Patent Publication Number: US-2023158088-A1

Title: Compositions for modulating gut microflora populations, enhancing drug potency and treating viral infections, and methods for making and using same

Description:
TECHNICAL FIELD 
     This invention generally relates to microbiology, pharmacology and antiviral therapies. In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, comprising combinations or consortia of microbes, such as non-pathogenic, live bacteria and/or bacterial spores, for the control, amelioration, prevention, and treatment of a disease or condition, for example, a viral infection such as a COVID19 infection. In alternative embodiment, these non-pathogenic, live bacteria and/or bacterial spores are administered to an individual in need thereof, thereby resulting in a modification or modulation of the individual&#39;s gut microfloral population(s). In alternative embodiments, by modulating or modifying the individual&#39;s gut microbial population(s) using compositions, products of manufacture and methods as provided herein, the pharmacodynamics of a drug or a vaccine, for example, antimicrobial such as an anti-bacterial, an antiviral or an antimalarial drug or a vaccine, administered to the individual is altered, for example, the pharmacodynamics of the drug is enhanced, for example, the individual&#39;s ability to absorb a drug is modified (for example, accelerated or slowed, or enhanced), or the dose efficacy of a drug is increased (for example, resulting in the requirement for a lower dose of drug to provide an intended effect), which can result in lowering the effective toxicity of the drug; or, alternatively the efficacy of a vaccine is enhanced or there are fewer or diminished side effects or negative reactions to the vaccine, for example, a diminished unwanted reaction to a vaccine carrier such as a liposome or nanolipid particle. For example, in alternative embodiments, the modulating or modifying of the individual&#39;s gut microbial population(s) increases the dose efficacy of the antimicrobial, for example, anti-bacterial, antiviral or antimalarial drug, thereby controlling, ameliorating, preventing and/or treating of that viral infection. In alternative embodiments, the amount, identity, presence, and/or ratio of gut microbiota in a subject is manipulated to facilitate one or more co-treatments, for example, in alternative embodiments, the combinations of microbes as provided herein are administered with an antimicrobial, for example, antibacterial, antiviral or antimalarial, therapy, which can comprise a drug, a small molecule, a vaccine, an antibody, a cell therapy, a natural killer (NK) cell therapy, angiotensin II receptor blockers, a defensin-mimetic, a nanobody, a peptide, an immune modulator, an immunotherapy, an anti-necrosis, a nucleoside, a quinoline compound, a protease inhibitor, a sphingosine kinase-2 (SK2) inhibitor, an interleukin receptor antagonist, a nanoviricide or other antimicrobial treatments. 
     BACKGROUND 
     The Coronavirus (SARS)-CoV-2, or COVID-19, and the potentially acute and life-threatening disease that it can cause, has quickly become a global pandemic (Rothan and Byrareddy 2020). SARS-CoV-2 is the seventh-known coronavirus to infect people (after 229E, NL63, OC43, HKU1, MERS, and SARS). Since its original discovery in China in December 2019, COVID-19 is now established in many countries and has caused immense disruption in social order, economic institutions, and is causing a severe strain on hospitals and clinics as more and more people with severe symptoms are seeking care. There are at present no specific antiviral drugs against COVID-19 infection, although drugs effective against other viruses like nucleoside analogs and HIV inhibitors could help treat COVID-19 infection and symptoms until new drugs become available (Wang et al. (2020) Journal of Medical Virology 92 (4): 441-47; Lu et al. (2020) BioScience Trends 14 (1). https://doi.org/10.5582/bst.2020.01020). In addition to these potential treatments and as the COVID-19 virus spreads, new and novel approaches for prevention of morbidity and mortality caused by this disease are desperately needed. 
     As of March 2021, several advances in the clinical treatment of (SARS)-CoV-2 have become available or are in late-stage clinical trials (Izda et al (2021) Clinical Immunology 222:108634). For instance, the adenosine nucleotide analog drug remdesivir, originally developed as an anti-viral drug against RNA viruses like Ebola, shows efficacy in the clinic for reducing morbidity/mortality and shortening the time of recovery of hospitalized COVID-19 patients (Beigel et al (2020) New England Journal of Medicine 383:1826). The REGN-COV2 antibody cocktail therapeutic developed by Regeneron Pharmaceuticals is a combination of antibodies specific to different parts of the SARS-CoV-2 spike protein and is shown to reduce viral load compared to placebo (Weinreich et al (2021) New England Journal of Medicine 384:238). Medications such as the Janus Kinase 1/2 inhibitor ruxolitinib (Rosee et al (2020) Leukemia 34:1805), the anti-IL-6 monoclonal antibody tocilizumab (Rosas et al (2021) New England J. of Med.), and corticosteroids such as dexamethasone (Horby et al (2021) New England J. of Med. 384:693) are intended to reduce hyperimmune responses that lead to cytokine storm in advanced hospitalized COVID-19 patients (Izda et al (2021) Clinical Immunology 222:108634). 
     In addition to immediate therapeutic treatments for COVID-19 related disease symptoms, there are now several highly effective and clinically available vaccines available that are directed against the spike protein against the (SARS)-CoV-2 coronavirus. For instance, the mRNA-based vaccines against the (SARS)-CoV-2 spike protein vaccines developed by Moderna (Baden et al (2021) New England J. Med.) 384:403) and by Pfizer (Polack et al (2020) 383:2603) show 94.1% and 95% efficacy, respectively, at preventing COVID-19 illness, including severe illness, in vaccinated individuals. The adenovirus-based DNA vector vaccines against the SARS-CoV-2 spike protein developed by Johnson and Johnson (Sadoff et al (2021) New England J. Med.) and by AstraZeneca (Madhi et al (2021) New England J. Med.) are also highly effective against SARS-CoV-2 and its variants. However, the current vaccines also have a number of side effects, and prevention of these or reduction in severity is desired. 
     SUMMARY 
     In alternative embodiments, provided are methods for:
         controlling, ameliorating or treating a viral infection such as a COVID-19 infection in an individual in need thereof,   lessoning the symptoms of or mortality of a viral infection,   enhancing the efficacy of an anti-viral drug, treatment, or a vaccine, or diminishing a side effects or a negative reaction to a vaccine, wherein optionally the vaccine is an antiviral vaccine, for example, diminishing an unwanted reaction to a vaccine carrier such as a liposome or nanolipid particle, or       

     enhancing the efficacy of a vaccine, or changing the gut microbiome in an individual in need thereof such that the individual has fewer or diminished side effects or negative reactions to an administered vaccine, wherein optionally the vaccine is an antiviral vaccine, and optionally the antiviral vaccine is an RNA-based vaccine, wherein optionally the RNA-based vaccine comprises RNA formulated in a liposome or a nanolipid particle, 
     the method comprising: 
     (a) administering or having administered to an individual in need thereof a formulation comprising at least two different species or genera (or types) of non-pathogenic bacteria, wherein each of the non-pathogenic bacteria comprise (or are in the form of) a plurality of non-pathogenic colony forming live bacteria, a plurality of non-pathogenic germinable bacterial spores, or a combination thereof; or, 
     (b) (i) providing a formulation comprising at least two different species or genera (or types) of non-pathogenic bacteria, wherein each of the non-pathogenic bacteria comprise (or are in the form of) a plurality of non-pathogenic colony forming live bacteria, a plurality of non-pathogenic germinable bacterial spores, or a combination thereof, and 
     (ii) administering or having administered to an individual in need thereof the formulation; 
     wherein the formulation comprises a or any combination of at least two different species or genera of non-pathogenic, live bacteria, or spore thereof, if the bacteria is spore forming, as described Tables 1, 4, 7, r 8 and/or 42, or live biotherapeutic compositions or combinations of bacteria as set forth in Tables 9 and/or 42, 
     and optionally the different species or genera (or types) of non-pathogenic, live bacteria or viable spores are present in approximately equal amounts, or each of the different species or genera (or types) of non-pathogenic, live bacteria or non-pathogenic germinable bacterial spores represent at least about 1%, 5%, 10%, 20%, 30%, 40%, or 50% or more, or between about 1% and 75%, of the total amount of non-pathogenic, live bacteria and non-pathogenic germinable bacterial spores in the formulation, 
     and optionally only or substantially only non-pathogenic, live bacteria are present in the formulation, or only or substantially only non-pathogenic germinable bacterial spores are present in the formulation, or approximately equal amounts of non-pathogenic, live bacteria and non-pathogenic germinable bacterial spores are present in the formulation. 
     In alternative embodiments of methods as provided herein:
         the method further comprises administering or having administered an antimicrobial drug or therapy, for example, an antiviral, antibacterial or antimalarial, drug or treatment, or an anti-bacterial or anti-viral vaccine, wherein optionally the vaccine is an adenovirus-based DNA vector vaccine or an RNA (for example, mRNA)-based vaccine,       

     and optionally the antimicrobial drug or therapy is administered before, during (concurrently with) and/or after administration a formulation as provided herein, for example, a formulation comprising a combination of microbes (for example, viable bacteria and/or spores), as provided herein, 
     and optionally a formulation as provided herein comprises both a combination of microbes (for example, viable bacteria and/or spores) as provided herein and an antimicrobial drug, for example, an antiviral, antibacterial or antimalarial, drug, 
     and optionally the antimicrobial (for example, antiviral) drug comprises: lopinavir; ritonavir; oseltamivir (for example, TAMIFLU™); lopinavir combined (formulated) with ritonavir, or KALETRA™; chloroquine phosphate, chloroquine diphosphate, hydroxychloroquine (for example, PLAQUENIL™) or oral chloroquine (for example, ARALEN™); remdesivir (for example, GS-5734™, Gilead Sciences); nevirapine, efavirenz, emtricitabine, tenofovir (or the combination efavirenz with emtricitabine and tenofovir, or ATRIPLA™); amprenavir (for example, AGENERASE™); nelfinavir (for example, VIRACEPT™); a thiazolide class drug, optionally nitazoxanide (or ALINIA™, NIZONIDE™) or tizoxanide (or 2-Hydroxy-N-(5-nitro-2-thiazolyl)benzamide); plitidepsin (also known as dehydrodidemnin B), or APLIDIN™ (PharmaMar, S.A.); an inhibitor or S-phase kinase-associated protein 2 (SKP2), or dioscin, or niclosamide, or NICLOCIDE™, FENASAL™, or PHENASAL™; ribavirin; an interferon such as interferon alpha, interferon beta, interferon type I, interferon type II and/or interferon type III, or a combination of ribavirin and interferon beta, or a combination of lopinavir and ritonavir and interferon-beta-1b; abacavir, actemra, acyclovir for example, (ACICLOVIR™) adefovir, amantadine, rintatolimod (for example, AMPLIGEN™), amprenavir (for example, AGENERASE™), aprepitant, arbidol, atazanavir, balavir, baloxavir marboxil (XOFLUZA™), bepotastine, bevirimat, bictegravir, biktarvy, brilacidin, cidofovir, caspofungin, lamivudine and zidovudine (for example, COMBVIR™) cobicstat, colisitin, cocaine, darunavir, delavirdine, descovy, didanosine, docosanol, dolutegravir, ecoliever, edoxudine, efavirenz, elvitegravir, emtricitabine, enfuvirtide, entecavir, epirubicin, epoprostenol, etravirine, famciclovir, fomivirsen, fosamprenavi, foscarnet, fosfonet, galidesivir, ibacitabine, icatibant, idoxuridine, ifenprodil, imiquimod, imunovir, indinavir, inosine, lamivudine, lopinavir, loviride, ledipasvir, leronlimab, maraviroc, methisazone, moroxydine, nelfinavir, nevirapine, nexavir, nitazoxanide, norvir, a nucleoside analogue (optionally brincidofovir, didanosine, favipiravir (also known as T-705, avigan, or favilavir, Toyama Chemical, Fujifilm, Japan), vidarabine, galidesivir (for example, BCX4430, IMMUCILLIN-A™) remdesivir (for example, GS-5734™, Gilead Sciences), cytarabine, gemcitabine, emtricitabine, zalcitabine, stavudine, telbivudine, zidovudine, idoxuridine and/or trifluridine or any combination thereof), oseltamivir (or TAMIFLU™), peginterferon alfa-2a, penciclovir, peramivir (for example, RAPIVAB™), perfenazine, pleconaril, plurifloxacin, podophyllotoxin, pyramidine, raltegravir, rifampicin, ribavirin, rilpivirine, rimantadine, ritonavir, saquinavir, sofosbuvir, telaprevir, tegobuv, tenofovir alafenamide, tenofovir disoproxil, tenofovir, tipranavir, trifluridine, trizivir, tromantadine, truvada, valaciclovir (for example, VALTREX™), valganciclovir, valrubicin, vapreotide, vicriviroc, vidarabine, viramidine, velpatasvir, vivecon, zalcitabine, zanamivir (for example, RELENZA™) or zidovudine; a serine protease inhibitor, optionally camostat; an anti-PD-1 checkpoint inhibitor, optionally camrelizumab; a compound or antibody capable of binding complement factor C5 and blocking membrane attack complex formation, optionally eculizumab; a cathepsin inhibitor, optionally a cathepsin K, B or L inhibitor, optionally relacatib; thalidomide, or thalidomide and glucocorticoid (optionally low-dose glucocorticoid), or and thalidomide and celecoxib; an antibacterial antibiotic or a macrolide drug, wherein optionally the macrolide drug comprises azithromycin (for example, ZITHROMAX™, or AZITHROCIN™), clarithromycin (for example, BIAXIN™) erythromycin (for example, ERYTHROCIN™), or fidaxomicin (for example, DIFICID™ or DIFICLIR™), troleandomycin (for example, TEKMISIN™), tylosin (for example, TYLOCINE™ or TYLAN™), solithromycin (for example, SOLITHERA™), oleandomycin (or SIGMAMYCINE™), midecamycin, roxithromycin, kitasamycin or turimycin, josamycin, carbomycin or magnamycin, and/or spiramycin; opaganib or YELIVA™; or, any two, three or more or combination thereof,
         the formulation comprises an inner core surrounded by an outer layer of polymeric material enveloping the inner core, wherein the non-pathogenic bacteria or the non-pathogenic germinable bacterial spores are substantially in the inner core, and optionally the polymeric material comprises a natural polymeric material;   the formulation is formulated or manufactured as or in: a nano-suspension delivery system; an encochleated formulation; or, as a multilayer crystalline, spiral structure with no internal aqueous space;   the formulation is formulated or manufactured as a delayed or gradual enteric release composition or formulation, and optionally the formulation comprises a gastro-resistant coating designed to dissolve at a pH of 7 in the terminal ileum, optionally an active ingredient is coated with an acrylic based resin or equivalent, optionally a poly(meth)acrylate, optionally a methacrylic acid copolymer B, NF, optionally EUDRAGIT S™ (Evonik Industries AG, Essen, Germany), which dissolves at pH 7 or greater, optionally comprises a multimatrix (MMX) formulation, and optionally manufactured as enteric coated to bypass the acid of the stomach and bile of the duodenum;   the plurality of non-pathogenic colony forming live bacteria are substantially dormant colony forming live bacteria, or the plurality of non-pathogenic colony forming live bacteria or the plurality of non-pathogenic germinable bacterial spores are lyophilized, wherein optionally the dormant colony forming live bacteria comprise live vegetative bacterial cells that have been rendered dormant by lyophilization or freeze drying in the absence of oxygen to maintain viability of strict anaerobic species;   the formulation comprises at least about 1×10 4  colony forming units (CFUs), or between about 1×10 1  and 1×10 13  CFUs, 1×10 2  and 1×10 10  CFUs, 1×10 2  and 1×10 8  CFUs, 1×10 3  and 1×10 7  CFUs, or 1×10 4  and 1×10 6  CFUs, of non-pathogenic live bacteria and/or non-pathogenic germinable bacterial spores;   the formulation comprises at least one (or any one, several, or all of) non-pathogenic bacteria or spore of the family or genus (or class):  Agathobaculum  (TaxID: 2048137),  Alistipes  (TaxID: 239759),  Anaeromassilibacillus  (TaxID: 1924093),  Anaerostipes  (TaxID: 207244),  Asaccharobacter  (TaxID: 553372),  Bacteroides  (TaxID: 816),  Barnesiella  (TaxID: 397864),  Bifidobacterium  (TaxID: 1678),  Blautia  (TaxID: 572511),  Butyricicoccus  (TaxID: 580596),  Clostridium  (TaxID: 1485),  Collinsella  (TaxID: 102106),  Coprococcus  (TaxID: 33042),  Dorea  (TaxID: 189330),  Eubacterium  (TaxID: 1730),  Faecalibacterium  (TaxID: 216851),  Fusicatenibacter  (TaxID: 1407607),  Gemmiger  (TaxID: 204475),  Gordonibacter  (TaxID: 644652),  Lachnoclostridium  (TaxID: 1506553),  Methanobrevibacter  (TaxID: 2172),  Parabacteroides  (TaxID: 375288), Romboutsia (TaxID: 1501226),  Roseburia  (TaxID: 841),  Ruminococcus  (TaxID: 1263),  Erysipelotrichaceae  (TaxID: 128827),  Coprobacillus  (TaxID: 100883),  Erysipelatoclostridium  sp. SNUG30099 (TaxID: 1982626),  Erysipelatoclostridium  (TaxID: 1505663), or a combination thereof,   the formulation comprises at least one (or any one, several, or all of) non-pathogenic bacteria or spore form thereof as set forth in Tables 1, 4, 7 or 8, or included in the combination of non-pathogenic bacteria and/or spores thereof (or spore derived from) as set forth in Tables 9 and/or 42;   the formulation comprises combination of non-pathogenic bacteria and/or spores thereof (or spore derived from) as set forth in Tables 9 and/or 42;   the formulation comprises water, sterile water, saline, sterile saline, a pharmaceutically acceptable preservative, a carrier, a buffer, a diluent, an adjuvant or a combination thereof;   the formulation is administered orally or rectally, or is formulated and/or administered as a liquid, a food, a gel, a candy, an ice, a lozenge, a tablet, pill or capsule, or a suppository or as an enema formulation, or the formulation is administered as an or is in a form for intra-rectal or intra-colonic administration;   the formulation is administered to the individual in need thereof in one, two, three, or four or more doses, and wherein the one, two, three, four or five or more doses are administered on a daily basis (optionally once a day, bid or tid or more), every other day, every third day, or about once a week, and optionally the two, three, or four or more doses are administered at least a week apart (or dosages are separated by about a week);   a formulation or a method as provided herein further comprises or further comprises administration of: an antimicrobial drug, for example, an antiviral, antibacterial or antimalarial, drug, and optionally the antimicrobial (for example, antiviral) drug comprises: lopinavir; ritonavir; oseltamivir (for example, TAMIFLU™); lopinavir combined (formulated) with ritonavir, or KALETRA™; chloroquine phosphate (for example, RESOCHIN™), chloroquine diphosphate, hydroxychloroquine (for example, PLAQUENIL™) or oral chloroquine (for example, ARALEN™); remdesivir (for example, GS-5734™, Gilead Sciences); nevirapine, efavirenz, emtricitabine, tenofovir (or the combination efavirenz with emtricitabine and tenofovir, or ATRIPLA™); amprenavir (for example, AGENERASE™); nelfinavir (for example, VIRACEPT™); a thiazolide class drug, optionally nitazoxanide (or ALINIA™, NIZONIDE™) or tizoxanide (or 2-Hydroxy-N-(5-nitro-2-thiazolyl)benzamide); plitidepsin (also known as dehydrodidemnin B), or APLIDIN™ (PharmaMar, S.A.); an inhibitor or S-phase kinase-associated protein 2 (SKP2), or dioscin, or niclosamide, or NICLOCIDE™, FENASAL™, or PHENASAL™; ribavirin; an interferon such as interferon alpha, interferon beta, interferon type I, interferon type II and/or interferon type III, or a combination of ribavirin and interferon beta, or a combination of lopinavir and ritonavir and interferon-beta-1b; abacavir, actemra, acyclovir for example, (ACICLOVIR™) adefovir, amantadine, ampligen, amprenavir (for example, AGENERASE™) aprepitant, atazanavir, balavir, baloxavir marboxil (XOFLUZA™), bepotastine, bevirimat, bictegravir, biktarvy, brilacidin, cidofovir, caspofungin, lamivudine and zidovudine (for example, COMBVIR™), cobicstat, colisitin, cocaine, danoprevir or danoprevir and ritonavir (for example, GANOVO™) darunavir (or darunavir and cobicstat, for example, PREZCOBIX™), delavirdine, descovy, didanosine, docosanol, dolutegravir, ecoliever, edoxudine, efavirenz, elvitegravir, emtricitabine, enfuvirtide, entecavir, epirubicin, epoprostenol, etravirine, famciclovir, fomivirsen, fosamprenavi, foscarnet, fosfonet, ibacitabine, icatibant, idoxuridine, ifenprodil, imiquimod, imunovir, indinavir, inosine, lamivudine, lopinavir, loviride, ledipasvir, leronlimab, maraviroc, methisazone, moroxydine, nelfinavir, nevirapine, nexavir, nitazoxanide, norvir, a nucleoside analogue (optionally brincidofovir, didanosine, favipiravir (also known as T-705, avigan, or favilavir, Toyama Chemical, Fujifilm, Japan), vidarabine, galidesivir (for example, BCX4430 by Biocryst, IMMUCILLIN-A™), remdesivir (for example, GS-5734™, Gilead Sciences), cytarabine, gemcitabine, emtricitabine, zalcitabine, stavudine, telbivudine, zidovudine, idoxuridine and/or trifluridine or any combination thereof), oseltamivir (or TAMIFLU™), peginterferon alfa-2a, penciclovir, peramivir (for example, RAPIVAB™), perfenazine, pleconaril, plurifloxacin, podophyllotoxin, pyramidine, raltegravir, rifampicin, ribavirin, rilpivirine, rimantadine, ritonavir, saquinavir, sofosbuvir, telaprevir, tegobuv, tenofovir alafenamide, tenofovir disoproxil, tenofovir, tipranavir, trifluridine, trizivir, tromantadine, truvada, valaciclovir (for example, VALTREX™), valganciclovir, valrubicin, vapreotide, vicriviroc, vidarabine, viramidine, velpatasvir, vivecon, zalcitabine, zanamivir (for example, RELENZA™) or zidovudine; a serine protease inhibitor, optionally camostat; an anti-PD-1 checkpoint inhibitor, optionally camrelizumab; a compound or antibody capable of binding complement factor C5 and blocking membrane attack complex formation, optionally eculizumab; a cathepsin inhibitor, optionally a cathepsin K, B or L inhibitor, optionally relacatib; thalidomide, or thalidomide and glucocorticoid (optionally low-dose glucocorticoid), or and thalidomide and celecoxib; an antibacterial antibiotic or a macrolide drug, wherein optionally the macrolide drug comprises azithromycin (for example, ZITHROMAX™, or AZITHROCIN™) clarithromycin (for example, BIAXIN™), erythromycin (for example, ERYTHROCIN™), or fidaxomicin (for example, DIFICID™ or DIFICLIR™) troleandomycin (for example, TEKMISIN™), tylosin (for example, TYLOCINE™ or TYLAN™), solithromycin (for example, SOLITHERA™), oleandomycin (or SIGMAMYCINE™), midecamycin, roxithromycin, kitasamycin or turimycin, josamycin, carbomycin or magnamycin, and/or spiramycin; opaganib or YELIVA™; an anti-interleukin-6 antibody (e.g., tocilizumab or tocilizumab and favipiravir, for example, ACTEMRA™); sarilumab (for example, KEVZARA™); umifenovir (for example, ARBIDOL™); colchicine, or COLCRYS™, MITIGARE™; a corticosteroid class drug such as budesonide (or RHINOCORT™ or PULMICORT™), prednisolone (or ORAPRED™), methyl-prednisolone, prednisone (or DELTASONE™ or ORASONE™) or hydrocortisone (or CORTEF™); an anti-androgen drug, or bicalutamide; a hydrocortisone or cortisol (or CORTEF™, SOLUCORTEF™), or hydrocortisone sodium succinate or hydrocortisone acetate or dexamethasome (or DEXTENZA™, OZURDEX™, NEOFORDEX™); famotidine, or PEPCID™; an antihistamine class drug such as azelastine, or ASTELIN™, OPTIVAR™ ALLERGODIL™, brompheniramine, fexofenadine or ALLEGRA™, pheniramine or AVIL™, or chlorpheniramine; a dendrimer, or an astodrimer sodium (Starpharma, Melbourne, Australia); a selective serotonin reuptake inhibitor (SSRI) class drug, optionally fluvoxamine, or LUVOX™, FAVERIN™, FLUVOXIN™; a nicotinic antagonist, a dopamine agonist or a noncompetitive N-Methyl-d-aspartic acid or N-Methyl-d-aspartate (NMDA) antagonist; an immunosuppressive drug, or tocilizumab or atlizumab, or ACTEMRA™, or ROACTEMRA™, or a calcineurin inhibitor (CNI), or ciclosporin or cyclosporine or cyclosporin); or, any two, three or more or combination thereof;       

     and optionally a formulation as provided herein further comprises an antibiotic, or a method as provided herein further comprises administration of an antibiotic, and optionally at least one dose of the antibiotic, for example, a macrolide drug such as azithromycin, is administered before a first administration of the formulation, optionally at least one dose of the antibiotic is administered one day or two days, or more, before a first administration of the formulation;
         and optionally a formulation as provided herein further comprises an inhibitor of an inhibitory immune checkpoint molecule, which can comprise a protein or polypeptide that binds to an inhibitory immune checkpoint protein, and optionally the inhibitor of the inhibitory immune checkpoint protein is an antibody or an antigen binding fragment thereof that specifically binds to the inhibitory immune checkpoint protein;   and optionally the inhibitor of the inhibitory immune checkpoint molecule targets a compound or protein comprising: a CTLA4 or CTLA-4 (cytotoxic T-lymphocyte-associated protein 4, also known as CD152, or cluster of differentiation 152); Programmed cell Death protein 1, also known as PD-1 or CD279; Programmed Death-Ligand 1 (PD-L1), also known as cluster of differentiation 274 (CD274) or B7 homolog 1 (B7-H1)); PD-L2; A2AR (adenosine A 2 , receptor, also known as ADORA2A); B7-H3; B7-H4; BTLA (B- and T-lymphocyte attenuator protein); KIR (Killer-cell Immunoglobulin-like Receptor); IDO (Indoleamine-pyrrole 2,3-dioxygenase); LAG3 (Lymphocyte-Activation Gene 3 protein); TIM-3; VISTA (V-domain Ig suppressor of T cell activation protein); or any combination thereof;   and optionally the inhibitor of an inhibitory immune checkpoint molecule comprises: ipilimumab or YERVOY®; pembrolizumab or KEYTRUDA®; nivolumab or OPDIVO®; atezolizumab or TECENTRIP®; avelumab or BAVENCIO®; durvalumab or IMFINZI®; AMP-224 (MedImmune), AMP-514 (an anti-programmed cell death 1 (PD-1) monoclonal antibody (mAb) (MedImmune)), PDR001 (a humanized mAb that targets PD-1), STI-A1110 or STI-A1010 (Sorrento Therapeutics), BMS-936559 (Bristol-Myers Squibb), BMS-986016 (Bristol-Myers Squibb), TSR-042 (Tesaro), JNJ-61610588 (Janssen Research &amp; Development), MSB-0020718C, AUR-012, enoblituzumab (also known as MGA271) (MacroGenics, Inc.), MBG453, LAG525 (Novartis), BMS-986015 (Bristol-Myers Squibb), or any combination thereof,   and optionally the inhibitor of the inhibitory immune checkpoint molecule, or the stimulatory immune checkpoint molecule, is administered by: intravenous (IV) injection, intramuscular (IM) injection, intratumoral injection or subcutaneous injection; or, is administered orally or by suppository; or the formulation further comprises at least one immune checkpoint inhibitor;       

     and optionally the viral infection treated by administration of a combination of microbes or formulations as provided herein, or by practicing a method as provided herein, comprises an infection caused by or associated with: a coronavirus (for example, COVID-19, SARS (Severe Acute Respiratory Syndrome) or MERS (Middle East Respiratory Syndrome))), an influenza virus (for example, influenza A, B or C), adeno-associated virus, aichi virus, coxsackievirus, dengue virus, ebolavirus, an encephalomyocarditis virus, an Epstein-Barr virus, hantaan virus, a hepatitis virus (for example, hepatitis A, B, C, E or delta virus), human respiratory syncytial virus (hRSV), human adenovirus, astrovirus, cytomegalovirus, entervirus, a herpes virus (for example, herpesvirus 1, 2, 6, 7, or 8), human immunodeficiency virus (HIV) (for example, HIV-1), human papillomavirus, parainfluenza virus, parvovirus, human respiratory syncytial virus, a rhinovirus, human spumaretrovirus, human T-lymphotropic virus, torovirus, lymphocytic choriomeningitis virus, measles virus, a polyomavirus (for example, Merkel cell or Wu polyomavirus), mumps virus, Norwalk virus, poliovirus, rabies virus, rosavirus, rotavirus (for example, rotavirus A, B or C), rubella virus, Semliki virus, simian virus, sindbis virus, tick-borne powassan virus, vaccinia virus, varicella-zoster virus, variola virus, equine encephalitis virus, vesicular stomatitis virus, West Nile virus, yellow fever virus or zika virus; 
     and optionally a method as provided herein is administered with (either before, during or after) administration of an antiviral vaccine, immune enhancer or adjuvant such as for example, NASOVAX™ vaccine by Altimmune, Inc. (Gaithersburg, Md.). 
     and/or
         the method comprises, or further comprises, administering, or having administered, or delivering, a genetically (or recombinantly) engineered cell, wherein optionally the genetically engineered cell is: a microbe or spore derived from a microbe as used in a method of any of the preceding claims, or a method as provided herein; or, a non-pathogenic bacteria or spore form thereof as set forth in Tables 1, 4, 7 or 8; or, a non-pathogenic bacteria or spore form thereof included in a combination of non-pathogenic bacteria and/or spores thereof (or spore derived from) as set forth in Tables 9 and 42,       

     and optionally the microbe is genetically engineered to express or secrete a heterologous or overexpress an endogenous immunomodulatory molecule, and optionally the immunomodulatory molecule is an immunomodulatory protein or peptide, and optionally the immunomodulatory molecule is an immunostimulatory molecule, 
     and optionally the microbe is genetically engineered to overexpress a pathway for production of at least one short chain fatty acid (SCFA), and optionally the SCFA comprises butyrate or butyric acid, propionate or acetate, 
     and optionally the microbe is genetically engineered by inserting a heterologous nucleic acid into the microbe, and optionally the heterologous nucleic acid encodes an exogenous membrane protein, 
     and optionally the immunostimulatory molecule, protein or peptide comprises a non-specific immunostimulatory protein, and optionally the non-specific immunostimulatory protein comprises a cytokine, and optionally the cytokine comprises an interferon (optionally an IFN-α2a, IFN-α2b), and interleukin (optionally IL-2, IL-4, IL-7, IL-12), an interferon (IFN), a TNF-α, a granulocyte colony-stimulating factor (G-CSF, also known as filgrastim, lenograstim or Neupogen®), a granulocyte monocyte colony-stimulating factor (GM-CSF, also known as molgramostim, sargramostim, Leukomax®, Mielogen® or Leukine®), or any combination thereof, 
     and optionally the immunostimulatory molecule, protein or peptide comprises a specific immunostimulatory protein or peptide, and optionally the specific immunostimulatory protein or peptide comprises an immunogen that can generate a specific humeral or cellular immune response or an immune response to a viral antigen, 
     and optionally the genetically engineered cell is a lymphocyte, and optionally the genetically engineered cell expresses a chimeric antigen receptor (CAR), and optionally the lymphocyte is a B cell or a T cell (CAR-T cell), and optionally the lymphocyte is a tumor infiltrating lymphocyte (TIL), 
     and optionally the microbe is genetically engineered to substantially decrease, reduce or eliminate the microbe&#39;s toxicity, 
     and optionally the microbe is genetically engineered to comprise a kill switch so the microbe can be rendered non-vital after administration of an appropriate trigger or signal, 
     and optionally the microbe is genetically engineered to secrete anti-inflammatory compositions or have an anti-inflammatory effect, 
     and optionally the genetically engineered cell is administered or delivered before administration of, simultaneously with, and/or after administration or delivery of the formulation. 
     In alternative embodiments, provided are formulations or pharmaceutical compositions comprising: 
     (a) a combination of microbes as set forth in Tables 9 and 42; 
     (b) a combination of microbes as used in a method as provided herein or as provided herein; and/or 
     (c) at least two different species or genera (or types) of non-pathogenic bacteria, wherein each of the non-pathogenic bacteria comprise (or are in the form of) a plurality of non-pathogenic colony forming live bacteria, a plurality of non-pathogenic germinable non-pathogenic bacterial spores, or a combination thereof, and the formulation comprises at least one (or any one, several, or all of) non-pathogenic bacteria or spore of the family or genus (or class):  Agathobaculum  (TaxID: 2048137),  Alistipes  (TaxID: 239759),  Anaeromassilibacillus  (TaxID: 1924093),  Anaerostipes  (TaxID: 207244),  Asaccharobacter  (TaxID: 553372),  Bacteroides  (TaxID: 816),  Barnesiella  (TaxID: 397864),  Bifidobacterium  (TaxID: 1678),  Blautia  (TaxID: 572511),  Butyricicoccus  (TaxID: 580596),  Clostridium  (TaxID: 1485),  Collinsella  (TaxID: 102106),  Coprococcus  (TaxID: 33042),  Dorea  (TaxID: 189330),  Eubacterium  (TaxID: 1730),  Faecalibacterium  (TaxID: 216851),  Fusicatenibacter  (TaxID: 1407607),  Gemmiger  (TaxID: 204475),  Gordonibacter  (TaxID: 644652),  Lachnoclostridium  (TaxID: 1506553),  Methanobrevibacter  (TaxID: 2172),  Parabacteroides  (TaxID: 375288), Romboutsia (TaxID: 1501226),  Roseburia  (TaxID: 841),  Ruminococcus  (TaxID: 1263),  Erysipelotrichaceae  (TaxID: 128827),  Coprobacillus  (TaxID: 100883),  Erysipelatoclostridium  sp. SNUG30099 (TaxID: 1982626),  Erysipelatoclostridium  (TaxID: 1505663), or a combination thereof. 
     In alternative embodiments, of formulations or pharmaceutical compositions as provided herein, or methods as provided herein:
         the formulation comprises at least one (or any one, several, or all of) non-pathogenic bacteria or spore form thereof as set forth in Tables 1, 4, 7 or 8, or included in the combination of non-pathogenic bacteria and/or spores thereof (or spore derived from) as set forth in Tables 9 and 42;   the formulation comprises an inner core surrounded by an outer layer of polymeric material enveloping the inner core, wherein the non-pathogenic bacteria or the non-pathogenic germinable bacterial spores are substantially in the inner core, and optionally the polymeric material comprises a natural polymeric material;   the plurality of non-pathogenic colony forming live bacteria are substantially dormant colony forming live bacteria, or the plurality of non-pathogenic colony forming live bacteria or the plurality of non-pathogenic germinable bacterial spores are lyophilized, wherein optionally the non-pathogenic dormant colony forming live bacteria comprise live vegetative bacterial cells that have been rendered dormant by lyophilization or freeze drying;   the formulation comprises at least 1×10 4  colony forming units (CFUs), or between about 1×10 2  and 1×10 8  CFUs, 1×10 3  and 1×10 7  CFUs, or 1×10 4  and 1×10 6  CFUs, of live non-pathogenic bacteria and/or non-pathogenic germinable bacterial spores;   the formulation or pharmaceutical composition comprises water, saline, a pharmaceutically acceptable preservative, a carrier, a buffer, a diluent, an adjuvant or a combination thereof;   the formulation or pharmaceutical composition is formulated for administration orally or rectally, or is formulated as a liquid, a food, a gel, a geltab, a candy, a lozenge, a tablet, pill or capsule, or a suppository;   the formulation or pharmaceutical composition further comprises: a biofilm disrupting or dissolving agent, an antibiotic, an inhibitor of an inhibitory immune checkpoint molecule and/or a stimulatory immune checkpoint molecule (or any composition for use in checkpoint blockade immunotherapy);   the inhibitor of an inhibitory immune checkpoint molecule comprises a protein or polypeptide that binds to an inhibitory immune checkpoint protein, and optionally the inhibitor of the inhibitory immune checkpoint molecule is an antibody or an antigen binding fragment thereof that binds to an inhibitory immune checkpoint protein;   the inhibitor of an inhibitory immune checkpoint molecule targets a compound or protein comprising: CTLA4 or CTLA-4 (cytotoxic T-lymphocyte-associated protein 4, also known as CD152, or cluster of differentiation 152); Programmed cell Death protein 1, also known as PD-1 or CD279; Programmed Death-Ligand 1 (PD-L1), also known as cluster of differentiation 274 (CD274) or B7 homolog 1 (B7-H1)); PD-L2; A2AR (adenosine A 2 , receptor, also known as ADORA2A); B7-H3; B7-H4; BTLA (B- and T-lymphocyte attenuator protein); KIR (Killer-cell Immunoglobulin-like Receptor); IDO (Indoleamine-pyrrole 2,3-dioxygenase); LAG3 (Lymphocyte-Activation Gene 3 protein); TIM-3; VISTA (V-domain Ig suppressor of T cell activation protein) or any combination thereof;   the inhibitor of an inhibitory immune checkpoint molecule comprises: ipilimumab or YERVOY®; pembrolizumab or KEYTRUDA®; nivolumab or OPDIVO®; atezolizumab or TECENTRIP®; avelumab or BAVENCIO®; durvalumab or IWINZI®; AMP-224 (MedImmune), AMP-514 (an anti-programmed cell death 1 (PD-1) monoclonal antibody (mAb) (MedImmune)), PDR001 (a humanized mAb that targets PD-1), STI-A1110 or STI-A1010 (Sorrento Therapeutics), BMS-936559 (Bristol-Myers Squibb), BMS-986016 (Bristol-Myers Squibb), TSR-042 (Tesaro), JNJ-61610588 (Janssen Research &amp; Development), MSB-0020718C, AUR-012, enoblituzumab (also known as MGA271) (MacroGenics, Inc.), MBG453, LAG525 (Novartis), BMS-986015 (Bristol-Myers Squibb), or any combination thereof, and/or   the stimulatory immune checkpoint molecule comprises a member of the tumor necrosis factor (TNF) receptor superfamily, optionally CD27, CD40, OX40, GITR (a glucocorticoid-Induced TNFR family Related gene protein) or CD137, or comprises a member of the B7-CD28 superfamily, optionally CD28 or Inducible T-cell co-stimulator (ICOS).       

     In alternative embodiments, provided are kits or products of manufacture comprising a formulation or pharmaceutical composition as provided herein, wherein optionally the product of manufacture is an implant. 
     In alternative embodiments, provided are uses of a formulation or pharmaceutical composition as provided herein, or a kit or product of manufacture as provided herein, for controlling, ameliorating or treating a cancer in an individual in need thereof. 
     In alternative embodiments, provided are uses of a formulation or a pharmaceutical composition as provided herein in the manufacture of a medicament for controlling, ameliorating or treating a cancer in an individual in need thereof. 
     In alternative embodiments, provided are formulations or pharmaceutical compositions as provided herein, or a kit as provided herein, for use in controlling, ameliorating or treating a cancer in an individual in need thereof. In alternative embodiments, the cancer is melanoma, advanced melanoma, cutaneous or intraocular melanoma, primary neuroendocrine carcinoma of the skin, breast cancer, a cancer of the head and neck, uterine cancer, rectal and colorectal cancer, a cancer of the head and neck, cancer of the small intestine, a colon cancer, a cancer of the anal region, a stomach cancer, lung cancer, brain cancer, non-small-cell lung cancer, ovarian cancer, angiosarcoma, bone cancer, osteosarcoma, prostate cancer; cancer of the bladder; cancer of the kidney or ureter or renal cell carcinoma, or carcinoma of the renal pelvis; a neoplasm of the central nervous system (CNS) or renal cell carcinoma. 
     The details of one or more exemplary embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims. 
     All publications, patents, patent applications cited herein are hereby expressly incorporated by reference for all purposes. 
    
    
     
       DESCRIPTION OF DRAWINGS 
       The drawings set forth herein are illustrative of exemplary embodiments provided herein and are not meant to limit the scope of the invention as encompassed by the claims. 
         FIG.  1    graphically summarizes the classification level of least common ancestors for each cluster. Microbial genome assemblies from NCBI RefSeq are classified into operational species units by clustering similar genome assemblies together. The least common ancestor in the NCBI hierarchy for the assemblies in each operational species unit (OSU) cluster is determined. For OSU&#39;s containing more than one microbial assembly, the rank of the least common ancestor is displayed. Most OSU&#39;s have a least common ancestor at the species or genus level, demonstrating consistency between the assigned OSU&#39;s and the pre-existing NCBI taxonomic tree, as described in Example 9, below. 
         FIG.  2    graphically shows the distribution of OSU cluster sizes. Microbial genome assemblies from NCBI RefSeq are classified into operational species units by clustering similar genome assemblies together. The cluster size distribution is visualized, as described in Example 9, below. 
         FIG.  3    graphically illustrates a principal component analysis (PCA) of microbiome composition obtained from fecal samples. Whole genome sequencing is performed on fecal samples from subjects with and without cancer as well as in remission. The reads are classified, and abundance of each operational species unit is estimated computationally. PCA is performed on centered-log-ratio transformed abundances, and the first two principal coordinates are plotted for cancer, remission, and control sample cohorts, as described in Example 9, below. 
         FIG.  4    graphically illustrates a PCA plot showing the relationship between longitudinal samples of the same patient. Whole genome sequencing is performed on fecal samples from subjects with and without cancer as well as in remission. The reads are classified, and abundance of each operational species unit is estimated computationally. PCA is performed on centered-log-ratio transformed abundances, and the first two principal coordinates are plotted for cancer and control sample cohorts, with longitudinal samples being connected by arrows. Later samples from the same subject are colored darker, as described in Example 9, below. 
         FIG.  5    graphically illustrates a volcano plot showing the differential abundance of species in cancer and control cohorts. Whole genome sequencing is performed on fecal samples from subjects with and without cancer and the reads are classified and abundance of each operational species unit is estimated computationally. The fold change difference and statistical significance (inverse p value, Mann Whitney U test) is calculated for abundances between cancer and control sample cohorts. The results are displayed on a volcano plot. Each point is an operational species unit, and the area of each point corresponds to the average abundance of that operational species unit across all samples, as described in Example 9, below. 
         FIG.  6    shows the distribution of abundances of specific organisms among the different patient samples in each cohort. Whole genome sequencing is performed on fecal samples from subjects with and without cancer and the reads are classified and abundance of each operational species unit is estimated computationally. Operational species units with significant differences between cancer and control are displayed, as described in Example 9, below. 
         FIG.  7    graphically illustrates the distribution of abundances of additional specific organisms among the different patient samples in each cohort, plotted as in  FIG.  6   . 
         FIG.  8    graphically illustrates a receiver operating characteristic (ROC) curve of the classifier developed based on stool species distribution. A random forest classifier is trained to classify operational species unit abundances for a sample as corresponding to cancer or control. An ROC curve is generated on 145 cancer samples and 88 control samples using leave-one-out cross validation. No hyperparameter optimization was performed, as described in Example 10, below. 
         FIG.  9    graphically illustrates correlations of species abundance with immune markers obtained from blood analysis. Immune markers with significant correlations to operational species unit relative abundances are plotted. P values are generated by a linear mixed model fit that model immune marker proportions as being linearly related to the logarithm of OSU abundance, with a random effect accounting for cancer and control groups. For CD3+CD56+, the logarithm of the immune marker proportion is used as the output of the mixed model. (a) positive correlations; (b) negative correlations, as described in Example 10, below. 
         FIG.  10    graphically illustrates the distribution of abundances of specific organisms in complete responders (CR), partial responders (PR), and non-responders (NR). Whole genome sequencing is performed on the initial time point fecal samples from subjects undergoing cancer immunotherapy and the reads are classified and abundance of each operational species unit is estimated computationally. Operational species unit abundances are correlated to response to therapy using a score of 2 for complete response, 1 for partial response, 0 for no response, using the Spearman rank correlation. Operational species unit abundances for several notable OSUs are displayed with the corresponding Spearman p values, as described in Example 10, below. 
         FIG.  11    graphically illustrates the first two principal components of a PCA of centered-log-ratio transformed microbial species abundance values obtained from fecal samples of FMT-treated mice 7 days post-treatment. Circles and Xs represent samples from mice treated with fecal material from two different non-responder patients. Squares and plusses represent samples from mice treated with fecal material from two different responder patients. The large symbols of each type indicate species composition of the human fecal material used for each transplant. 
         FIG.  12    graphically illustrates principal components 2 and 3 of a PCA of centered-log-ratio transformed microbial species abundance values obtained from fecal samples of FMT-treated mice 7 days post-treatment. Symbols are as described for  FIG.  11   . 
         FIG.  13    graphically illustrates principal components 3 and 4 of a PCA of centered-log-ratio transformed microbial species abundance values obtained from fecal samples of FMT-treated mice 7 days post-treatment. Symbols are as described for  FIG.  11   . 
         FIG.  14    graphically illustrates the first two components of a t-Distributed Stochastic Neighbor Embedding (tSNE) of centered-log-ratio transformed microbial species abundance values obtained from fecal samples of FMT-treated mice 7 days post-treatment. Circles and Xs represent samples from mice treated with fecal material from two different non-responder patients. Squares and plusses represent samples from mice treated with fecal material from two different responder patients. 
         FIG.  15    graphically illustrates the first two components of a tSNE of centered-log-ratio transformed microbial species abundance values obtained from fecal samples of FMT-treated mice 7, 13, and 27 days post-treatment. Shading intensity of the points indicates different donors. Circles, 7 days post-treatment; Xs, 13 days post-treatment; squares, 27 days post-treatment. 
         FIG.  16    illustrates Table 2, as discussed in Example 7, below. 
         FIG.  17    illustrates Table 3, as discussed in Example 9, below. 
         FIG.  18    illustrates Table 5, as discussed in Example 10, below. 
         FIG.  19    illustrates Table 6, as discussed in Example 10, below. 
         FIG.  20    graphically illustrates exemplary flow cytometry analysis of peripheral blood samples from a patient undergoing immunotherapy are shown, as described in Example 9, below. 
         FIG.  21    graphically illustrates flow cytometry data from immune-phenotyping 73 blood samples obtained from human subjects with and without cancer. Statistical analysis was performed to find significantly different differences in immune markers between cancer and control sample cohorts, using a Mann Whitney U test and filtering for a false discovery rate of 0.05. Markers passing the FDR filter are plotted. The box denotes the 25th, 50th, and 75th percentiles of the data, and each point is a single sample; as discussed in detail in Example 9, below. 
         FIG.  22    graphically illustrates principal component analysis of flow cytometry data from immune-phenotyping 73 blood samples obtained from human subjects with and without cancer. Principal component analysis is performed on the immune marker percentages and the first two components are plotted by stage of cancer. The P value is computed using permutational multivariate analysis of variance (PERMANOVA); as discussed in detail in Example 9, below. 
         FIG.  23    graphically illustrates the results of a statistical analysis performed on metabolomics data on plasma obtained from a third-party provider (as “a volcano plot”). A Mann Whitney U test is used to find significantly different metabolites between cancer and control cohorts. Metabolites enriched in cancer samples appear on the right side of the plot and those enriched in control samples occur on the left, with higher points on the y-axis corresponding to increased statistical significance, as discussed in detail in Example 9, below. 
         FIG.  24    graphically illustrates the results of a principal component analysis comparing immune flow cytometry data to whole genome sequencing data. The primary principal component for the whole genome sequencing data and the second principal component for immune flow cytometry data are plotted against each other, revealing a strong correlation and suggesting that the microbiome may play a role in affecting the immune system and vice versa, as discussed in detail in Example 9, below. 
         FIG.  25    graphically illustrates the results of a principal component analysis performed on the plasma metabolomics of cancer and control samples, showing clear separation between cancer and control samples, as discussed in detail in Example 9, below. 
         FIG.  26    graphically illustrates the distribution of Euclidean distances in a centered-log-transformed space between successive longitudinal fecal whole genome sequencing samples for both cancer and control cohorts. The plot shows a higher average distance between longitudinal cancer samples than control, as discussed in detail in Example 9, below. 
         FIG.  27    graphically illustrates a heatmap of the Spearman correlations calculated between each flow gate (CD11b+, CD3+, CD8-HLADR+ and FoxP3+) for humans and each organism in the gut whose mean abundance is greater than or equal to 0.0005; as discussed in detail in Example 9, below. 
         FIG.  28    depicts in table form the results of a statistical analysis performed on metabolomics data on plasma obtained from a third-party provider. A Mann Whitney U test is used to find significantly different metabolites between cancer and control cohorts. The top 100 metabolites ranked by p value are reported, as discussed in detail in Example 9, below. 
         FIG.  29    graphically illustrates data from studies where mice inoculated with CT-26 colon cancer cells were treated with microbial mix 4 and anti-CTLA-4 therapy, the data showing that the anti-CTLA-4 therapy with microbial mix 4 (or “microbe mix 4”) had minimal tumor growth in contrast to the other groups, tumor volume is shown as a function of time since tumor inoculation, as described in Example 15, below. 
         FIG.  30    illustrates a plot summarizing data from a FACS analysis of whole blood obtained from the animals at the end of a study (as described in Example 15) that indicated that CD4 and CD8 T-lymphocyte activity are increased by treatment with a microbial mix 4 in conjunction with anti-CTLA-4. 
         FIG.  31    graphically illustrates data from studies where mice inoculated with CT-26 colon cancer cells were treated with microbial mix 2, mix 5 and anti-CTLA4 therapy, the data showing that the anti-CTLA-4 therapy with microbial mix 2 (or “microbe mix 2”) had minimal tumor growth in contrast to the other groups, tumor volume is shown as a function of time since tumor inoculation, as described in Example 15, below. 
         FIG.  32    graphically illustrates a principal component analysis on metabolome profile from all samples at timepoint T7. Downward cones, Control; circles, Microbe; squares, Drug; and upward cones, Combo; as described in detail in Example 15, below. 
         FIG.  33    graphically illustrates data of concentrations of pterin and biopterin in mouse samples over time; in order from lightest to darkest lines and symbols, groups are indicated as follows: Control, Microbe, Drug, Combo; as described in detail in Example 15, below. 
         FIG.  34    graphically illustrates data from studies where mice inoculated with CT-26 colon cancer cells were treated with microbial mix 4 and prebiotic (ellagic acid) therapy, the data showing that the prebiotic therapy (ellagic acid) with microbial mix 4 had minimal tumor growth in contrast to the other groups, tumor volume is shown as a function of time since tumor inoculation, as described in Example 16, below. 
         FIG.  35    graphically illustrates flow cytometry data from a immune-phenotyping of mice subjected to cancer receiving the different microbial treatments, where measurements were conducted on both peripheral blood and on the tumor itself, with stains for various cell surface markers, where final tumor volume is a function of CD3+ proportion in CD45 cells (left image) or CD4 to CD8 ratio in CD3+ cells (right image), as discussed in detail in Example 16, below. 
         FIG.  36    graphically illustrates Spearman correlations between immune cell populations and final tumor volume for all treatment groups and magnitude is plotted by GI location (small intestine, cecum and colon); as discussed in detail in Example 17, below. 
         FIG.  37    graphically illustrates the statistically significant correlation between final tumor volume for all treatment groups and the IA/IE (MHC II) immune cell populations in the colon for all treatment groups; as discussed in detail in Example 17, below. 
         FIG.  38    graphically illustrates flow cytometry data on mice 22 days post-inoculation and CD3+ percentage is displayed against tumor volume at day 28 post-inoculation; as discussed in detail in Example 17, below. 
         FIG.  39    graphically illustrates tumor volumes for mice remaining alive (10 mice initially per group) 28 days post tumor inoculation; as discussed in detail in Example 17, below. 
         FIG.  40    graphically illustrates tumor volumes over time for mice treated with anti-PD1 alone or in conjunction with microbial mix 2; as discussed in detail in Example 17, below. 
         FIG.  41    graphically illustrates tumor volumes that were measured 28 days post inoculation and displayed by both pre-treatment and treatment groups; as discussed in detail in Example 17, below. 
         FIG.  42 A-B  graphically illustrates tumor volumes that were measured at multiple time points post-inoculation. Mean and standard error of the mean are displayed for each treatment group within water ( FIG.  42 A ) and antibiotic ( FIG.  42 B ) pre-treatment groups; as discussed in detail in Example, 22 below. 
         FIG.  43    graphically illustrates tumor volume distribution with and without microbial mix 2 being administered for each FMT donor. The box denotes the 25th, 50th, and 75th percentiles of the data, and each point is a single mouse; as discussed in detail in Example 17, below. 
         FIG.  44    graphically illustrates the mean tumor volume over time for mice receiving microbial mix 2 vs Vehicle for each fecal transplant donor. Error bars are standard error of the mean; as discussed in detail in Example 17, below. 
         FIG.  45    graphically illustrates the mean tumor volume over time for mice receiving microbial mix 2 vs Vehicle for each fecal transplant donor. Each dot denotes an individual mouse&#39;s tumor volume; as discussed in detail in Example, 17 below. 
         FIG.  46 A-D  graphically illustrates images of the gastrointestinal tract at day 21 for mice pre-treated with either water or antibiotics and treatments including vehicle, anti-CTLA-4, anti-CTLA-4 in combination with microbial mix 4+ ellagic acid and anti-CTLA-4 in combination with microbial mix 2; as discussed in detail in Example 17, below. 
         FIG.  47    illustrates Table 33, as discussed in Example 24, below. 
         FIG.  48    graphically illustrates the CyTOF gating strategy used to classify immune cell populations based on metal-labeled peptide markers, and cell counts for a representative sample; as discussed in detail in Example 24, below. 
         FIG.  49    illustrates Table 40, as discussed in Example 25, below. 
         FIG.  50    illustrates Table 41, as discussed in Example 25, below. 
         FIG.  51    graphically represents survival of mice following FMT treatment and challenge with influenza A/CA/04/2009 (H1N1pdm) virus; Kaplan-Meier survival curves were generated and compared by the Log-rank (Mantel-Cox) test followed by pairwise comparison using the Gehan-Breslow-Wilcoxon test in PRISM 9.0.2™ (GraphPad Software Inc.); mean body weights were analyzed by one-way analysis of variance (ANOVA) followed by Tukey&#39;s multiple comparison tests using PRISM™; the mean day of death was calculated using PRISM™ and differences in mean day of death were evaluated by one-way ANOVA; no significant difference in survival post-infection was observed between infected HC-FMT or NR-FMT treated mice. 
         FIG.  52    graphically illustrates mean body weights of mice following FMT treatment, then challenge with influenza A/CA/04/2009 (H1N1pdm) virus. 
         FIG.  53    is a box plot showing lung virus titers of mice following FMT treatment and challenge with influenza A/CA/04/2009 (H1N1pdm) virus. 
         FIG.  54    illustrates lung scores of visible pathogenicity of mice following FMT treatment and challenge with influenza A/CA/04/2009 (H1N1pdm) virus. 
         FIG.  55    graphically illustrates lung weights of mice following FMT treatment and challenge with influenza A/CA/04/2009 (H1N1pdm) virus. 
         FIG.  56    graphically illustrates lung cytokine concentrations of IL-1a, IL-1b, IL-2, and IL-3 of mice treated with HC- or NR-FMT, before (uninfected) and following challenge with influenza A/CA/04/2009 (H1N1pdm) virus (infected). Welch&#39;s t-test was applied to identify those with significant differential abundance between and non-responders FMT HC-FMT and NR-FMT recipients (N=9 for each group). P-values are shown for groups in cases where they are less than 0.05. 
         FIG.  57    graphically illustrates lung cytokine concentrations of IL-4, IL-5, IL-6, and IL-10 of mice treated with HC- or NR-FMT, before (uninfected) and following challenge with influenza A/CA/04/2009 (H1N1pdm) virus (infected). Welch&#39;s t-test was applied to identify those with significant differential abundance between and non-responders FMT HC-FMT and NR-FMT recipients (N=9 for each group). P-values are shown for groups in cases where they are less than 0.05. 
         FIG.  58    graphically illustrates lung cytokine concentrations of IL-12p70, IL-17, MCP-1, and IFN-γ of mice treated with HC- or NR-FMT, before (uninfected) and following challenge with influenza A/CA/04/2009 (H1N1pdm) virus (infected). Welch&#39;s t-test was applied to identify those with significant differential abundance between and non-responders FMT HC-FMT and NR-FMT recipients (N=9 for each group). P-values are shown for groups in cases where they are less than 0.05. 
         FIG.  59    graphically illustrates lung cytokine concentrations of TNFα, MIP-1α, GM-CSF, and RANTES of mice treated with HC- or NR-FMT, before (uninfected) and following challenge with influenza A/CA/04/2009 (H1N1pdm) virus (infected); Welch&#39;s t-test was applied to identify those with significant differential abundance between and non-responders FMT HC-FMT and NR-FMT recipients (N=9 for each group); P-values are shown for groups in cases where they are less than 0.05. 
         FIG.  60    presents metagenomic analyses of FMT preparations made from feces from the HC and NR human donors; each slice of the donut plot indicates the fractional abundance of a microbial taxon, in most case a species or strain, in the complete metagenome; taxa that fall below 1.0% total abundance are grouped together as “Other”. 
     
    
    
     Like reference symbols in the various drawings indicate like elements. 
     DETAILED DESCRIPTION 
     In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, comprising novel combinations of microbes, also called live biotherapeutic compositions such as non-pathogenic, live (optionally dormant) bacteria and/or bacterial spores, for example, such as the exemplary combinations of microbes as listed in Table 9, Example 10 and Table 42, Example 25. In alternative embodiments, the compositions, products of manufacture, kits and methods as provided herein are used as a therapy (for example, as a mono-therapy or as a co-therapy, or co-treatment) for the control, amelioration and/or treatment of a disease or condition, for example, a viral infection such as a coronavirus infection. In alternative embodiments, the compositions, products of manufacture, kits and/or methods as provided herein are administered to an individual receiving a drug, for example, an anti-viral therapy, thereby resulting in a modification or modulation of the patient&#39;s gut microfloral population(s), thus resulting in an enhancement of the drug therapy, for example, lowering the dosage or amount of drug needed for effective therapy, or the frequency with which a drug must be administered to be effective. In alternative embodiments, by modulating or modifying the individual&#39;s gut microbial population(s) using compositions, products of manufacture and methods as provided herein, the pharmacodynamics of a drug administered to the patient is altered, for example, the pharmacodynamics of the drug is enhanced, for example, the individual&#39;s ability to absorb a drug is modified (for example, accelerated or slowed, or enhanced), or the dose efficacy of a drug is increased (for example, resulting in needing a lower dose of drug for an intended effect), or the gut microbes act orthogonally on the drug target (for example, resulting in the presence of the microbe being essential for the drug to have the intended effect). For example, in alternative embodiments, by modulating or modifying the patient&#39;s gut microbial population(s) using compositions, products of manufacture and methods as provided herein the dose efficacy of a drug, for example, an anti-viral drug, vaccine, or therapy, is increased, thereby enhancing the control, amelioration or treatment of that viral infection. 
     In alternative embodiments, the amount, identity, presence, and/or ratio of gut microbiota in a subject is manipulated to facilitate a mono-therapy or one or more co-treatments; for example, in alternative embodiments, combinations of microbes as provided herein are administered with (for example, concurrent with, or before and/or after) an anti-viral treatment. 
     Described here for the first time are novel combinations of specific microbes, for example, bacteria, including for example microbes found in a human gut or recombinantly engineered or cultured microbes, which can be administered as a mono-therapy or as a co-therapy for, in alternative embodiments, patients having or suspected of having or at increased risk of having a viral infection such as a coronavirus infection, where in alternative embodiments the patients are already undergoing an immune checkpoint inhibitor treatment, or are already undergoing a chemotherapy, a radiation therapy, an immune checkpoint inhibitor, a Chimeric Antigen Receptor (CAR) T-cell therapy (CAR-T) or other immunotherapy or cancer treatment. 
     In alternative embodiments, provided are therapeutic compositions, including formulations and pharmaceutical compositions, comprising non-pathogenic (optionally dormant) live microbes such as bacteria and/or germination-competent bacterial spores, which can be used for the prevention, amelioration or treatment of a viral infection or the side effects of an anti-viral therapy, for example, a drug therapy or anti-viral vaccine, or can be used or administered before, with or after a chemotherapy, a radiation therapy, an immune checkpoint inhibitor, a Chimeric Antigen Receptor (CAR) T-cell therapy (CAR-T) or other immunotherapy or cancer treatment. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein, or used to practice methods as provided herein, comprise colony forming (optionally dormant) live bacteria and/or germinable bacterial spores which can be used in mono- or co-therapies, for example, as an adjuvant to an antineoplastic treatment administered to a cancer patient, or administered with or as a supplement to a chemotherapy, a radiation therapy, an immune checkpoint inhibitor, a Chimeric Antigen Receptor (CAR) T-cell therapy (CAR-T) or other immunotherapy or cancer treatment. 
     In some embodiments, a therapeutic composition as provided herein acts or is used as a probiotic composition which can be administered with, before and/or after a chemotherapy, a radiation therapy, an immune checkpoint inhibitor, a Chimeric Antigen Receptor (CAR) T-cell therapy (CAR-T) or other immunotherapy or cancer treatment. In alternative embodiments, therapeutic compositions (for example, the formulations) as provided herein, comprise the bacteria and/or spores and an antineoplastic active agent such as an immune checkpoint inhibitor. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein, or used to practice methods as provided herein, comprise colony forming (optionally dormant) live bacteria and/or germinable bacterial spores for use as a mono-therapy or in combination with (for example, as a co-therapy) or supplementary to a drug (which can be a small molecule or a protein, for example, a therapeutic antibody) blocking an immune checkpoint for inducing immuno-stimulation in a cancer patient. The therapeutic composition as provided herein and the drug (for example, an antibody) can be administered separately or together, or at different time points or at the same time, or can be administered sequentially or concurrently. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein comprise colony forming (optionally dormant) live bacteria and/or germinable bacterial spores which can be used as an adjuvant to an anti-cancer or antineoplastic treatment, for example, an immune checkpoint treatment, administered to a cancer patient. In alternative embodiments, the therapeutic composition comprises the antineoplastic or immune checkpoint active agents. In alternative embodiments, the therapeutic composition, formulations or pharmaceutical compositions as provided herein are administered with or after, or both with and after, administration of the antineoplastic or immune checkpoint active agent. 
     In alternative embodiments, the formulation or pharmaceutical composition further comprises, or is manufactured with, an outer layer of polymeric material (for example, natural polymeric material) enveloping, or surrounding, a core that comprises the combination of microbes as provided herein. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein, or used to practice methods as provided herein, can comprise a pharmaceutically acceptable carrier, diluent, and/or adjuvant. In other embodiments a pharmaceutically acceptable preservative is present. In yet other embodiments, a pharmaceutically acceptable germinate is present. In still other embodiments the therapeutic composition contains, or further comprises, a nutrient such as inulin, beta-glucan, mannitol, mucin, L-tryptophan, tryptamine, 5-hydroxytryptophan, or niacin, or an immunostimulant such as polyinosinic-polycytidylic acid (poly I.C) at an effective dose of 0.005, 0.05, 0.5, 5.0 milligrams per kilogram body weight 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein, or used to practice methods as provided herein, are in the form of a tablet, geltab or capsule, for example, a polymer capsule such as a gelatin or a hydroxypropyl methylcellulose (HPMC, or hypromellose) capsule (for example, VCAPS PLUS™ (Capsugel, Lonza)). In other embodiments, the therapeutic compositions, formulations or pharmaceutical compositions are in or are manufactured as a food or drink, for example, an ice, candy, lolly or lozenge, or any liquid, for example, in a beverage. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein, or used to practice methods as provided herein, comprise at least one bacterial type that is not detectable, of low natural abundance, or not naturally found, in a healthy or normal subject&#39;s (for example, human) gastrointestinal tract. In alternative embodiments, the gastrointestinal tract refers to the stomach, the small intestine, the large intestine and the rectum, or combinations thereof. 
     In alternative embodiments, provided are methods of ameliorating or treating cancer and/or at least one symptom resulting from a cancer therapy or of a condition of the gastrointestinal tract. 
     In alternative embodiments, by administration of a therapeutic composition, formulation or pharmaceutical composition as provided herein to a subject, or practicing a method as provided herein, the microbiome population or composition of the subject is modulated or altered. 
     In alternative embodiments, the term “microbiome” encompasses the communities of microbes that can live sustainably and/or transiently in and on a subject&#39;s body, for example, in the gut of a human, including bacteria, viruses and bacterial viruses, archaea, and eukaryotes. In alternative embodiments, the term “microbiome” encompasses the “genetic content” of those communities of microbes, which includes the genomic DNA, RNA (ribosomal-, messenger-, and transfer-RNA), the epigenome, plasmids, and all other types of genetic information. 
     In alternative embodiments, the term “subject” refers to any animal subject including humans, laboratory animals (for example, primates, rats, mice), livestock (for example, cows, sheep, goats, pigs, turkeys, and chickens), and household pets (for example, dogs, cats, and rodents). The subject may be suffering from a disease, for example, a cancer. 
     In alternative embodiments, the term “type” or “types” when used in conjunction with “bacteria” or “bacterial” refers to bacteria differentiated at the genus level, the species level, the sub-species level, the strain level, or by any other taxonomic method known in the art. 
     In alternative embodiments, the phrase “dormant live bacteria” refers to live vegetative bacterial cells that have been rendered dormant by lyophilization or freeze drying. Such dormant live vegetative bacterial cells are capable of resuming growth and reproduction immediately upon resuscitation. 
     In alternative embodiments, the term “spore” also includes “endospore”, and these terms can refer to any bacterial entity which is in a dormant, non-vegetative and non-reproductive stage, including spores that are resistant to environmental stress such as desiccation, temperature variation, nutrient deprivation, radiation, and chemical disinfectants. In alternative embodiments, “spore germination” refers to the dormant spore beginning active metabolism and developing into a fully functional vegetative bacterial cell capable of reproduction and colony formation. In alternative embodiments, “germinant” is a material, composition, and/or physical-chemical process capable of inducing vegetative growth of a dormant bacterial spore in a host organism or in vitro, either directly or indirectly. 
     In alternative embodiments, the term “colony forming” refers to a vegetative bacterium that is capable of forming a colony of viable bacteria or a spore that is capable of germinating and forming a colony of viable bacteria. 
     In alternative embodiments, the term “natural polymeric material” comprises a naturally occurring polymer that is not easily digestible by human enzymes so that it passes through most of the human digestive system essentially intact until it reaches the large or small intestine. 
     In alternative embodiments, therapeutic compositions, formulations or pharmaceutical compositions as provided herein comprise population(s) of non-pathogenic dormant live bacteria and/or bacterial spores. The dormant live bacteria can be capable of colony formation and, in the case of spores, germination and colony formation. Thus, in alternative embodiments, compositions are useful for altering a subject&#39;s gastrointestinal biome, for example, by increasing the population of those bacterial types or microorganisms, or are capable of altering the microenvironment of the gastrointestinal biome, for example, by changing the chemical microenvironment or disrupting or degrading intestinal mucin or biofilm, thereby providing treatment of cancer, gastrointestinal conditions, and symptoms resulting from cancer therapy, ultimately increasing the health of the subject to whom they are administered. 
     In alternative embodiments, the terms “purify,” purified,” and “purifying” are used interchangeably to describe a population&#39;s known or unknown composition of bacterial type(s), amount of that bacterial type(s), and/or concentration of the bacterial type(s); a purified population does not have any undesired attributes or activities, or if any are present, they can be below an acceptable amount or level. In alternative embodiments, the various populations of bacterial types are purified, and the terms “purified,” “purify,” and “purifying” refer to a population of desired bacteria and/or bacterial spores that have undergone at least one process of purification; for example, a process comprising screening of individual colonies derived from fecal matter for a desired phenotype, such as their effectiveness in enhancing the pharmacodynamics of a drug (such as a cancer drug, for example, a drug inhibitory to an immune checkpoint), for example, the individual&#39;s ability to absorb a drug is modified (for example, accelerated or slowed, or enhanced), or the dose efficacy of a drug is increased (for example, resulting in needing a lower dose of drug for an intended effect), or the immune system is primed for improved drug efficacy, or a selection or enrichment of the desired bacterial types. 
     Enrichment can be accomplished by increasing the amount and/or concentration of the bacterial types, such as by culturing in a media that selectively favors the growth of certain types of microbes, by screening pure microbial isolates for the desired genotype, or by a removal or reduction in unwanted bacterial types. 
     In alternative embodiments, bacteria used to practice compositions and methods provided herein are derived from fecal material donors that are in good health, have microbial biomes associated with good health, and are typically free from antibiotic administration during the collection period and for a period of time prior to the collection period such that no antibiotic remains in the donor&#39;s system. In alternative embodiments, the donor subjects do not suffer from and have no family history of renal cancer, bladder cancer, breast cancer, prostate cancer, lymphoma, leukemia, autoimmune disease. In alternative embodiments, donor subjects are free from irritable bowel disease, irritable bowel syndrome, celiac disease, Crohn&#39;s disease, colorectal cancer, anal cancer, stomach cancer, sarcomas, any other type of cancer, or a family history of these diseases. In alternative embodiments, donor subjects do not have and have no family history of mental illness, such as anxiety disorder, depression, bipolar disorder, autism spectrum disorders, panic disorders, obsessive-compulsive disorder, attention-deficit disorders, eating disorders (for example bulimia, anorexia), mood disorder or schizophrenia. In yet other embodiments the donor subjects have no knowledge or history of food allergies or sensitivities. 
     In alternative embodiments, the health of fecal matter donors is screened prior to the collection of fecal matter, such as at 1, 2, 3, 4, 8, 16, 20, 24, 28, 32, 36, 40, 44, 48, or 52 weeks pre-collection. In alternative embodiments, fecal matter donors are also screened post-collection, such as at 1, 2, 3, 4, 8, 16, 20, 24, 28, 32, 36, 40, 44, 48, or 52 weeks post-collection. Pre- and post-screening can be conducted daily, weekly, bi-weekly, monthly, or yearly. In alternative embodiments, individuals who do not test positive for pathogenic bacteria and/or viruses (for example, coronavirus, HIV, hepatitis, polio, adeno-associated virus, pox, coxsackievirus, etc.) pre- and post-collection are considered verified donors. 
     In alternative embodiments, to purify bacteria and/or bacterial spores, fecal matter is collected from donor subjects and placed in an anaerobic chamber within a short time after elimination, such as no more than 1 minute, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, or 60 minutes or more after elimination. In alternative embodiments, fecal matter is collected from donor subjects are placed in an anaerobic chamber within between about 1 minute and 48 hours, or more, after elimination from the donor. 
     Bacteria from a sample of the collected fecal matter can be collected in several ways. For example, the sample can be mixed with anoxic nutrient broth, dilutions of the resulting mixture conducted, and bacteria present in the dilutions grown on solid anoxic media. Alternatively, bacteria can be isolated by streaking a sample of the collected material directly on anoxic solid media for growth of isolated colonies. In alternative embodiments, to increase the ease of isolating bacteria from fecal samples mixed with anoxic nutrient broth, the resulting mixture can be shaken, vortexed, blended, filtered, and centrifuged to break up and/or remove large non-bacterial matter. 
     In alternative embodiments, purification of the isolated bacteria and/or bacterial spores by any means known in the art, for example, contamination by undesirable bacterial types, host cells, and/or elements from the host microbial environment can be eliminated by reiterative streaking to single colonies on solid media until at least two replicate streaks from serial single colonies show only a single colony morphology. Purification can also be accomplished by reiterative serial dilutions to obtain a single cell, for example, by conducting multiple 10-fold serial dilutions to achieve an ultimate dilution of 10 −2 , 10 −3 , 10 −4 , 10 −5 , 10 −6 , 10 −7 , 10 −8 , 10 −9  or greater. Any methods known to those of skill in the art can also be applied. 
     Confirmation of the presence of only a single bacterial type can be confirmed in multiple ways such as, gram staining, PCR, DNA sequencing, enzymatic analysis, metabolic profiling/analysis, antigen analysis, and flow cytometry using appropriate distinguishing reagents. 
     In alternative embodiments, purified population(s) of vegetative bacteria that are incorporated into therapeutic bacterial compositions as provided herein, or used to practice methods as provided herein, are fermented in growth media. Suitable growth media include Nutrient Broth (Thermo Scientific™ Oxoid™), Anaerobe Basal Broth (Thermo Scientific™ Oxoid™), Reinforced Clostridial Medium (Thermo Scientific™ Oxoid™), Schaedler Anaerobic Broth (Thermo Scientific™ Oxoid™), MRS Broth (Millipore-Sigma™), Vegitone  Actinomyces  Broth (Millipore-Sigma™), Vegitone Infusion Broth (Millipore-Sigma™), Vegitone Casein Soya Broth (Millipore-Sigma™), or one of the following media available from Anaerobe Systems: Brain Heart Infusion Broth (BHI),  Campylobacter -Thioglycollate Broth (CAMPY-THIO), Chopped Meat Broth (CM), Chopped Meat Carbohydrate Broth (CMC), Chopped Meat Glucose Broth (CMG), Cycloserine Cefoxitin Mannitol Broth with Taurocholate Lysozyme Cysteine (CCMB-TAL), Oral Treponeme Enrichment Broth (OTEB), MTGE-Anaerobic Enrichment Broth (MTGE), Thioglycollate Broth with Hemin, Vit. K, without indicator, (THIO), Thioglycollate Broth with Hemin, Vit. K, without indicator, (THIO),  Lactobacilli -MRS Broth (LMRS),  Brucella  Broth (BRU-BROTH), Peptone Yeast Extract Broth (PY), PY Glucose (PYG), PY Arabinose, PY Adonitol, PY Arginine, PY Amygdalin, PYG Bile, PY Cellobiose, PY DL-Threonine, PY Dulcitol, PY Erythritol, PY Esculin, PYG Formate/Fumarate for FA/GLCf, PY Fructose, PY Galactose, PYG Gelatin, PY Glycerol, Indole-Nitrate Broth, PY Inositol, PY Inulin, PY Lactate for FA/GLCf, PY Lactose, PY Maltose, PY Mannitol, PY Mannose, PY Melezitose, PY Melibiose, PY Pyruvic Acid, PY Raffinose, PY Rhamnose, PY Ribose, PY Salicin, PY Sorbitol, PY Starch, PY Sucrose, PY Trehalose, PY Xylan, PY Xylose, Reinforced Clostridial Broth (RCB), Yeast Casitone Fatty Acids Broth with Carbohydrates (YCFAC Broth). In alternative embodiments, growth media includes or is supplemented with reducing agents such as L-cysteine, dithiothreitol, sodium thioglycolate, and sodium sulfide. In alternative embodiments, fermentation is conducted in stirred-tank fermentation vessels, performed in either batch or fed-batch mode, with nitrogen sparging to maintain anaerobic conditions. pH is controlled by the addition of concentrated base, such as NH 4 OH or NaOH. In the case of fed-batch mode, the feed is a primary carbon source for growth of the microorganisms, such as glucose. In alternative embodiments, the post-fermentation broth is collected, and/or the bacteria isolated by ultrafiltration or centrifugation and lyophilized or freeze dried prior to formulation. 
     In alternative embodiments, purified and isolated vegetative bacterial cells used in therapeutic bacterial compositions as provided herein, or used to practice methods as provided herein, have been made dormant; noting that bacterial spores are already in a dormancy state. Dormancy of the vegetative bacterial cells can be accomplished by, for example, incubating and maintaining the bacteria at temperatures of less than 4° C., freezing and/or lyophilization of the bacteria. Lyophilization can be accomplished according to normal bacterial freeze-drying procedures as used by those of skill in the art, such as those reported by the American Type Culture Collection (ATCC) on the ATCC website (see, for example, (https://www.atcc.org). 
     In alternative embodiments, the purified population of dormant live bacteria and/or bacterial spores has undetectable levels of pathogenic activities, such as the ability to cause infection and/or inflammation, toxicity, an autoimmune response, an undesirable metabolic response (for example diarrhea), or a neurological response. 
     In alternative embodiments, all of the types of dormant live bacteria or bacterial spores present in a purified population are obtained from fecal material treated as described herein or as otherwise known to those of skill in the art. In other embodiments, one or more of the types of dormant live bacteria or bacterial spores present in a purified population is generated individually in culture and combined with one or more types obtained from fecal material. In alternative embodiments, all of the types of dormant live bacteria or bacterial spores present in a purified population are generated individually in culture. In still other embodiments, one or all of the types of dormant live bacteria and/or bacterial spores present in a purified population are non-naturally occurring or engineered. In yet other embodiments, non-naturally occurring or engineered non-bacterial microorganisms are present, with or without dormant live bacteria and/or bacterial spores. 
     In alternative embodiments, bacterial compositions used in compositions as provided herein, or to practice methods as provided herein, comprise combinations of different bacteria, for example, comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more bacterial types, or more than 20 bacterial types, or between about 2 and 30 bacterial types. 
     In alternative embodiments, the bacterial compositions comprise at least about 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 , or more (or between about 10 2  to 10 15 ) microbes, for example, dormant live bacteria and/or bacterial spores. In some embodiments each bacterial type is equally represented in the total number of dormant live bacteria and/or bacterial spores. In other embodiments, at least one bacterial type is represented in a higher amount than the other bacterial type(s) found in the composition. 
     In alternative embodiments, a population of different bacterial types used in compositions as provided herein, or to practice methods as provided herein, can increase microbe populations found in the subject&#39;s gastrointestinal tract by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900% or 1000%, or between about 5% and 2000%, as compared to the subject&#39;s microbiome gastrointestinal population prior to treatment. 
     In alternative embodiments, the combination of microbes, for example, combination of bacterial cells and/or spores, used in compositions as provided herein, or to practice methods as provided herein, are mixed with pharmaceutically acceptable excipients, such as diluents, carriers, adjuvants, binders, fillers, salts, lubricants, glidants, disintegrants, coatings, coloring agents, etc. Examples of such excipients are acacia, alginate, alginic acid, aluminum acetate, benzyl alcohol, butyl paraben, butylated hydroxy toluene, citric acid, calcium carbonate, candelilla wax, croscarmellose sodium, confectioner sugar, colloidal silicone dioxide, cellulose, plain or anhydrous calcium phosphate, carnuba wax, corn starch, carboxymethylcellulose calcium, calcium stearate, calcium disodium EDTA, copolyvidone, calcium hydrogen phosphate dihydrate, cetylpyridine chloride, cysteine HCL, crossprovidone, calcium phosphate di or tri basic, dibasic calcium phosphate, disodium hydrogen phosphate, dimethicone, erythrosine sodium, ethyl cellulose, gelatin, glyceryl monooleate, glycerin, glycine, glyceryl monostearate, glyceryl behenate, hydroxy propyl cellulose, hydroxyl propyl methyl cellulose, hypromellose, HPMC phthalate, iron oxides or ferric oxide, iron oxide yellow, iron oxide red or ferric oxide, lactose hydrous or anhydrous or monohydrate or spray dried, magnesium stearate, microcrystalline cellulose, mannitol, methyl cellulose, magnesium carbonate, mineral oil, methacrylic acid copolymer, magnesium oxide, methyl paraben, providone or PVP, PEG, polysorbate 80, propylene glycol, polyethylene oxide, propylene paraben, polaxamer 407 or 188, potassium bicarbonate, potassium sorbate, potato starch, phosphoric acid, polyoxy140 stearate, sodium starch glycolate, starch pregelatinized, sodium carmellose, sodium lauryl sulfate, starch, silicon dioxide, sodium benzoate, stearic acid, sucrose, sorbic acid, sodium carbonate, saccharin sodium, sodium alginate, silica gel, sorbiton monooleate, sodium stearyl fumarate, sodium chloride, sodium metabisulfite, sodium citrate dihydrate, sodium starch, sodium carboxy methyl cellulose, succinic acid, sodium propionate, titanium dioxide, talc, triacetin, and triethyl citrate. 
     In alternative embodiments, the combinations of microbes, for example, combination of bacterial cells and/or spores, used in compositions as provided herein, or to practice methods as provided herein, are fabricated as colonic or microflora-triggered delivery systems, as described for example, in Basit et al, J. Drug Targeting, 17:1, 64-71; Kotla, Int J Nanomedicine. 2016; 11: 1089-1095; Bansai et al, Polim Med. 2014 April-June; 44(2):109-18; or, Shah et al, Expert Opin Drug Deliv. 2011 June; 8(6):779-96. 
     In alternative embodiments, combinations of microbes, for example, combination of bacterial cells and/or spores, used in compositions as provided herein, or to practice methods as provided herein, are encapsulated in at least one polymeric material, for example, a natural polymeric material, such that there is a core of bacterial cells and/or spores surrounded by a layer of the polymeric material, for example, a polysaccharide. Examples of suitable polymeric materials are those that have been demonstrated to remain intact through the GI tract until reaching the small or large intestine, where they are degraded by microbial enzymes in the intestines. Exemplary natural polymeric materials can include, but are not restricted to, chitosan, inulin, guar gum, xanthan gum, amylose, alginates, dextran, pectin, khava, and  albizia  gum (Dafe et al. (2017) Int J Biol Macromol; Kofla et al. (2016) Int J Nanomedicine 11:1089-1095). 
     In alternative embodiments, compositions provided herein are suitable for therapeutic administration to a human or other mammal in need thereof. In alternative embodiments the compositions are produced by a process comprising, for example: (a) obtaining fecal material from a mammalian donor subject, (b) subjecting the fecal material to at least one purification treatment under conditions that produce a single bacterial type population of bacteria and/or bacterial spores, or a combination of bacterial types and/or bacterial spores, (c) optionally combining the purified population with another purified population obtained from the same or different fecal material, from cultured conditions, or from a genetic stock center such as ATCC or DSMZ, (d) if the microbes, for example, bacterial cells, are not dormant, then treating the purified population(s) under conditions that cause vegetative bacterial cells to become dormant, and (e) placing the dormant bacteria and/or bacterial spores in a vehicle for administration. 
     In alternative embodiments, formulations and pharmaceutical compositions, and microbes, for example, bacterial cells and/or spores, used in compositions as provided herein or to practice methods as provided herein, are formulated for oral or gastric administration to a mammalian subject. In particular embodiments, the composition is formulated for oral administration as a solid, semi-solid, gel or liquid form, such as in the form of a pill, tablet, capsule, lozenge, food, extract or beverage. Examples of suitable foods are those that require little mastication, such as yogurt, puddings, gelatins, and ice cream. Examples of extracts include crude and processed pomegranate juice, strawberry, raspberry and blackberry. Examples of suitable beverages include cold beverages, such as juices (pomegranate, raspberry, blackberry, blueberry, cranberry, acai, cloudberry, etc., and combinations thereof) and teas (green, black, etc.) and oaked wine. 
     In alternative embodiments, formulations and pharmaceutical compositions further comprise, or methods as provided herein further comprise administration of, at least one antibiotic (including anti-bacterials or anti-virals), for example, a tetracycline class drug such as doxycycline, chlortetracycline, tetracycline hydrochloride, oxytetracycline, demeclocycline, methacycline or minocycline, penicillin, amoxycillin, erythromycin, vancomycin, clarithromycin, roxithromycin, azithromycin, spiramycin, oleandomycin, josamycin, kitsamysin, flurithromycin, nalidixic acid, oxolinic acid, norfloxacin, perfloxacin, amifloxacin, ofloxacin, ciprofloxacin, sparfloxacin, levofloxacin, rifabutin, rifampicin, rifapentin, sulfisoxazole, sulfamethoxazole, sulfadiazine, sulfadoxine, sulfasalazine, sulfaphenazole, dapsone, sulfacytidine, linezolid or any combination thereof. In alternative embodiments, the antibiotic or a combination of antibiotics are administered before, during and/or after administration of formulations and pharmaceutical compositions as provided herein. 
     Gradual or Delayed Release Formulations 
     In alternative embodiments, exemplary formulations comprise, contain or are coated by an enteric coating to protect a microbe, for example, a bacteria, in a formulation and pharmaceutical compositions as provided herein to allow it to pass through the stomach and small intestine (for example, protect the administered combination of microbes such that a substantial majority of the microbes remain viable), although spores are typically resistant to the stomach and small intestines. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated with a delayed release composition or formulation, coating or encapsulation. In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are designed or formulated for implantation of living microbes, for example, bacteria or spores, into the gut, including the intestine and/or the distal small bowel and/or the colon. In this embodiment the living microbes, for example, bacteria pass the areas of danger, for example, stomach acid and pancreatic enzymes and bile, and reach the intestine substantially undamaged to be viable and implanted in the GI tract. 
     In alternative embodiments, a formulation or pharmaceutical preparation, or the combination of microbes contained therein, is liquid, frozen or freeze-dried. In alternative embodiments, for example, for an encapsulated formulation, all are in powdered form. In alternative embodiments, if a formulation or pharmaceutical preparation as provided herein is in a powdered, lyophilate or freeze-dried form, the powder, lyophilate or freeze-dried form can be in a container such as a bottle, cartridge, packet or packette, or sachet, and the powder, lyophilate or freeze-dried form can be hydrated or reconstituted by a liquid, for example by adding water, saline, juice, milk and the like to the powder, lyophilate or freeze-dried form, for example, the powdered, lyophilate or freeze-dried form can be added to the liquid. In alternative embodiments, a powdered, lyophilate or freeze-dried form as provided herein is in a bottle or container, and the liquid is added to the bottle or container, and this mixture can be consumed by an individual in need thereof. In alternative embodiments, a powdered, lyophilate or freeze-dried form as provided herein is in a cartridge that can be part of a container or bottle, and the powdered, lyophilate or freeze-dried form can be mixed with the liquid, for example, as described in U.S. Pat. No. 8,590,753. In alternative embodiments, a powdered, lyophilate or freeze-dried form as provided herein can be contained in or can be added to a container or bottle as described for example, in U.S. Pat. Nos. 10,315,815; 10,315,803; 10,281,317; 10,183,116; 9,809,374; 9,345,831; 9,173,999; 7,874,420. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release using cellulose acetate (CA) and polyethylene glycol (PEG), for example, as described by Defang et al. (2005) Drug Develop. &amp; Indust. Pharm. 31:677-685, who used CA and PEG with sodium carbonate in a wet granulation production process. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release using a hydroxypropylmethylcellulose (HPMC), a microcrystalline cellulose (MCC) and magnesium stearate, as described for example, in Huang et al. (2004) European J. of Pharm. &amp; Biopharm. 58: 607-614). 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release using for example, a poly(meth)acrylate, for example a methacrylic acid copolymer B, a methyl methacrylate and/or a methacrylic acid ester, a polyvinylpyrrolidone (PVP) or a PVP-K90 and a EUDRAGIT® RL PO™, as described for example, in Kuksal et al. (2006) AAPS Pharm. 7(1), article 1, E1 to E9. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. 20100239667. In alternative embodiments, the composition comprises a solid inner layer sandwiched between two outer layers. The solid inner layer can comprise the non-pathogenic bacteria and/or spores, and one or more disintegrants and/or exploding agents, or one or more effervescent agents or a mixture. Each outer layer can comprise a substantially water soluble and/or crystalline polymer or a mixture of substantially water soluble and/or crystalline polymers, for example, a polyglycol. These can be adjusted to achieve delivery of the living components to the intestine. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. 20120183612, which describes stable pharmaceutical formulations comprising active agents in a non-swellable diffusion matrix. In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are released from a matrix in a sustained, invariant and, if several active agents are present, independent manner and the matrix is determined with respect to its substantial release characteristics by ethylcellulose and at least one fatty alcohol to deliver bacteria distally. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. No. 6,284,274, which describes a bilayer tablet containing an active agent (for example, an opiate analgesic), a polyalkylene oxide, a polyvinylpyrrolidone and a lubricant in the first layer and a second osmotic push layer containing polyethylene oxide or carboxy-methylcellulose. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. No. 20030092724, which describes sustained release dosage forms in which a nonopioid analgesic and opioid analgesic are combined in a sustained release layer and in an immediate release layer, sustained release formulations comprising microcrystalline cellulose, EUDRAGIT RSPO™, CAB-O-SIL™, sodium lauryl sulfate, povidone and magnesium stearate. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. 20080299197, describing a multi-layered tablet for a triple combination release of active agents to an environment of use, for example, in the GI tract. In alternative embodiments, a multi-layered tablet is used, and it can comprise two external drug-containing layers in stacked arrangement with respect to and on opposite sides of an oral dosage form that provides a triple combination release of at least one active agent. In one embodiment the dosage form is an osmotic device, or a gastro-resistant coated core, or a matrix tablet, or a hard capsule. In these alternative embodiments, the external layers may contain biofilm dissolving agents and internal layers can comprise viable/living bacteria, for example, a formulation comprising at least two different species or genera (or types) of non-pathogenic bacteria as used to practice methods as provided herein. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated as multiple layer tablet forms, for example, where a first layer provides an immediate release of a formulation or pharmaceutical preparation as provided herein and a second layer provides a controlled-release of another (or the same) bacteria or drug, or another active agent, for example, as described for example, in U.S. Pat. No. 6,514,531 (disclosing a coated trilayer immediate/prolonged release tablet), U.S. Pat. No. 6,087,386 (disclosing a trilayer tablet), U.S. Pat. No. 5,213,807 (disclosing an oral trilayer tablet with a core comprising an active agent and an intermediate coating comprising a substantially impervious/impermeable material to the passage of the first active agent), and U.S. Pat. No. 6,926,907 (disclosing a trilayer tablet that separates a first active agent contained in a film coat from a core comprising a controlled-release second active agent formulated using excipients which control the drug release, the film coat can be an enteric coating configured to delay the release of the active agent until the dosage form reaches an environment where the pH is above four). 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. 20120064133, which describes a release-retarding matrix material such as: an acrylic polymer, a cellulose, a wax, a fatty acid, shellac, zein, hydrogenated vegetable oil, hydrogenated castor oil, polyvinylpyrrolidine, a vinyl acetate copolymer, a vinyl alcohol copolymer, polyethylene oxide, an acrylic acid and methacrylic acid copolymer, a methyl methacrylate copolymer, an ethoxyethyl methacrylate polymer, a cyanoethyl methacrylate polymer, an aminoalkyl methacrylate copolymer, a poly(acrylic acid), a poly(methacrylic acid), a methacrylic acid alkylamide copolymer, a poly(methyl methacrylate), a poly(methacrylic acid anhydride), a methyl methacrylate polymer, a polymethacrylate, a poly(methyl methacrylate) copolymer, a polyacrylamide, an aminoalkyl methacrylate copolymer, a glycidyl methacrylate copolymer, a methyl cellulose, an ethylcellulose, a carboxymethylcellulose, a hydroxypropylmethylcellulose, a hydroxymethyl cellulose, a hydroxyethyl cellulose, a hydroxypropyl cellulose, a crosslinked sodium carboxymethylcellulose, a crosslinked hydroxypropylcellulose, a natural wax, a synthetic wax, a fatty alcohol, a fatty acid, a fatty acid ester, a fatty acid glyceride, a hydrogenated fat, a hydrocarbon wax, stearic acid, stearyl alcohol, beeswax, glycowax, castor wax, carnauba wax, a polylactic acid, polyglycolic acid, a co-polymer of lactic and glycolic acid, carboxymethyl starch, potassium methacrylate/divinylbenzene copolymer, crosslinked polyvinylpyrrolidone, polyvinylalcohols, polyvinylalcohol copolymers, polyethylene glycols, non-crosslinked polyvinylpyrrolidone, polyvinylacetates, polyvinylacetate copolymers or any combination thereof. In alternative embodiments, spherical pellets are prepared using an extrusion/spheronization technique, of which many are well known in the pharmaceutical art. The pellets can comprise one or more formulations or pharmaceutical preparations as provided herein. 
     In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are formulated for delayed or gradual enteric release as described in U.S. Pat. App. Pub. 20110218216, which describes an extended release pharmaceutical composition for oral administration, and uses a hydrophilic polymer, a hydrophobic material and a hydrophobic polymer or a mixture thereof, with a microenvironment pH modifier. The hydrophobic polymer can be ethylcellulose, cellulose acetate, cellulose propionate, cellulose butyrate, methacrylic acid-acrylic acid copolymers or a mixture thereof. The hydrophilic polymer can be polyvinylpyrrolidone, hydroxypropylcellulose, methylcellulose, hydroxypropylmethyl cellulose, polyethylene oxide, acrylic acid copolymers or a mixture thereof. The hydrophobic material can be a hydrogenated vegetable oil, hydrogenated castor oil, carnauba wax, candellia wax, beeswax, paraffin wax, stearic acid, glyceryl behenate, cetyl alcohol, cetostearyl alcohol or and a mixture thereof. The microenvironment pH modifier can be an inorganic acid, an amino acid, an organic acid or a mixture thereof. Alternatively, the microenvironment pH modifier can be lauric acid, myristic acid, acetic acid, benzoic acid, palmitic acid, stearic acid, oxalic acid, malonic acid, succinic acid, adipic acid, sebacic acid, fumaric acid, maleic acid; glycolic acid, lactic acid, malic acid, tartaric acid, citric acid, sodium dihydrogen citrate, gluconic acid, a salicylic acid, tosylic acid, mesylic acid or malic acid or a mixture thereof. 
     In alternative embodiments, therapeutic combinations or formulations, or pharmaceuticals or the pharmaceutical preparations as provided herein, or as used in methods as provided herein, are formulated as a delayed or gradual enteric release composition or formulation, and optionally the formulation comprises a gastro-resistant coating designed to dissolve at a pH of 7 in the terminal ileum, for example, an active ingredient is coated with an acrylic based resin or equivalent, for example, a poly(meth)acrylate, for example a methacrylic acid copolymer B, NF, which dissolves at pH 7 or greater, for example, comprises a multimatrix (MMX) formulation. In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are powders that can be included into a suitable carrier, for example, such as a liquid, a tablet or a suppository. In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are ‘powders for reconstitution’ as a liquid to be drunk, placed down a naso-duodenal tube or used as an enema for patients to take home and self-administer enemas. In alternative embodiments, compositions and formulations as provided herein, and compositions and formulations used to practice methods as provided herein, are micro-encapsulated, formed into tablets and/or placed into capsules, especially enteric-coated capsules. In alternative embodiments, compositions as provided herein are formulated to be effective in a given mammalian subject in a single administration or over multiple administrations. In some embodiments, a substrate or prebiotic required by the bacterial type in a formulation as provided herein is administered for a period of time in advance of the administration of the combination of microbes, for example, bacterial compositions, as provided herein. Such administration (for example, of prebiotics) pre-loads the gastrointestinal tract with the substrates needed by the bacterial types of the composition and increases the potential for the bacterial composition to have adequate resources to perform the required metabolic reactions. In other embodiments, the composition is administered simultaneously with the substrates required by the bacterial types a formulation as provided herein. In still other embodiments the substrate or prebiotic is administered alone. In alternative embodiments, efficacy is measured by an increase in the population of those bacterial types in the subject&#39;s intestinal tract, or an increase in the population of those bacterial types originally found in the subject&#39;s intestinal tract before treatment. 
     In alternative embodiments, compositions as provided herein comprise, further comprise, or have added to: at least one probiotic or prebiotic, wherein optionally the prebiotic comprises an inulin, a beta-glucan, a polyol, lactulose, extracts of artichoke, chicory root, oats, barley, various legumes, garlic, kale, beans or flacks or an herb, wherein optionally the probiotic comprises a cultured or stool-extracted microorganism or bacteria, or a bacterial component, and optionally the bacteria or bacterial component comprises or is derived from a  Bacteroidetes , a  Firmicutes , a  Lactobacilli , a  Bifidobacteria , an  Erysipelatoclostridium , a  Ruminococcus , a  Clostridium , a  Collinsella , an  E. coli , a  Streptococcus fecalis  and equivalents. 
     In alternative embodiments, compositions as provided herein comprise, further comprise, or have added to: at least one congealing agent, wherein optionally the congealing agent comprises an arrowroot or a plant starch, a powdered flour, a powdered potato or potato starch, an absorbant polymer, an Absorbable Modified Polymer, and/or a corn flour or a corn starch; or, further comprise an additive selected from one or more of a saline, a media, a defoaming agent, a surfactant agent, a lubricant, an acid neutralizer, a marker, a cell marker, a drug, an antibiotic, a contrast agent, a dispersal agent, a buffer or a buffering agent, a sweetening agent, a debittering agent, a flavoring agent, a pH stabilizer, an acidifying agent, a preservative, a desweetening agent and/or coloring agent, vitamin, mineral and/or dietary supplement, or a prebiotic nutrient; or, further comprise, or have added to: at least one Biofilm Disrupting Compound, wherein optionally the biofilm disrupting compound comprises an enzyme, a deoxyribonuclease (DNase), N-acetylcysteine, an auranofin, an alginate lyase, glycoside hydrolase dispersin B; a Quorum-sensing inhibitor, a ribonucleic acid III inhibiting peptide, Salvadorapersica extracts, Competence-stimulating peptide, Patulin and penicillic acid; peptides—cathelicidin-derived peptides, small lytic peptide, PTP-7, nitric oxide, neo-emulsions; ozone, lytic bacteriophages, lactoferrin, xylitol hydrogel, synthetic iron chelators, a statin (optionally lovastatin (optionally MEVACOR™), simvastatin (optionally ZOCOR™), atorvastatin (optionally LIPITOR™), pravastatin (optionally PRAVACHOL™), fluvastain (optionally LESCOL™) or rosuvastatin (optionally CRESTOR™)), cranberry components, curcumin, silver nanoparticles, Acetyl-11-keto-β-boswellic acid (AKBA), barley coffee components, probiotics, sinefungin, S-adenosylmethionine, S-adenosyl-homocysteine, Delisea furanones, N-sulfonyl homoserine lactones or any combination thereof. 
     In alternative embodiments, compositions as provided herein comprise, further comprise, or have added to: a flavoring or a sweetening agent, an aspartamine, a  stevia , monk fruit, a sucralose, a saccharin, a cyclamate, a xylitol, a vanilla, an artificial vanilla or chocolate or strawberry flavor, an artificial chocolate essence, or a mixture or combination thereof. 
     Products of Manufacture and Kits 
     Provided are products of manufacture, for example, implants or pharmaceuticals, and kits, containing components for practicing methods as provided herein, for example, including a formulation comprising a combination of microbes as provided herein, such as for example, freshly isolated microbes, cultured microbes, or genetically engineered microbes, or at least two different species or genera (or types) of non-pathogenic bacteria, wherein each of the non-pathogenic bacteria comprise (or are in the form of) a plurality of non-pathogenic colony forming live bacteria, a plurality of non-pathogenic germinable bacterial spores, or a combination thereof, and optionally including instructions for practicing methods as provided herein. 
     Companion Diagnostics and Patient Biomarkers 
     Provided are biomarkers indicative of patient response or non-response to a composition or method as provided herein, including for example, an anti-viral treatment or vaccine, a chemotherapy, a radiation therapy, an immune checkpoint inhibitor (for example, a checkpoint inhibitor therapy), a Chimeric Antigen Receptor (CAR) T-cell therapy (CAR-T) or other immunotherapy or a cancer treatment. These biomarkers may be in the form of microbial species abundance in the gut (or abundance in the colon), microbial gene expression or protein expression, or abundance of a metabolite in a stool sample or a sample of bacteria taken from the gut. Alternatively, the biomarkers may be metabolite concentration, cytokine profile, or protein expression in the blood. These biomarkers are used to develop a diagnostic screen to predict in advance whether a patient will naturally respond to therapy or will require microbial intervention to enable the composition or method as provided herein, for example, checkpoint inhibitors or CAR-T therapy, to function efficaciously or more efficaciously as compared to their effectiveness in the patient if a composition or method as provided herein had not been administered. 
     Genetic Modification of Microbial Therapeutics 
     In alternative embodiments, microbes, for example, bacteria, used in compositions as provided herein, or used to practice methods as provided herein, are genetically engineered. In alternative embodiments, microbes are genetically engineered to increase their efficacy, for example, to increase the efficacy of an anti-viral drug or treatment as provided or described herein. 
     In alternative embodiments, one several or all of a combination of microbes as provided herein, or used to practice methods as provided herein, are genetically engineered. In alternative embodiments, microbes are genetically engineered to substantially decrease, reduce or eliminate their toxicity. In alternative embodiments, microbes are genetically engineered to comprise a kill switch so they can be rendered non-vital after administration of an appropriate trigger or signal. In alternative embodiments, microbes are genetically engineered to secrete anti-inflammatory compositions or have an anti-inflammatory effect. In alternative embodiments, microbes are genetically engineered to secrete an anti-cancer substance. 
     Microbes, for example, bacteria, used in compositions as provided herein, or used to practice methods as provided herein, can be genetically engineered using any method known in the art, for example, as discussed in the Examples, below. For example, one or more gene sequence(s) and/or gene cassette(s) may be expressed on a high-copy plasmid, a low-copy plasmid, or a chromosome. In some embodiments, expression from the plasmid is used to increase expression of an inserted, for example, heterologous nucleic acid, for example, a gene or protein encoding sequence or an inhibitory nucleic acid such as an antisense or siRNA-encoding nucleic acid. The inserted nucleic acid of interest can be inserted into a bacterial chromosome at one or more integration sites. 
     For example, in alternative embodiments, microbes are genetically engineered to comprise one or more gene sequence(s) and/or gene cassette(s) for producing a non-native anti-inflammation and/or gut barrier function enhancer molecule. In alternative embodiments, the anti-inflammation and/or gut barrier function enhancer molecule comprises a short-chain fatty acid, butyrate, propionate, acetate, IL-2, IL-22, superoxide dismutase (SOD), GLP-2, GLP-1, IL-10, IL-27, TGF-.beta.1, TGF-.beta.2, N-acylphosphatidylethanolamines (NAPES), elafin (also known as peptidase inhibitor 3 or SKALP), trefoil factor, melatonin, PGD 2 , kynurenic acid, and kynurenine. A molecule may be primarily anti-inflammatory, for example, IL-10, or primarily gut barrier function enhancing, for example, GLP-2. In alternative embodiments, microbes are genetically engineered to comprise one or more gene sequence(s) and/or gene cassette(s) that are inhibitory to the activity of, or substantially or completely inhibit expression of, bacterial virulence factors, toxins, or antibiotic resistance functions. 
     Bacterial Strains 
     In alternative embodiments, bacterial strains used in formulations as provided herein, or in methods as provided herein, are identified by their sequence identities to 16S rDNA. 
     For example, in alternative embodiments, a  Clostridium  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:1: 
     
       
         
           
               
               
            
               
                   
                   Clostridiums  sp. AF36-4 16S ribosomal RNA gene 
               
               
                   
                 SEQ ID 1 
               
               
                   
                 TTTAACATGAGAGTTTGATCCTGGCTCAGGATGAA 
               
               
                   
                   
               
               
                   
                 CGCTGGCGGCGTGCTTAACACATGCAAGTCGAACG 
               
               
                   
                   
               
               
                   
                 AAGCACCTCTCCCGAAGATTGACACAGCTTGCTGT 
               
               
                   
                   
               
               
                   
                 AGATTGATTCATTTGAGGTGACTGAGTGGCGGACG 
               
               
                   
                   
               
               
                   
                 GGTGAGTAACGCGTGGGTAACCTGCCTCATAGAGG 
               
               
                   
                   
               
               
                   
                 GGGACAACAGTTGGAAACGACTGCTAATACCGCAT 
               
               
                   
                   
               
               
                   
                 AGTAAGAAAGATTCGCATGTTTCTTTCTTGAAAGA 
               
               
                   
                   
               
               
                   
                 TTTATCGCTATGAGATGGACCCGCGTCTGATTAGC 
               
               
                   
                   
               
               
                   
                 TAGTTGGTAAGGTAACGGCTTACCAAGGCGACGAT 
               
               
                   
                   
               
               
                   
                 CAGTAGCCGGCTTGAGAGAGTGAACGGCCACATTG 
               
               
                   
                   
               
               
                   
                 GGACTGAGACACGGCCCAAACTCCTACGGGAGGCA 
               
               
                   
                   
               
               
                   
                 GCAGTGGGGAATATTGCACAATGGGGGAAACCCTG 
               
               
                   
                   
               
               
                   
                 ATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCG 
               
               
                   
                   
               
               
                   
                 GTATGTAAAGCTCTATCAGCAGGGAAGATAATGAC 
               
               
                   
                   
               
               
                   
                 GGTACCTGACTAAGAAGCCCCGGCTAACTACGTGC 
               
               
                   
                   
               
               
                   
                 CAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTA 
               
               
                   
                   
               
               
                   
                 TCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGG 
               
               
                   
                   
               
               
                   
                 CAAGGCAAGTCAGATGTGAAAGCCCGGGGCTCAAC 
               
               
                   
                   
               
               
                   
                 CCCGGTACTGCATTTGAAACTGTCTAGCTAGAGTG 
               
               
                   
                   
               
               
                   
                 CAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTG 
               
               
                   
                   
               
               
                   
                 AAATGCGTAGATATTAGGAGGAACACCAGTGGCGA 
               
               
                   
                   
               
               
                   
                 AGGCGGCTTACTGGACTGTAACTGACACTGAGGCA 
               
               
                   
                   
               
               
                   
                 CGAAAGCGTGGGGAGCAAACAGGATTAGATACCCT 
               
               
                   
                   
               
               
                   
                 GGTAGTCCACGCCGTAAACGATGAATACTAGGTGT 
               
               
                   
                   
               
               
                   
                 CGGGGCCCACAGGGCTTCGGTGCCGCAGCAAACGC 
               
               
                   
                   
               
               
                   
                 ATTAAGTATTCCACCTGGGGAGTACGTTCGCAAGA 
               
               
                   
                   
               
               
                   
                 ATGAAACTCAAAGGAATTGACGGGGACCCGCACAA 
               
               
                   
                   
               
               
                   
                 GCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCG 
               
               
                   
                   
               
               
                   
                 AAGAACCTTACCAAGTCTTGACATCCTTCTGACCG 
               
               
                   
                   
               
               
                   
                 TTCCTTAGCCGGAACTTCCCTTCGGGGCAGAAGTG 
               
               
                   
                   
               
               
                   
                 ACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGT 
               
               
                   
                   
               
               
                   
                 GAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACC 
               
               
                   
                   
               
               
                   
                 CTTATCCTTAGTAGCCAGCGGTTCGGCCGGGCACT 
               
               
                   
                   
               
               
                   
                 CTGGGGAGACTGCCGGAGATAATCCGGAGGAAGGT 
               
               
                   
                   
               
               
                   
                 GGGGATGACGTCAAATCATCATGCCCCTTATGACT 
               
               
                   
                   
               
               
                   
                 TGGGCTACACACGTGCTACAATGGCGGTAACAAAG 
               
               
                   
                   
               
               
                   
                 GGAAGCAGCCTCGCGAGAGTGAGCAAACCCCAAAA 
               
               
                   
                   
               
               
                   
                 ATGCCGTCTCAGTTCGGATTGTAGTCTGCAACTCG 
               
               
                   
                   
               
               
                   
                 ACTACATGAAGCTGGAATCGCTAGTAATCGCAGAT 
               
               
                   
                   
               
               
                   
                 CAGAATGCJGCGGTGAATACGTTCCCGGGTCTTGT 
               
               
                   
                   
               
               
                   
                 ACACACCGCCCGTCACACCATGGGAGTCGGATATG 
               
               
                   
                   
               
               
                   
                 CCCGAAGCCAGTGACCCAACCGCAAGGAGGGAGCT 
               
               
                   
                   
               
               
                   
                 GTCGAAGGTGGAGCCGATAACTGGGGTGAAGTCGT 
               
               
                   
                   
               
               
                   
                 AACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATC 
               
               
                   
                   
               
               
                   
                 ACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Dorea  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:2: 
     
       
         
           
               
               
            
               
                   
                   Dorea  sp. AM58-8 16S ribosomal RNA gene 
               
               
                   
                 SEQ ID 2 
               
               
                   
                 TTTTTACGAGAGTTTGATCCTGGCTCAGGATGAAC 
               
               
                   
                   
               
               
                   
                 GCTGGCGGCGTGCTTAACACATGCAAGTCGAACGA 
               
               
                   
                   
               
               
                   
                 AGCACTTAAGTTTGATTCTTCGGATGAAGACTTTT 
               
               
                   
                   
               
               
                   
                 GTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGG 
               
               
                   
                   
               
               
                   
                 TAACCTGCCTCATACAGGGGGATAACAGTTAGAAA 
               
               
                   
                   
               
               
                   
                 TGACTGCTAATACCGCATAAGACCACAGCACCGCA 
               
               
                   
                   
               
               
                   
                 TGGTGCAGGGGTAAAAACTCCGGTGGTATGAGATG 
               
               
                   
                   
               
               
                   
                 GACCCGCGTCTGATTAGCTGGTTGGTGGGGTAACG 
               
               
                   
                   
               
               
                   
                 GCCTACCAAGCGACGATCAGTAGCCGACCTGAGAG 
               
               
                   
                   
               
               
                   
                 GGTGACCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
                   
               
               
                   
                 AACTCCTACGGGAGGCAGCAGTGGGGAATATTGCA 
               
               
                   
                   
               
               
                   
                 CAATGGGGGAAACCCTGATGCAGCGACGCCGCGTG 
               
               
                   
                   
               
               
                   
                 AAGGATGAAGTATTTCGGTATGTAAACTTCTATCA 
               
               
                   
                   
               
               
                   
                 GCAGGGAAGAAAATGACGGTACCTGACTAAGAAGC 
               
               
                   
                   
               
               
                   
                 CCCGGCTAACTACGTGCCAGCAGCCGCGGTAATAC 
               
               
                   
                   
               
               
                   
                 GTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGT 
               
               
                   
                   
               
               
                   
                 AAAGGGAGCGTAGACGGTATGGCAAGTCTGATGTG 
               
               
                   
                   
               
               
                   
                 AAAGGCCAGGGCTCAACCCTGGGACTGCATTGGAA 
               
               
                   
                   
               
               
                   
                 ACTGTCGAACTAGAGTGTCGGAGAGGCAAGTGGAA 
               
               
                   
                   
               
               
                   
                 TTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGG 
               
               
                   
                   
               
               
                   
                 AGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGA 
               
               
                   
                   
               
               
                   
                 TGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAA 
               
               
                   
                   
               
               
                   
                 ACAGGATTAGATACCCTGGTAGTCCACGCCGTAAA 
               
               
                   
                   
               
               
                   
                 CGATGACTACTAGGTGTCGGGTAGCAGAGCTATTC 
               
               
                   
                   
               
               
                   
                 GGTGCCGCAGCCAACGCAATAAGTAGTCCACCTGG 
               
               
                   
                   
               
               
                   
                 GGAGTACGTTCGCAAGAATGAAACTCAAAGGAATT 
               
               
                   
                   
               
               
                   
                 GACGGGGACCCGCACAAGCGGTGGAGCATGTGGTT 
               
               
                   
                   
               
               
                   
                 TAATTCGAAGCAACGCGAAGAACCTTACCTGCTCT 
               
               
                   
                   
               
               
                   
                 TGACATCTCCCTGACCGGCAAGTAATGTTGCCTTT 
               
               
                   
                   
               
               
                   
                 CCTTCGGGACAGGGATGACAGGTGGTGCATGGTTG 
               
               
                   
                   
               
               
                   
                 TCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC 
               
               
                   
                   
               
               
                   
                 CCGCAACGAGCGCAACCCCTATCTTTAGTAGCCAG 
               
               
                   
                   
               
               
                   
                 CGGTTCGGCCGGGCACTCTAGAGAGACTGCCAGGG 
               
               
                   
                   
               
               
                   
                 ATAACCTGGAGGAAGGTGGGGATGACGTCAAATCA 
               
               
                   
                   
               
               
                   
                 TCATGCCCCTTATGAGCAGGGCTACACACGTGCTA 
               
               
                   
                   
               
               
                   
                 CAATGGCGTAAACAAAGGGAAGCGAGCCTGCGAGG 
               
               
                   
                   
               
               
                   
                 GTAAGCAAATCTCAAAAATAACGTCTCAGTTCGGA 
               
               
                   
                   
               
               
                   
                 TTGTAGTCTGCAACTCGACTACATGAAGCTGGAAT 
               
               
                   
                   
               
               
                   
                 CGCTAGTAATCGCGAATCAGAATGTCGCGGTGAAT 
               
               
                   
                   
               
               
                   
                 ACGTTCCCGGGTCTTGTACACACCGCCCGTCACAC 
               
               
                   
                   
               
               
                   
                 CATGGGAGTTGGTAACGCCCGAAGTCAGTGACCCA 
               
               
                   
                   
               
               
                   
                 ACCGCAAGGAGGGAGCTGCCGAAGGTGGGACCGAT 
               
               
                   
                   
               
               
                   
                 AACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCG 
               
               
                   
                   
               
               
                   
                 GAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, an  Erysipelotrichaceae  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:3: 
     
       
         
           
               
               
            
               
                   
                   Erysipelotrichaceae   bacterium  GAM147 
               
               
                   
                 16S ribosomal RNA gene 
               
               
                   
                 SEQ ID 3 
               
               
                   
                 AATGGAGAGTTTGATCCTGGCTCAGGATGAACGCT 
               
               
                   
                   
               
               
                   
                 GGCGGCGTGCCTAATACATGCAAGTCGAACGCTTC 
               
               
                   
                   
               
               
                   
                 ACTTCGGTGAAGAGTGGCGAACGGGTGAGTAATAC 
               
               
                   
                   
               
               
                   
                 ATAAGTAACCTGGCATCTACAGGGGGATAACTGAT 
               
               
                   
                   
               
               
                   
                 GGAAACGTCAGCTAAGACCGCATAGGTGTAGAGAT 
               
               
                   
                   
               
               
                   
                 CGCATGAACTCTATATGAAAAGTGCTACGGGACTG 
               
               
                   
                   
               
               
                   
                 GTAGATGATGGACTTATGGCGCATTAGCTTGTTGG 
               
               
                   
                   
               
               
                   
                 TAGGGTAACGGCCTACCAAGGCGACGATGCGTAGC 
               
               
                   
                   
               
               
                   
                 CGACCTGAGAGGGTGACCGGCCACACTGGGACTGA 
               
               
                   
                   
               
               
                   
                 GACACGGCCCAGACTCCTACGGGAGGCAGCAGTAG 
               
               
                   
                   
               
               
                   
                 GGAATTTTCGGCAATGGGGGAAACCCTGACCGAGC 
               
               
                   
                   
               
               
                   
                 AACGCCGCGTGAAGGAAGAAGTAATTCGTTATGTA 
               
               
                   
                   
               
               
                   
                 AACTTCTGTCATAGAGGAAGAACGGTGGATATAGG 
               
               
                   
                   
               
               
                   
                 AAATGATATCCAAGTGACGGTACTCTATAAGAAAG 
               
               
                   
                   
               
               
                   
                 CCACGGCTAACTACGTGCCAGCAGCCGCGGTAATA 
               
               
                   
                   
               
               
                   
                 CGTAGGTGGCGAGCGTTATCCGGAATTATTGGGCG 
               
               
                   
                   
               
               
                   
                 TAAAGAGGGAGCAGGCGGCACTAAGGGTCTGTGGT 
               
               
                   
                   
               
               
                   
                 GAAAGATCGAAGCTTAACTTCGGTAAGCCATGGAA 
               
               
                   
                   
               
               
                   
                 ACCGTAGAGCTAGAGTGTGTGAGAGGATCGTGGAA 
               
               
                   
                   
               
               
                   
                 TTCCATGTGTAGCGGTGAAATGCGTAGATATATGG 
               
               
                   
                   
               
               
                   
                 AGGAACACCAGTGGCGAAGGCGACGATCTGGCGCA 
               
               
                   
                   
               
               
                   
                 TAACTGACGCTCAGTCCCGAAAGCGTGGGGAGCAA 
               
               
                   
                   
               
               
                   
                 ATAGG 
               
               
                   
                   
               
               
                   
                 ATTAGATACCCTAGTAGTCCACGCCGTAAACGATG 
               
               
                   
                   
               
               
                   
                 AGTACTAAGTGTTGGGGGTCAAACCTCAGTGCTGC 
               
               
                   
                   
               
               
                   
                 AGTTAACGCAATAAGTACTCCGCCTGAGTAGTACG 
               
               
                   
                   
               
               
                   
                 TTCGCAAGAATGAAACTCAAAGGAATTGACGGGGG 
               
               
                   
                   
               
               
                   
                 CCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGA 
               
               
                   
                   
               
               
                   
                 AGCAACGCGAAGAACCTTACCAGGTCTTGACATCG 
               
               
                   
                   
               
               
                   
                 ATCTAAAGGCTCCAGAGATGGAGAGATAGCTATAG 
               
               
                   
                   
               
               
                   
                 AGAAGACAGGTGGTGCATGGTTGTCGTCAGCTCGT 
               
               
                   
                   
               
               
                   
                 GTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCG 
               
               
                   
                   
               
               
                   
                 CAACCCCTGTTGCCAGTTGCCAGCATTAAGTTGGG 
               
               
                   
                   
               
               
                   
                 GACTCTGGCGAGACTGCCGGTGACAAGCCGGAGGA 
               
               
                   
                   
               
               
                   
                 AGGCGGGGATGACGTCAAATCATCATGCCCCTTAT 
               
               
                   
                   
               
               
                   
                 GACCTGGGCTACACACGTGCTACAATGGACAGAGC 
               
               
                   
                   
               
               
                   
                 AGAGGGAAGCGAAGCCGCGAGGTGGAGCGAAACCC 
               
               
                   
                   
               
               
                   
                 ATAAAACTGTTCTCAGTTCGGACTGCAGTCTGCAA 
               
               
                   
                   
               
               
                   
                 CTCGACTGCACGAAGATGGAATCGCTAGTAATCGCG 
               
               
                   
                   
               
               
                   
                 ATCAGCATGTCGCGGTGAATACGTTCTCGGGCCTT 
               
               
                   
                   
               
               
                   
                 AGTACACACCGCCCGTCACACCATGAGAGTCGGTAA 
               
               
                   
                   
               
               
                   
                 CACCCGAAGCCGGTGGCCTAACCGCAAGGAAGGAG 
               
               
                   
                   
               
               
                   
                 CTGTCTAAGGTGGGACTGATGATTGGGGTGAAGTC 
               
               
                   
                   
               
               
                   
                 GTAACAAGGTATCCCTACGGGAACGTGGGGATGGA 
               
               
                   
                   
               
               
                   
                 TCACCTCCTTTCTAGGGAGA 
               
            
           
         
       
     
     In alternative embodiments, a  Firmicutes  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence 50 identity to SEQ ID NO:4: 
     
       
         
           
               
               
            
               
                   
                   Firmicutes  bacterium AF12-30 16S 
               
               
                   
                 ribosomal RNA gene 
               
               
                   
                 SEQ ID 4 
               
               
                   
                 GAACATGAGAGTTTGATCCTGGCTCAGGATGAACGC 
               
               
                   
                   
               
               
                   
                 TGGCGGCGTGCTTAACACATGCAAGTCGAACGAAG 
               
               
                   
                   
               
               
                   
                 CGCCTTATTTGATTTTCTTCGGAACTGAAGATTTG 
               
               
                   
                   
               
               
                   
                 GTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGG 
               
               
                   
                   
               
               
                   
                 TAACCTGCCCTGTACAGGGGGATAACAATCAGAAA 
               
               
                   
                   
               
               
                   
                 TGACTGCTAATACCGCATAAGACCACAGCACCGCA 
               
               
                   
                   
               
               
                   
                 TGGTGCAGGGGTAAAAACTCCGGTGGTACAGGATG 
               
               
                   
                   
               
               
                   
                 GACCCGCGTCTGATTAGCTGGTTGGTGAGGTAACG 
               
               
                   
                   
               
               
                   
                 GCTCACCAAGGCGACGATCAGTAGCCGGCTTGAGA 
               
               
                   
                   
               
               
                   
                 GAGTGAACGGCCACATTGGGACTGAGACACGGCCC 
               
               
                   
                   
               
               
                   
                 AAACTCCTACGGGAGGCAGCAGTGGGGAATATTGC 
               
               
                   
                   
               
               
                   
                 ACAATGGGGGGAACCCTGATGCAGCGACGCCGCGT 
               
               
                   
                   
               
               
                   
                 GAGTGAAGAAGTATCTCGGTATGTAAAGCTCTATC 
               
               
                   
                   
               
               
                   
                 AGCAGGGAAGAAAATGACGGTACCTGACTAAGAAG 
               
               
                   
                   
               
               
                   
                 CCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATA 
               
               
                   
                   
               
               
                   
                 CGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTG 
               
               
                   
                   
               
               
                   
                 TAAAGGGTGCGTAGGTGGTATGGCAAGTCAGAAGT 
               
               
                   
                   
               
               
                   
                 GAAAACCCAGGGCTTAACTCTGGGACTGCTTTTGA 
               
               
                   
                   
               
               
                   
                 AACTGTCAGACTGGAGTGCAGGAGAGGTAAGCGGA 
               
               
                   
                   
               
               
                   
                 ATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAG 
               
               
                   
                   
               
               
                   
                 GAGGAACATCAGTGGCGAAGGCGGCTTACTGGACT 
               
               
                   
                   
               
               
                   
                 GAAACTGACACTGAGGCACGAAAGCGTGGGGAGCA 
               
               
                   
                   
               
               
                   
                 AACAGGATTAGATACCCTGGTAGTCCACGCCGTAA 
               
               
                   
                   
               
               
                   
                 ACGATGAATACTAGGTGTCGGGGCCGTAGAGGCTT 
               
               
                   
                   
               
               
                   
                 CGGTGCCGCAGCCAACGCAGTAAGTATTCCACCTG 
               
               
                   
                   
               
               
                   
                 GGGAGTACGTTCGCAAGAATGAAACTCAAAGGAAT 
               
               
                   
                   
               
               
                   
                 TGACGGGGACCCGCACAAGCGGTGGAGCATGTGGT 
               
               
                   
                   
               
               
                   
                 TTAATTCGAAGCAACGCGAAGAACCTTACCTGGTC 
               
               
                   
                   
               
               
                   
                 TTGACATCCTTCTGACCGGTCCTTAACCGGACCTT 
               
               
                   
                   
               
               
                   
                 TCCTTCGGGACAGGAGTGACAGGTGGTGCATGGTT 
               
               
                   
                   
               
               
                   
                 GTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGT 
               
               
                   
                   
               
               
                   
                 CCCGCAACGAGCGCAACCCCTATCTTTAGTAGCCA 
               
               
                   
                   
               
               
                   
                 GCATTTCAGGTGGGCACTCTAGAGAGACTGCCAGG 
               
               
                   
                   
               
               
                   
                 GATAACCTGGAGGAAGGTGGGGACGACGTCAAATC 
               
               
                   
                   
               
               
                   
                 ATCATGCCCCTTATGACCAGGGCTACACACGTGCT 
               
               
                   
                   
               
               
                   
                 ACAATGGCGTAAACAGAGGGAAGCAGCCTCGTGAG 
               
               
                   
                   
               
               
                   
                 AGTGAGCAAATCCCAAAAATAACGTCTCAGTTCGG 
               
               
                   
                   
               
               
                   
                 ATTGTAGTCTGCAACTCGACTACATGAAGCTGGAA 
               
               
                   
                   
               
               
                   
                 TCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAA 
               
               
                   
                   
               
               
                   
                 TACGTTCCCGGGTCTTGTACACACCGCCCGTCACA 
               
               
                   
                   
               
               
                   
                 CCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCC 
               
               
                   
                   
               
               
                   
                 AACCGTAAGGAGGGAGCTGCCGAAGGCGGGACCGA 
               
               
                   
                   
               
               
                   
                 TAACTGGGGTGAAGTCGTAACAAGGTAGCCGTATC 
               
               
                   
                   
               
               
                   
                 GGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Ruminococcus  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:5: 
     
       
         
           
               
               
            
               
                   
                   Ruminococcus  sp. OF03-6AA 16S 
               
               
                   
                 ribosomal RNA gene 
               
               
                   
                 SEQ ID 5 
               
               
                   
                 TTCTAGTGGCGGACGGGTGAGTAACGCGTGGGTAA 
               
               
                   
                   
               
               
                   
                 CCTGCCTTGTACAGGGGGATAACAGTCAGAAATGA 
               
               
                   
                   
               
               
                   
                 CTGCTAATACCGCATAAGCGCACAGGACCGCATGG 
               
               
                   
                   
               
               
                   
                 TCCGGTGTGAAAAACTCCGGTGGTATAAGATGGAC 
               
               
                   
                   
               
               
                   
                 CCGCGTTGGATTAGCTAGTTGGCAGGGTAACGGCC 
               
               
                   
                   
               
               
                   
                 TACCAAGCGACGATCCATAGCCGGCCTGAGAGGGT 
               
               
                   
                   
               
               
                   
                 GAACGGCCACATTGGGACTGAGACACGGCCCAGAC 
               
               
                   
                   
               
               
                   
                 TCCTACGGGAGGCAGCAGTGGGGAATATTGCACAA 
               
               
                   
                   
               
               
                   
                 TGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAG 
               
               
                   
                   
               
               
                   
                 GAAGAAGTATCTCGGTATGTAAACTTCTATCAGC 
               
               
                   
                   
               
               
                   
                 AGGGAAGAAAATGACGGTACCTGACT 
               
               
                   
                   
               
               
                   
                 AAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCG 
               
               
                   
                   
               
               
                   
                 GTAATACGTAGGGGGCAAGCGTTATCCGGATTTAC 
               
               
                   
                   
               
               
                   
                 TGGGTGTAAAGGGAGCGTAGACGGATGGACAAGTC 
               
               
                   
                   
               
               
                   
                 TGATGTGAAAGGCTGGGGCTCAACCCCGGGACTGC 
               
               
                   
                   
               
               
                   
                 ATTGGAAACTGCCCGTCTTGAGTGCCGGAGAGGTA 
               
               
                   
                   
               
               
                   
                 AGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGA 
               
               
                   
                   
               
               
                   
                 TATTAGGAGGAACACCAGTGGCGAAGGCGGCTTAC 
               
               
                   
                   
               
               
                   
                 TGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGG 
               
               
                   
                   
               
               
                   
                 GGAGCAAACAGGATTAGATACCCTGGTAGTCCACG 
               
               
                   
                   
               
               
                   
                 CGGTAAACGATGAATGCTAGGTGTCGGGTGACAAA 
               
               
                   
                   
               
               
                   
                 GTCATTCGGTGCCGCCGCAAACGCATTAAGCATTC 
               
               
                   
                   
               
               
                   
                 CACCTGGGGAGTACGTTCGCAAGAATGAAACTCAA 
               
               
                   
                   
               
               
                   
                 AGGAATTGACGGGGACCCGCACAAGCGGTGGAGCA 
               
               
                   
                   
               
               
                   
                 TGTGGTTTAATTCGAAGCAACGCGAAGAACCTTAC 
               
               
                   
                   
               
               
                   
                 CAAGTCTTGACATCCCTCTGACCGGAACTTAACCG 
               
               
                   
                   
               
               
                   
                 TTCCTTCCCTTCGGGGCAGAGGAGACAGGTGGTGC 
               
               
                   
                   
               
               
                   
                 ATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGG 
               
               
                   
                   
               
               
                   
                 TTAAGTCCCGCAACGAGCGCAACCCCTATCCTCAG 
               
               
                   
                   
               
               
                   
                 TAGCCAGCAGTTCGGCTGGGCACTCTGTGGAGACT 
               
               
                   
                   
               
               
                   
                 GCCAGGGATAACCTGGAGGAAGGC 
               
               
                   
                   
               
               
                   
                 GGGGATGACGTCAAATCATCATGCCCCTTATGATT 
               
               
                   
                   
               
               
                   
                 TGGGCTACACACGTGCTACAATGGCGTAAACAAAG 
               
               
                   
                   
               
               
                   
                 GGAAGCGAACCTGCGAGGGTGGGCAAATCCCAAAA 
               
               
                   
                   
               
               
                   
                 ATAACGTCCCAGTTCGGACTGTAGTCTGCAACCCG 
               
               
                   
                   
               
               
                   
                 ACTACACGAAGCTGGAATCGCTAGTAATCGCGGAT 
               
               
                   
                   
               
               
                   
                 CAG 
               
               
                   
                   
               
               
                   
                 AATGCCGCGGTGAATACGTTCCCGGGTCTTGTACA 
               
               
                   
                   
               
               
                   
                 CACCGCCCGTCACACCATGGGAGTCAGTAACGCCC 
               
               
                   
                   
               
               
                   
                 GAAGTCAGTGACCTAACCGTAAGGAGGGAGCTGCC 
               
               
                   
                   
               
               
                   
                 GAAGGCGGGACCGATGACTGGGGTGAAGTCGTAAC 
               
               
                   
                   
               
               
                   
                 AAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACC 
               
               
                   
                   
               
               
                   
                 TCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Collinsella  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:6: 
     
       
         
           
               
               
            
               
                   
                   Collinsella  sp. AM34-10 16S 
               
               
                   
                 ribosomal RNA gene 
               
               
                   
                 SEQ ID 6 
               
               
                   
                 TTTGGACGGAGAGTTCGATCCTGGCTCAGGATGAA 
               
               
                   
                   
               
               
                   
                 CGCTGGCGGCGCGCCTAACACATGCAAGTCGAACG 
               
               
                   
                   
               
               
                   
                 GCACCTGCCTTCGGGCAGAAGCGAGTGGCGAACGG 
               
               
                   
                   
               
               
                   
                 CTGAGTAACACGTGGAGAACCTGCCCCCTCCCCCG 
               
               
                   
                   
               
               
                   
                 GGATAGCCGCCCGAAAGGACGGGTAATACCGGATA 
               
               
                   
                   
               
               
                   
                 CCCCGGGGTGCCGCATGGCACCCCGGCTAAAGCCC 
               
               
                   
                   
               
               
                   
                 CGACGGGAGGGGATGGCTCCGCGGCCCATCAGGTA 
               
               
                   
                   
               
               
                   
                 GACGGCGGGGTGACGGCCCACCGTGCCGACAACGG 
               
               
                   
                   
               
               
                   
                 GTAGCCGGGTTGAGAGACCGACCGGCCAGATTGGG 
               
               
                   
                   
               
               
                   
                 ACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC 
               
               
                   
                   
               
               
                   
                 AGTGGGGAATCTTGCGCAATGGGGGGAACCCTGAC 
               
               
                   
                   
               
               
                   
                 GCAGCGACGCCGCGTGCGGGACGGAGGCCTTCGGG 
               
               
                   
                   
               
               
                   
                 TCGTAAACCGCTTTCAGCAGGGAAGAGTCAAGACT 
               
               
                   
                   
               
               
                   
                 GTACCTGCAGAAGAAGCCCCGGCTAACTACGTGCC 
               
               
                   
                   
               
               
                   
                 AGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTAT 
               
               
                   
                   
               
               
                   
                 CCGGATTCATTGGGCGTAAAGCGCGCGTAGGCGGC 
               
               
                   
                   
               
               
                   
                 CCGGCAGGCCGGGGGTCGAAGCGGGGGGCTCAACC 
               
               
                   
                   
               
               
                   
                 CCCCGAAGCCCCCGGAACCTCCGCGGCTTGGGTCC 
               
               
                   
                   
               
               
                   
                 GGTAGGGGAGGGTGGAACACCCGGTGTAGCGGTGG 
               
               
                   
                   
               
               
                   
                 AATGCGCAGATATCGGGTGGAACACCGGTGGCGAA 
               
               
                   
                   
               
               
                   
                 GGCGGCCCTCTGGGCCGAGACCGACGCTGAGGCGC 
               
               
                   
                   
               
               
                   
                 GAAAGCTGGGGGAGCGAACAGGATTAGATACCCTG 
               
               
                   
                   
               
               
                   
                 GTAGTCCCAGCCGTAAACGATGGACGCTAGGTGTG 
               
               
                   
                   
               
               
                   
                 GGGGGACGATCCCCCCGTGCCGCAGCCAACGCATT 
               
               
                   
                   
               
               
                   
                 AAGCGTCCCGCCTGGGGAGTACGGCCGCAAGGCTA 
               
               
                   
                   
               
               
                   
                 AAACTCAAAGGAATTGACGGGGGCCCGCACAAGCA 
               
               
                   
                   
               
               
                   
                 GCGGAGCATGTGGCTTAATTCGAAGCAACGCGAAG 
               
               
                   
                   
               
               
                   
                 AACCTTACCAGGGCTTGACATATGGGTGAAGCGGG 
               
               
                   
                   
               
               
                   
                 GGAGACCCCGTGGCCGAGAGGAGCCCATACAGGTG 
               
               
                   
                   
               
               
                   
                 GTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGT 
               
               
                   
                   
               
               
                   
                 TGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCG 
               
               
                   
                   
               
               
                   
                 CGTGTTGCCATCGGGTGATGCCGGGAACCCACGCG 
               
               
                   
                   
               
               
                   
                 GGACCGCCGCCGTCAAGGCGGAGGAGGGCGGGGAC 
               
               
                   
                   
               
               
                   
                 GACGTCAAGTCATCATGCCCCTTATGCCCTGGGCT 
               
               
                   
                   
               
               
                   
                 GCACACGTGCTACAATGGCCGGTACAGAGGGATGC 
               
               
                   
                   
               
               
                   
                 CACCCCGCGAGGGGGAGCGGATCCCGGAAAGCCGG 
               
               
                   
                   
               
               
                   
                 CCCCAGTTCGGATTGGGGGCTGCAACCCGCCCCCA 
               
               
                   
                   
               
               
                   
                 TGAAGTCGGAGTTGCTAGTAATCGCGGATCAGCAT 
               
               
                   
                   
               
               
                   
                 GCCGCGGTGAATGCGTTCCCGGGCCTTGTACACAC 
               
               
                   
                   
               
               
                   
                 CGCCCGTCACACCACCCGAGTCGTCTGCACCCGAA 
               
               
                   
                   
               
               
                   
                 GTCGCCGGCCCAACCGCAAGGGGGGAGGCGCCGAA 
               
               
                   
                   
               
               
                   
                 GGTGTGGAGGGTGAGGGGGGTGAAGTCGTAACAAG 
               
               
                   
                   
               
               
                   
                 GTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCC 
               
               
                   
                   
               
               
                   
                 TTTCTAGGGAG 
               
            
           
         
       
     
     In alternative embodiments, a  Coprobacillus  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:7: 
     
       
         
           
               
            
               
                   Coprobacillus  sp. 8_1_38FAA 16S ribosomal 
               
               
                 RNA gene 
               
               
                 SEQ ID 7 
               
               
                 AATGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAAT 
               
               
                   
               
               
                 ACATGCAAGTCGAACGCTTCACTTCGGTGAAGAGTGGCGAACGGGTGAGT 
               
               
                   
               
               
                 AATACATAAGTAACCTGGCCTTTACAGGGGGATAACTATTGGAAACGATA 
               
               
                   
               
               
                 GCTAAGACCGCATAGGTGTCAAAACCGCATGGAGATGACATGAAATATGC 
               
               
                   
               
               
                 TACGGCATAGGTAGAGGATGGACTTATGGCGCATTAGCTAGTTGGAGGGG 
               
               
                   
               
               
                 TAACGGCCCACCAAGGCGACGATGCGTAGCCGACCTGAGAGGGTGACCGG 
               
               
                   
               
               
                 CCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAG 
               
               
                   
               
               
                 GGAATTTTCGGCAATGGGGGAAACCCTGACCGAGCAACGCCGCGTGAAGG 
               
               
                   
               
               
                 AAGAAGTAATTCGTTATGTAAACTTCTGTCATAGAGGAAGAACGGTGCGT 
               
               
                   
               
               
                 GTAGGGAATGACATGCAAGTGACGGTACTCTATAAGAAAGCCACGGCTAA 
               
               
                   
               
               
                 CTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCGAGCGTTATCCGGAA 
               
               
                   
               
               
                 TTATTGGGCGTAAAGAGGGAGCAGGCGGCACTAAGGGTCTGTGGTGAAAG 
               
               
                   
               
               
                 ATCGAAGCTTAACTTCGGTAAGCCATGGAAACCGTAGAGCTAGAGTGTGT 
               
               
                   
               
               
                 GAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGACGATCTGGCGCATAACTGACGCTCAGT 
               
               
                   
               
               
                 CCCGAAAGCGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGAGTACTAAGTGTTGGGAGTCAAATCTCAGTGCTGCAGTTA 
               
               
                   
               
               
                 ACGCAATAAGTACTCCGCCTGAGTAGTACGTTCGCAAGAATGAAACTCAA 
               
               
                   
               
               
                 AGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGA 
               
               
                   
               
               
                 AGCAACGCGAAGAACCTTACCAGGTCTTGACATCGATCTAAAGGCTCCAG 
               
               
                   
               
               
                 AGATGGAGAGATAGCTATAGAGAAGACAGGTGGTGCATGGTTGTCGTCAG 
               
               
                   
               
               
                 CTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGT 
               
               
                   
               
               
                 TGCCAGTTGCCAGCATTAAGTTGGGGACTCTGGCGAGACTGCCGGTGACA 
               
               
                   
               
               
                 AGCCGGAGGAAGGCGGGGATGACGTCAAATCATCATGCCCCTTATGACCT 
               
               
                   
               
               
                 GGGCTACACACGTGCTACAATGGACAGAGCAGAGGGAAGCGAAGCCGCGA 
               
               
                   
               
               
                 GGTGGAGCGAAACCCAGAAAACTGTTCTCAGTTCGGACTGCAGTCTGCAA 
               
               
                   
               
               
                 CTCGACTGCACGAAGTTGGAATCGCTAGTAATCGCGAATCAGCATGTCGC 
               
               
                   
               
               
                 GGTGAATACGTTCTCGGGCCTTGTACACACCGCCCGTCACACCATGAGAG 
               
               
                   
               
               
                 TCGGTAACACCCGAAGCCGGTGGCCTAACCGCAAGGAAGGAGCTGTCTAA 
               
               
                   
               
               
                 GGTGGGACTGATGATTGGGGTGAAGTCGTAACAAGGTATCCCTACGGGAA 
               
               
                   
               
               
                 CGTGGGGATGGATCACCTCCTTTCTAGGGAGA 
               
            
           
         
       
     
     In alternative embodiments, a  Dorea  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:8: 
     
       
         
           
               
            
               
                   Dorea  sp. OM07-5 16S ribosomal RNA gene 
               
               
                 SEQ ID 8 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAGCGAAGCACCTAAGAAAGATTCTTCGGATGAATTC 
               
               
                   
               
               
                 TTTTGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTC 
               
               
                   
               
               
                 ATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCAC 
               
               
                   
               
               
                 GGTACTGCATGGTACAGTGGTAAAAACTCCGGTGGTATGAGATGGACCCG 
               
               
                   
               
               
                 CGTCTGATTAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCGACGATCAG 
               
               
                   
               
               
                 TAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 AACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAAGGATGAAGTATTTCGGTATGTAAACTTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAAC 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGCATTGCAAGCCAGATGTGAAAGC 
               
               
                   
               
               
                 CCGGGGCTCAACCCCGGGACrGCATTTGGACCGGCAGGCCGGGGGTCGAA 
               
               
                   
               
               
                 GCGGGGGGCTCAACCCCCCGAAGCCCCCGGAACCTCCGCGGCTTGGGTCC 
               
               
                   
               
               
                 GGTAGGGGAGGGTGGAACACCCGGTGTAGCGGTGGAATGCGCAGATATCG 
               
               
                   
               
               
                 GGTGGAACACCGGTGGCGAAGGCGGCCCTCTGGGCCGAGACCGACGCTGA 
               
               
                   
               
               
                 GGCGCGAAAGCTGGGGGAGCGAACAGGATTAGATACCCrGGTAGTCCCAG 
               
               
                   
               
               
                 CCGTAAACGATGGACGCTAGGTGTGGGGGGACGATCCCCCCGTGCCGCAG 
               
               
                   
               
               
                 CCAACGCATTAAGCGTCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTGGCTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATATGGGTGAAGCGGG 
               
               
                   
               
               
                 GGAGACCCCGTGGCCGAGAGGAGCCCATACAGGTGGTGCATGGCTGTCGT 
               
               
                   
               
               
                 CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCC 
               
               
                   
               
               
                 CGCCGCGTGTTGCCATCGGGTGATGCCGGGAACCCACGCGGGACCGCCGC 
               
               
                   
               
               
                 CGTCAAGGCGGAGGAGGGCGGGGACGACGTCAAGTCATCATGCCCCTTAT 
               
               
                   
               
               
                 GCCCTGGGCTGCACACGTGCTACAATGGCCGGTACAGAGGGATGCCACCC 
               
               
                   
               
               
                 CGCGAGGGGGAGCGGATCCCGGAAAGCCGGCCCCAGTTCGGATTGGGGGC 
               
               
                   
               
               
                 TGCAACCCGCCCCCATGAAGTCGGAGTTGCTAGTAATCGCGGATCAGCAT 
               
               
                   
               
               
                 GCCGCGGTGAATGCGTTCCCGGGCCTTGTACACACCGCCCGTCACACCAC 
               
               
                   
               
               
                 CCGAGTCGTCTGCACCCGAAGTCGCCGGCCCAACCGCAAGGGGGGAGGCG 
               
               
                   
               
               
                 CCGAAGGTGTGGAGGGTGAGGGGGGTGAAGTCGTAACAAGGTAGCCGTAC 
               
               
                   
               
               
                 CGGAAGGTGCGGCTGGATCACCTCCTTTCTAGGGAG 
               
            
           
         
       
     
     In alternative embodiments, a  Faecalibacterium prausnitzii  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:9: 
     
       
         
           
               
            
               
                   Faecalibacterium prausnitzii  A2-165 
               
               
                 16S ribosomal RNA gene 
               
               
                 SEQ ID 9 
               
               
                 TCCTTAGAAAGGAGGTGATCCAGCCGCAGGTTCTCCTACGGCTACCTTGT 
               
               
                   
               
               
                 TACGACTTCACCCCAATCACCAGTTTTACCTTCGGCGGCGTCCTCCTTGC 
               
               
                   
               
               
                 GGTTAGACTACCGACTTCGGGTCCCCCCGGCTCTCATGGTGTGACGGGCG 
               
               
                   
               
               
                 GTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATGCTGATCCACGAT 
               
               
                   
               
               
                 TACTAGCAATTCCGACTTCGTGCAGGCGAGTTGCAGCCTGCAGTCCGAAC 
               
               
                   
               
               
                 TGGGACGTTGTTTCTGAGTTTTGCTCCACCTCGCGGTCTTGCTTCTCTTT 
               
               
                   
               
               
                 GTTTAACGCCATTGTAGTACGTGTGTAGCCCAAGTCATAAAGGGCATGAT 
               
               
                   
               
               
                 GATTTGACGTCATCCCCACCTTCCTCCGTTTTGTCAACGGCAGTCCTGCC 
               
               
                   
               
               
                 AGAGTCCTCTTGCGTAGTAACTGACAGTAAGGGTTGCGCTCGTTGCGGGA 
               
               
                   
               
               
                 CTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTG 
               
               
                   
               
               
                 TCTCTGCGTCCCGAAGGAAAATACTGTTTCCAGCATCGTCGCAGGATGTC 
               
               
                   
               
               
                 AAGACTTGGTAAGGTTCTTCGCGTTGCGTCGAATTAAACCACATACTCCA 
               
               
                   
               
               
                 CTGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCG 
               
               
                   
               
               
                 TACTCCCCAGGTGGATTACTTATTGTGTTAACTGCGGCACTGAAGGGGTC 
               
               
                   
               
               
                 AATCCTCCAACACCTAGTAATCATCGTTTACGGTGTGGACTACCAGGGTA 
               
               
                   
               
               
                 TCTAATCCTGTTTGCTACCCACACTTTCGAGCCTCAGCGTCAGTTGGTGC 
               
               
                   
               
               
                 CCAGTAGGCCGCCTTCGCCACTGGTGTTCCTCCCGATATCTACGCATTCC 
               
               
                   
               
               
                 ACCGCTACACCGGGAATTCCGCCTACCTCTGCACTACTCAAGAAAAACAG 
               
               
                   
               
               
                 TTTTGAAAGCAGTTTATGGGTTGAGCCCATAGATTTCACTTCCAACTTGT 
               
               
                   
               
               
                 CTTCCCGCCTGCGCTCCCTTTACACCCAGTAATTCCGGACAACGCTTGTG 
               
               
                   
               
               
                 ACCTACGTTTTACCGCGGCTGCTGGCACGTAGTTAGCCGTCACTTCCTTG 
               
               
                   
               
               
                 TTGAGTACCGTCATTATCTTCCTCAACAACAGGAGTTTACAATCCGAAGA 
               
               
                   
               
               
                 CCTTCTTCCTCCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATTGTGCA 
               
               
                   
               
               
                 ATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCC 
               
               
                   
               
               
                 AATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGCCTTGGTGG 
               
               
                   
               
               
                 GCCATTACCTCACCAACTAGCTAATCGGACGCGAGGCCATCTCAAAGCGG 
               
               
                   
               
               
                 ATTGCTCCTTTTCCCTCTGCTCGATGCCGAGCTGTGGGCTTATGCGGTAT 
               
               
                   
               
               
                 TAGCAGTCGTTTCCAACTGTTGTCCCCCTCTTTGAGGCAGGTTCCTCACG 
               
               
                   
               
               
                 CGTTACTCACCCGTTCGCCACTCGCTTGAGAAAGCAAGCTCTCTCTCGCT 
               
               
                   
               
               
                 CGTTCGACTTGCATGTGTTAGGCGCGCCGCCAGCGTTCGTCCTGAGCCAG 
               
               
                   
               
               
                 GATCAAACTCTTTATAAA 
               
               
                   
               
            
           
         
       
     
     In alternative embodiments, a  Clostridium coccoides  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:10: 
     
       
         
           
               
            
               
                   Clostridium coccoides  strain 8F 16S 
               
               
                 ribosomal RNA gene 
               
               
                 SEQ ID 10 
               
               
                 TTTGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACA 
               
               
                   
               
               
                 TGCAAGTCGAGCGAAGCGCTAAGACAGATTTCTTCGGATTGAAGTCTTTG 
               
               
                   
               
               
                 TGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACA 
               
               
                   
               
               
                 GGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGCGCACAGGAC 
               
               
                   
               
               
                 CGCATGGTCTGGTGTGAAAAACTCCGGTGGTATGAGATGGACCCGCGTCT 
               
               
                   
               
               
                 GATTAGCTAGTTGGAGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCC 
               
               
                   
               
               
                 GGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTC 
               
               
                   
               
               
                 CTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATG 
               
               
                   
               
               
                 CAGCGACGCCGCGTGAAGGAAGAAGTATCTCGGTATGTAAACTTCTATCA 
               
               
                   
               
               
                 GCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGT 
               
               
                   
               
               
                 GCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTG 
               
               
                   
               
               
                 GGTGTAAAGGGAGCGTAGACGGAAGAGCAAGTCTGATGTGAAAGGCTGGG 
               
               
                   
               
               
                 GCTTAACCCCAGGACTGCATTGGAAACTGTTGTTCTAGAGTGCCGGAGAG 
               
               
                   
               
               
                 GTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAA 
               
               
                   
               
               
                 CACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGA 
               
               
                   
               
               
                 AAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAA 
               
               
                   
               
               
                 CGATGAATACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAGCAAAC 
               
               
                   
               
               
                 GCAATAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAG 
               
               
                   
               
               
                 GAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAG 
               
               
                   
               
               
                 CAACGCGAAGAACCTTACCAAGTCTTGACATCCCTCTGACCGTCCCGTAA 
               
               
                   
               
               
                 CGGGGGCTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTC 
               
               
                   
               
               
                 AGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTT 
               
               
                   
               
               
                 ATCCTTAGTAGCCAGCACATGATGGTGGGCACTCTAGGGAGACTGCCGGG 
               
               
                   
               
               
                 GATAACCCGGAGGAAGGCGGGGACGACGTCAAATCATCATGCCCCTTATG 
               
               
                   
               
               
                 ATTTGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGAGACA 
               
               
                   
               
               
                 GCGATGTTGAGCGAATCCCAAAAATAACGTCCCAGTTCGGACTGCAGTCT 
               
               
                   
               
               
                 GCAACTCGACTGCACGAAGCTGGAATCGCTAGTAATCGCGGATCAGAATG 
               
               
                   
               
               
                 CCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATG 
               
               
                   
               
               
                 GGAGTCAGTAACGCCCGAAGTCAGTGACCTAACCGAAAGGAAGGAGCTGC 
               
               
                   
               
               
                 CGAAGGCGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCCGTATC 
               
               
                   
               
               
                 GGAAGGTGCGGCTGGATCCCC 
               
            
           
         
       
     
     In alternative embodiments, a  Bifidobacterium bifidum  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:11: 
     
       
         
           
               
            
               
                   Bifidobacterium bifidum  NCIMB 41171 16S 
               
               
                 ribosomal RNA gene 
               
               
                 SEQ ID 11 
               
               
                 TTTTGTGGAGGGTTCGATTCTGGCTCAGGATGAACGCTGGCGGCGTGCTT 
               
               
                   
               
               
                 AACACATGCAAGTCGAACGGGATCCATCAAGCTTGCTTGGTGGTGAGAGT 
               
               
                   
               
               
                 GGCGAACGGGTGAGTAATGCGTGACCGACCTGCCCCATGCTCCGGAATAG 
               
               
                   
               
               
                 CTCCTGGAAACGGGTGGTAATGCCGGATGTTCCACATGATCGCATGTGAT 
               
               
                   
               
               
                 TGTGGGAAAGATTCTATCGGCGTGGGATGGGGTCGCGTCCTATCAGCTTG 
               
               
                   
               
               
                 TTGGTGAGGTAACGGCTCACCAAGGCTTCGACGGGTAGCCGGCCTGAGAG 
               
               
                   
               
               
                 GGCGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGG 
               
               
                   
               
               
                 CAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCC 
               
               
                   
               
               
                 GCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTTGTTTGGGAGCA 
               
               
                   
               
               
                 AGCCTTCGGGTGAGTGTACCTTTCGAATAAGCGCCGGCTAACTACGTGCC 
               
               
                   
               
               
                 AGCAGCCGCGGTAATACGTAGGGCGCAAGCGTTATCCGGATTTATTGGGC 
               
               
                   
               
               
                 GTAAAGGGCTCGTAGGCGGCTCGTCGCGTCCGGTGTGAAAGTCCATCGCT 
               
               
                   
               
               
                 TAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAG 
               
               
                   
               
               
                 ACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACAC 
               
               
                   
               
               
                 CGATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAG 
               
               
                   
               
               
                 CGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGG 
               
               
                   
               
               
                 TGGACGCTGGATGTGGGGCACGTTCCACGTGTTCCGTGTCGGAGCTAACG 
               
               
                   
               
               
                 CGTTAAGCGTCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGA 
               
               
                   
               
               
                 AATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGC 
               
               
                   
               
               
                 AACGCGAAGAACCTTACCTGGGCTTGACATGTTCCCGACGACGCCAGAGA 
               
               
                   
               
               
                 TGGCGTTTCCCTTCGGGGCGGGTTCACAGGTGGTGCATGGTCGTCGTCAG 
               
               
                   
               
               
                 CTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGC 
               
               
                   
               
               
                 CCCGTGTTGCCAGCACGTTATGGTGGGAACTCACGGGGGACCGCCGGGGT 
               
               
                   
               
               
                 TAACTCGGAGGAAGGTGGGGATGACGTCAGATCATCATGCCCCTTACGTC 
               
               
                   
               
               
                 CAGGGCTTCACGCATGCTACAATGGCCGGTACAGCGGGATGCGACATGGC 
               
               
                   
               
               
                 GACATGGAGCGGATCCCTGAAAACCGGTCTCAGTTCGGATCGGAGCCTGC 
               
               
                   
               
               
                 AACCCGGCTCCGTGAAGGCGGAGTCGCTAGTAATCGCGGATCAGCAACGC 
               
               
                   
               
               
                 CGCGGTGAATGCGTTCCCGGGCCTTGTACACACCGCCCGTCAAGTCATGA 
               
               
                   
               
               
                 AAGTGGGCAGCACCCGAAGCCGGTGGCCTAACCCCTTGTGGGATGGAGCC 
               
               
                   
               
               
                 GTCTAAGGTGAGGCTCGTGATTGGGACTAAGTCGTAACAAGGTAGCCGTA 
               
               
                   
               
               
                 CCGGAAGGTGCGGCTGGATCACCTCCTTTCTACGGAG 
               
            
           
         
       
     
     In alternative embodiments, a  Ruminococcus lactaris  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:12: 
     
       
         
           
               
            
               
                   Ruminococcus lactaris  16S ribosomal RNA gene 
               
               
                 SEQ ID 12 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAGCGAAGCACTTTGCTTTGATTTCTTCGGGATGAAG 
               
               
                   
               
               
                 AGCTTAGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCC 
               
               
                   
               
               
                 TCATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACC 
               
               
                   
               
               
                 ACAGCACCGCATGGTGCAGGGGTAAAAACTCCGGTGGTATGAGATGGACC 
               
               
                   
               
               
                 CGCGTCTGATTAGTTAGTTGGTGGGGTAACGGCCTACCAAGGCGACGATC 
               
               
                   
               
               
                 AGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCC 
               
               
                   
               
               
                 CAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAAC 
               
               
                   
               
               
                 CCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGC 
               
               
                   
               
               
                 TCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTA 
               
               
                   
               
               
                 ACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGA 
               
               
                   
               
               
                 TTTACTGGGTGTAAAGGGAGCGTAGACGGAGCAGCAAGTCTGATGTGAAA 
               
               
                   
               
               
                 ACCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTTGATCTGGAGTGC 
               
               
                   
               
               
                 CGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTA 
               
               
                   
               
               
                 GGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGA 
               
               
                   
               
               
                 GGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACG 
               
               
                   
               
               
                 CCGTAAACGATGACTACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGC 
               
               
                   
               
               
                 AGCCAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAA 
               
               
                   
               
               
                 CTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAA 
               
               
                   
               
               
                 TTCGAAGCAACGCGAAGAACCTTACCTGCTCTTGACATCCCGGTGACGGC 
               
               
                   
               
               
                 AGAGTAATGTCTGCTTTTCTTCGGAACACCGGTGACAGGTGGTGCATGGT 
               
               
                   
               
               
                 TGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGC 
               
               
                   
               
               
                 AACCCCTATCTTCAGTAGCCAGCGGTAAGGCCGGGCACTCTGGAGAGACT 
               
               
                   
               
               
                 GCCAGGGATAACCTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCC 
               
               
                   
               
               
                 CTTATGAGCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGC 
               
               
                   
               
               
                 GAACCCGCGAGGGTGGGCAAATCCCAAAAATAACGTCTCAGTTCGGATTG 
               
               
                   
               
               
                 TAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATC 
               
               
                   
               
               
                 AGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCAC 
               
               
                   
               
               
                 ACCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCGTAAGGAGGG 
               
               
                   
               
               
                 AGCTGCCGAAGGTGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGC 
               
               
                   
               
               
                 CGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Blautia obeum  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:13: 
     
       
         
           
               
            
               
                   Blautia obeum  16S ribosomal RNA gene 
               
               
                 SEQ ID 13 
               
               
                 TTTATCAGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTT 
               
               
                   
               
               
                 AACACATGCAAGTCGAACGGGAAACTTTTCATTGAAGCTTCGGCAGATTT 
               
               
                   
               
               
                 GGTCTGTTTCTAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTT 
               
               
                   
               
               
                 ATACAGGGGGATAACAACCAGAAATGGTTGCTAATACCGCATAAGCGCAC 
               
               
                   
               
               
                 AGGACCGCATGGTCCGGTGTGAAAAACTCCGGTGGTATAAGATGGACCCG 
               
               
                   
               
               
                 CGTTGGATTAGCTAGTTGGCAGGGTAACGGCCTACCAAGGCGACGATCCA 
               
               
                   
               
               
                 TAGCCGGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAAGGAAGAAGTATCTCGGTATGTAAACTTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGCCCCGGCTAAC 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGACTGGCAAGTCTGATGTGAAAGG 
               
               
                   
               
               
                 CGGGGGCTCAACCCCTGGACTGCATTGGAAACTGTTAGTCTTGAGTGCCG 
               
               
                   
               
               
                 GAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGG 
               
               
                   
               
               
                 CTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGAATACTAGGTGTTGGGGAGCAAAGCTCTTCGGTGCCGCCG 
               
               
                   
               
               
                 CAAACGCATTAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATCCCTCTGACCGTTC 
               
               
                   
               
               
                 CTTAACCGGAACnTCCTTCGGGACAGAGGAGACAGGTGGTGCATGGTTGT 
               
               
                   
               
               
                 CGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAAC 
               
               
                   
               
               
                 CCCTATCCCCAGTAGCCAGCGGTTCGGCCGGGCACTCTGAGGAGACTGCC 
               
               
                   
               
               
                 AGGGATAACCTGGAGGAAGGCGGGGATGACGTCAAATCATCATGCCCCTT 
               
               
                   
               
               
                 ATGATTTGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGAG 
               
               
                   
               
               
                 CCTGCGAAGGTAAGCAAATCCCAAAAATAACGTCCCAGTTCGGACTGCAG 
               
               
                   
               
               
                 TCTGCAACTCGACTGCACGAAGCTGGAATCGCTAGTAATCGCGGATCAGA 
               
               
                   
               
               
                 ATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACC 
               
               
                   
               
               
                 ATGGGAGTCAGTAACGCCCGAAGTCAGTGACCTAACTGCAAAGAAGGAGC 
               
               
                   
               
               
                 TGCCGAAGGCGGGACCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGT 
               
               
                   
               
               
                 ATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Coprococcus comes  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:14: 
     
       
         
           
               
            
               
                   Coprococcus comes  16S ribosomal RNA gene 
               
               
                 SEQ ID 14 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAACGAAGCACTTTAACCTGATTCTTCGGATGAAGGT 
               
               
                   
               
               
                 TTTTGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTC 
               
               
                   
               
               
                 ATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCAC 
               
               
                   
               
               
                 AGAGCCGCATGGCTCGGTGGGAAAAACrCCGGTGGTATGAGATGGACCCG 
               
               
                   
               
               
                 CGTCTGATTAGGTAGTTGGTGGGGTAACGGCCTACCAAGCCAACGATCAG 
               
               
                   
               
               
                 TAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 AACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAA 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGCTGTGTAAGTCTGAAGTGAAAGC 
               
               
                   
               
               
                 CCGGGGCTCAACCCCGGGACTGCTTTGGAAACTATGCAGCTAGAGTGTCG 
               
               
                   
               
               
                 GAGAGGTAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGTTGAGG 
               
               
                   
               
               
                 CTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGACTACTAGGTGTCGGGGAGCAAAGCTCTTCGGTGCCGCAG 
               
               
                   
               
               
                 CAAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCTGCTCTTGACATCCCGGTGACCGGCG 
               
               
                   
               
               
                 TGTAATGACGCCTTTTCTTCGGAACACCGGTGACAGGTGGTGCATGGTTG 
               
               
                   
               
               
                 TCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAA 
               
               
                   
               
               
                 CCCTTATCTTCAGTAGCCAGCAATTCGGATGGGCACTCTGGAGAGACTGC 
               
               
                   
               
               
                 CAGGGATAACCTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCT 
               
               
                   
               
               
                 TATGAGCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGA 
               
               
                   
               
               
                 GCCTGCGAGGGTAAGCAAATCTCAAAAATAACGTCTCAGTTCGGATTGTA 
               
               
                   
               
               
                 GTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAG 
               
               
                   
               
               
                 CATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACAC 
               
               
                   
               
               
                 CATGGGAGTTGGTAACGCCCGAAGTCAGTGACCCAACCGTAAGGAGGGAG 
               
               
                   
               
               
                 CTGCCGAAGGTGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCCG 
               
               
                   
               
               
                 TATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Dorea longicatena  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:15: 
     
       
         
           
               
            
               
                   Dorea longicatena  16S ribosomal RNA gene 
               
               
                 SEQ ID 15 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAGCGAAGCGCTTAAGTTTGATTCTTCGGATGAAGAC 
               
               
                   
               
               
                 TTTTGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTC 
               
               
                   
               
               
                 ATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCAC 
               
               
                   
               
               
                 GGTACCGCATGGTACAGTGGTAAAAACTCCGGTGGTATGAGATGGACCCG 
               
               
                   
               
               
                 CGTCTGATTAGGTAGTTGGTGGGGTAACGGCCTACCAAGCCGACGATCAG 
               
               
                   
               
               
                 TAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAAGGATGAAGTATTTCGGTATGTAAACTTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAAC 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGCACGGCAAGCCAGATGTGAAAGC 
               
               
                   
               
               
                 CCGGGGCTCAACCCCGGGACTGCATTTGGAACTGCTGAGCTAGAGTGTCG 
               
               
                   
               
               
                 GAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATGACTGACGTTGAGG 
               
               
                   
               
               
                 CTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGACTGCTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAG 
               
               
                   
               
               
                 CTAACGCAATAAGCAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCTGATCTTGACATCCCGATGACCGCTT 
               
               
                   
               
               
                 CGTAATGGAAGTTTTTCTTCGGAACATCGGTGACAGGTGGTGCATGGTTG 
               
               
                   
               
               
                 TCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAA 
               
               
                   
               
               
                 CCCCTATCTTCAGTAGCCAGCAGGTTAAGCTGGGCACTCTGGAGAGACTG 
               
               
                   
               
               
                 CCAGGGATAACCTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCC 
               
               
                   
               
               
                 TTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGAGAAGCG 
               
               
                   
               
               
                 AACTCGCGAGGGTAAGCAAATCTCAAAAATAACGTCTCAGTTCGGATTGT 
               
               
                   
               
               
                 AGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCAGATCA 
               
               
                   
               
               
                 GAATGCTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACA 
               
               
                   
               
               
                 CCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCGTAAGGAGGGA 
               
               
                   
               
               
                 GCTGCCGAAGGTGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCC 
               
               
                   
               
               
                 GTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Bifidobacterium catenulatum  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:16: 
     
       
         
           
               
            
               
                   Bifidobacterium catenuiatum  16S ribosomal 
               
               
                 RNA gene 
               
               
                 SEQ ID 16 
               
               
                 TTTTGTGGAGGGTTCGATTCTGGCTCAGGATGAACGCrGGCGGCGTGCTT 
               
               
                   
               
               
                 AACACATGCAAGTCGAACGGGATCCAGGCAGCTTGCTGCCTGGTGAGAGT 
               
               
                   
               
               
                 GGCGAACGGGTGAGTAATGCGTGACCGACCrGCCCCATACACCGGAATAG 
               
               
                   
               
               
                 CTCCTGGAAACGGGTGGTAATGCCGGATGCTCCGACTCCTCGCATGGGGT 
               
               
                   
               
               
                 GTCGGGAAAGATTTCATCGGTATGGGATGGGGTCGCGTCCrATCAGGTAG 
               
               
                   
               
               
                 TCGGCGGGGTAACGGCCCACCGAGCCTACGACGGGTAGCCGGCCTGAGAG 
               
               
                   
               
               
                 GGCGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGG 
               
               
                   
               
               
                 CAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCC 
               
               
                   
               
               
                 GCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCA 
               
               
                   
               
               
                 AGCCTTCGGGTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCC 
               
               
                   
               
               
                 AGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGC 
               
               
                   
               
               
                 GTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCT 
               
               
                   
               
               
                 TAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAG 
               
               
                   
               
               
                 ACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACAC 
               
               
                   
               
               
                 CAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAG 
               
               
                   
               
               
                 CGTGGGGAGCGAACAGGATTAGGAACACCAGTGGCGAAGGCGGCTTACTG 
               
               
                   
               
               
                 GACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAG 
               
               
                   
               
               
                 ATACCCTGGTAGTCCACGCCGTAAACGATGACTACTAGGTGTCGGGGAGC 
               
               
                   
               
               
                 AAAGCTCTTCGGTGCCGCAGCAAACGCAATAAGTAGTCCACCTGGGGAGT 
               
               
                   
               
               
                 ACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCG 
               
               
                   
               
               
                 GTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGCTCT 
               
               
                   
               
               
                 TGACATCCCGGTGACCGGCGTGTAATGACGCCTTTTCTTCGGAACACCGG 
               
               
                   
               
               
                 TGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTT 
               
               
                   
               
               
                 AAGTCCCGCAACGAGCGCAACCCTTATCTTCAGTAGCCAGCAATTCGGAT 
               
               
                   
               
               
                 GGGCACTCTGGAGAGACTGCCAGGGATAACCTGGAGGAAGGTGGGGATGA 
               
               
                   
               
               
                 CGTCAAATCATCATGCCCCTTATGAGCAGGGCTACACACGTGCTACAATG 
               
               
                   
               
               
                 GCGTAAACAAAGGGAAGCGAGCCTGCGAGGGTAAGCAAATCTCAAAAATA 
               
               
                   
               
               
                 ACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAAT 
               
               
                   
               
               
                 CGCTAGTAATCGCGAATCAGCATGTCGCGGTGAATACGTTCCCGGGTCTT 
               
               
                   
               
               
                 GTACACACCGCCCGTCACACCATGGGAGTTGGTAACGCCCGAAGTCAGTG 
               
               
                   
               
               
                 ACCCAACCGTAAGGAGGGAGCTGCCGAAGGTGGGACCGATAACTGGGGTG 
               
               
                   
               
               
                 AAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTT 
               
               
                   
               
               
                 TCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, an  Akkermansia muciniphila  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:17: 
     
       
         
           
               
            
               
                   Akkermansia muciniphila  16S ribosomal 
               
               
                 RNA sequence 
               
               
                 SEQ ID 17 
               
               
                 ATGGAGAGTTTGATTCTGGCTCAGAACGAACGCTGGCGGCGTGGATAAGA 
               
               
                   
               
               
                 CATGCAAGTCGAACGAGAGAATTGCTAGCTTGCTAATAATTCTCTAGTGG 
               
               
                   
               
               
                 CGCACGGGTGAGTAACACGTGAGTAACCTGCCCCCGAGAGCGGGATAGCC 
               
               
                   
               
               
                 CTGGGAAACTGGGATTAATACCGCATAGTATCGAAAGATTAAAGCAGCAA 
               
               
                   
               
               
                 TGCGCTTGGGGATGGGCTCGCGGCCTATTAGTTAGTTGGTGAGGTAACGG 
               
               
                   
               
               
                 CTCACCAAGGCGATGACGGGTAGCCGGTCTGAGAGGATGTCCGGCCACAC 
               
               
                   
               
               
                 TGGAACTGAGACACGGTCCAGACACCTACGGGTGGCAGCAGTCGAGAATC 
               
               
                   
               
               
                 ATTCACAATGGGGGAAACCCTGATGGTGCGACGCCGCGTGGGGGAATGAA 
               
               
                   
               
               
                 GGTCTTCGGATTGTAAACCCCTGTCATGTGGGAGCAAATTAAAAAGATAG 
               
               
                   
               
               
                 TACCACAAGAGGAAGAGACGGCTAACTCTGTGCCAGCAGCCGCGGTAATA 
               
               
                   
               
               
                 CAGAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGG 
               
               
                   
               
               
                 CTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCA 
               
               
                   
               
               
                 CATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTG 
               
               
                   
               
               
                 TAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGG 
               
               
                   
               
               
                 TTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGGAGCGAAAGG 
               
               
                   
               
               
                 GATTAGATACCCCTGTAGTCCTGGCAGTAAACGGTGCACGCTTGGTGTGC 
               
               
                   
               
               
                 GGGGAATCGACCCCCTGCGTGCCGGAGCTAACGCGTTAAGCGTGCCGCCT 
               
               
                   
               
               
                 GGGGAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGACCCGC 
               
               
                   
               
               
                 ACAAGCGGTGGAGTATGTGGCTTAATTCGATGCAACGCGAAGAACCTTAC 
               
               
                   
               
               
                 CTGGGCTTGACATGTAATGAACAACATGTGAAAGCATGCGACTCTTCGGA 
               
               
                   
               
               
                 GGCGTTACACAGGTGCTGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGT 
               
               
                   
               
               
                 TTGGTTAAGTCCAGCAACGAGCGCAACCCCTGTTGCCAGTTACCAGCACG 
               
               
                   
               
               
                 TGAAGGTGGGGACTCTGGCGAGACTGCCCAGATCAACTGGGAGGAAGGTG 
               
               
                   
               
               
                 GGGACGACGTCAGGTCAGTATGGCCCTTATGCCCAGGGCTGCACACGTAC 
               
               
                   
               
               
                 TACAATGCCCAGTACAGAGGGGGCCGAAGCCGCGAGGCGGAGGAAATCCT 
               
               
                   
               
               
                 AAAAACTGGGCCCAGTTCGGACTGTAGGCTGCAACCCGCCTACACGAAGC 
               
               
                   
               
               
                 CGGAATCGCTAGTAATGGCGCATCAGCTACGGCGCCGTGAATACGTTCCC 
               
               
                   
               
               
                 GGGTCTTGTACACACCGCCCGTCACATCATGGAAGCCGGTCGCACCCGAA 
               
               
                   
               
               
                 GTATCTGAAGCCAACCGCAAGGAGGCAGGGTCCTAAGGTGAGACTGGTAA 
               
               
                   
               
               
                 CTGGGATGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATC 
               
               
                   
               
               
                 ACCTCCTTTCTATGGA 
               
            
           
         
       
     
     In alternative embodiments, a  Ruminococcus gnavus  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:18: 
     
       
         
           
               
            
               
                   Ruminococcus gnavus  16S ribosomal RNA gene 
               
               
                 SEQ ID 18 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAGCGAAGCACCTTGACGGATTTCTTCGGATTGAAGC 
               
               
                   
               
               
                 CTTGGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTC 
               
               
                   
               
               
                 GTACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCAC 
               
               
                   
               
               
                 AGTACCGCATGGTACGGTGTGAAAAACTCCGGTGGTATGAGATGGACCCG 
               
               
                   
               
               
                 CGTCTGATTAGGTAGTTGGTGGGGTAACGGCCTACCAAGCCGACGATCAG 
               
               
                   
               
               
                 TAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 AACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAGCGATGAAGTATTTCGGTATGTAAAGCTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAAC 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGC 
               
               
                   
               
               
                 CCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCG 
               
               
                   
               
               
                 GAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGG 
               
               
                   
               
               
                 CTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGAATACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAG 
               
               
                   
               
               
                 CAAACGCAATAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCTGGTCTTGACATCCCTCTGACCGCTC 
               
               
                   
               
               
                 TTTAATCGGAGCTTTCCTTCGGGACAGAGGAGACAGGTGGTGCATGGTTG 
               
               
                   
               
               
                 TCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAA 
               
               
                   
               
               
                 CCCCTATCTTTACTAGCCAGCATTTTGGATGGGCACTCTAGAGAGACTGC 
               
               
                   
               
               
                 CAGGGATAACCTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCT 
               
               
                   
               
               
                 TATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGA 
               
               
                   
               
               
                 GCCCGCGAGGGGGAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTA 
               
               
                   
               
               
                 GTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAG 
               
               
                   
               
               
                 AATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACAC 
               
               
                   
               
               
                 CATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCGCAAGGAGGGAG 
               
               
                   
               
               
                 CTGCCGAAGGTGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCCG 
               
               
                   
               
               
                 TATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGA 
               
            
           
         
       
     
     In alternative embodiments, a  Ruminococcus  torques species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO: 19: 
     
       
         
           
               
            
               
                   Ruminococcus torques  16S ribosomal RNA gene 
               
               
                 SEQ ID 19 
               
               
                 TTTAACGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTA 
               
               
                   
               
               
                 ACACATGCAAGTCGAGCGAAGCACTTTGCTTAGATTCTTCGGATGAAGAG 
               
               
                   
               
               
                 GATTGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTC 
               
               
                   
               
               
                 ATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCAC 
               
               
                   
               
               
                 AGCACCGCATGGTGCGGGGGTAAAAACTCCGGTGGTATGAGATGGACCCG 
               
               
                   
               
               
                 CGTCTGATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCGACGATCAG 
               
               
                   
               
               
                 TAGCCGACCTGAGAGGGTGGCCGGCCACATTGGGACTGAGACACGGCCCA 
               
               
                   
               
               
                 AACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCC 
               
               
                   
               
               
                 TGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTC 
               
               
                   
               
               
                 TATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAA 
               
               
                   
               
               
                 TACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATT 
               
               
                   
               
               
                 TACTGGGTGTAAAGGGAGCGTAGACGGATGGGCAAGTCTGATGTGAAAAC 
               
               
                   
               
               
                 CCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTTCATCTAGAGTGCTG 
               
               
                   
               
               
                 GAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGG 
               
               
                   
               
               
                 AGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGG 
               
               
                   
               
               
                 CTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCC 
               
               
                   
               
               
                 GTAAACGATGACTACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAG 
               
               
                   
               
               
                 CAAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACT 
               
               
                   
               
               
                 CAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT 
               
               
                   
               
               
                 CGAAGCAACGCGAAGAACCTTACCTGCTCTTGACATCCCGCTGACCGGAC 
               
               
                   
               
               
                 GGTAATGCGTCCTTCCCTTCGGGGCAGCGGAGACAGGTGGTGCATGGTTG 
               
               
                   
               
               
                 TCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAA 
               
               
                   
               
               
                 CCCCTATCTTTAGTAGCCAGCGGCCAGGCCGGGCACTCTAGAGAGACTGC 
               
               
                   
               
               
                 CGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCT 
               
               
                   
               
               
                 TATGAGCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGA 
               
               
                   
               
               
                 GACCGCGAGGTGGAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTA 
               
               
                   
               
               
                 GTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAG 
               
               
                   
               
               
                 AATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACAC 
               
               
                   
               
               
                 CATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCGTAAGGAGGGAG 
               
               
                   
               
               
                 CTGCCGAAGGCGGGACCGATAACTGGGGGTGAAGTCGTAACAAGGTAGCC 
               
               
                   
               
               
                 GTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, a  Clostridium scindens  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:20: 
     
       
         
           
               
            
               
                   Clostridium scindens  16S ribosomal RNA gene 
               
               
                 SEQ ID 20 
               
               
                 GAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACAT 
               
               
                   
               
               
                 GCAAGTCGAACGAAGCGCCTGGCCCCGACTTCTTCGGAACGAGGAGCCTT 
               
               
                   
               
               
                 GCGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGCAACCTGCCTTGCAC 
               
               
                   
               
               
                 TGGGGGATAACAGCCAGAAATGGCTGCTAATACCGCATAAGACCGAAGCG 
               
               
                   
               
               
                 CCGCATGGCGCGGCGGCCAAAGCCCCGGCGGTGCAAGATGGGCCCGCGTC 
               
               
                   
               
               
                 TGATTAGGTAGTTGGCGGGGTAACGGCCCACCAAGCCGACGATCAGTAGC 
               
               
                   
               
               
                 CGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCAGACT 
               
               
                   
               
               
                 CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGAT 
               
               
                   
               
               
                 GCAGCGACGCCGCGTGAAGGATGAAGTATTTCGGTATGTAAACTTCTATC 
               
               
                   
               
               
                 AGCAGGGAAGAAGATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACG 
               
               
                   
               
               
                 TGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACT 
               
               
                   
               
               
                 GGGTGTAAAGGGAGCGTAGACGGCGATGCAAGCCAGATGTGAAAGCCCGG 
               
               
                   
               
               
                 GGCTCAACCCCGGGACTGCATTTGGAACTGCGTGGCTGGAGTGTCGGAGA 
               
               
                   
               
               
                 GGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGA 
               
               
                   
               
               
                 ACACCAGTGGCGAAGGCGGCCTGCTGGACGATGACTGACGTTGAGGCTCG 
               
               
                   
               
               
                 AAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAA 
               
               
                   
               
               
                 ACGATGACTACTAGGTGTCGGGTGGCAAGGCCATTCGGTGCCGCAGCAAA 
               
               
                   
               
               
                 CGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAA 
               
               
                   
               
               
                 GGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAA 
               
               
                   
               
               
                 GCAACGCGAAGAACCTTACCTGATCTTGACATCCCGATGCCAAAGCGCGT 
               
               
                   
               
               
                 AACGCGCTCTTTCTTCGGAACATCGGTGACAGGTGGTGCATGGTTGTCGT 
               
               
                   
               
               
                 CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCC 
               
               
                   
               
               
                 TATCTTCAGTAGCCAGCATTTTGGATGGGCACTCTGGAGAGACTGCCAGG 
               
               
                   
               
               
                 GAGAACCTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATG 
               
               
                   
               
               
                 ACCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAGGCGAACCC 
               
               
                   
               
               
                 GCGAGGGTGGGCAAATCCCAAAAATAACGTGTCAGTTCGGATTGTAGTCT 
               
               
                   
               
               
                 GCAACTCGACTACATGAAGTTGGAATCGCTAGTAATCGCGAATCAGAATG 
               
               
                   
               
               
                 TCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATG 
               
               
                   
               
               
                 GGAGTCAGTAACGCCCGAAGCCGGTGACCCAACCCGTAAGGGAGGGAGCC 
               
               
                   
               
               
                 GTCGAAGGTGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCCGTA 
               
               
                   
               
               
                 TCGGAAGGTGCGGCTGGATCACCTCCTTC 
               
            
           
         
       
     
     In alternative embodiments, a  Enterococcus hirae  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to SEQ ID NO:21: 
     
       
         
           
               
            
               
                   Enterococcus hirae  16S ribosomal RNA gene 
               
               
                 SEQ ID 21 
               
               
                 TGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACA 
               
               
                   
               
               
                 TGCAAGTCGAACGCTTCTTTTTCCACCGGAGCTTGCTCCACCGGAAAAAG 
               
               
                   
               
               
                 AGGAGTGGCGAACGGGTGAGTAACACGTGGGTAACCTGCCCATCAGAAGG 
               
               
                   
               
               
                 GGATAACACTTGGAAACAGGTGCTAATACCGTATAACAATCGAAACCGCA 
               
               
                   
               
               
                 TGGTTTTGATTTGAAAGGCGCTTTCGGGTGTCGCTGATGGATGGACCCGC 
               
               
                   
               
               
                 GGTGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCGACGATGCAT 
               
               
                   
               
               
                 AGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAA 
               
               
                   
               
               
                 ACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCT 
               
               
                   
               
               
                 GACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCT 
               
               
                   
               
               
                 GTTGTTAGAGAAGAACAAGGATGAGAGTAACTGTTCATCCCTTGACGGTA 
               
               
                   
               
               
                 TCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACG 
               
               
                   
               
               
                 TAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCG 
               
               
                   
               
               
                 GTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATT 
               
               
                   
               
               
                 GGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTA 
               
               
                   
               
               
                 GCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTC 
               
               
                   
               
               
                 TCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGA 
               
               
                   
               
               
                 TTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTGGA 
               
               
                   
               
               
                 GGGTTTCCGCCCTTCAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGG 
               
               
                   
               
               
                 GGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCAC 
               
               
                   
               
               
                 AAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCA 
               
               
                   
               
               
                 GGTCTTGACATCCTTTGACCACTCTAGAGATAGAGCTTCCCCTTCGGGGG 
               
               
                   
               
               
                 CAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTT 
               
               
                   
               
               
                 GGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCCATCATTT 
               
               
                   
               
               
                 AGTTGGGCACTCTAGCAAGACTGCCGGTGACAAACCGGAGGAAGGTGGGG 
               
               
                   
               
               
                 ATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTAC 
               
               
                   
               
               
                 AATGGGAAGTACAACGAGTCGCAAAGTCGCGAGGCTAAGCTAATCTCTTA 
               
               
                   
               
               
                 AAGCTTCrCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCCG 
               
               
                   
               
               
                 GAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGG 
               
               
                   
               
               
                 CCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTC 
               
               
                   
               
               
                 GGTGAGGTAACCTTTTGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGG 
               
               
                   
               
               
                 GGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT 
               
               
                   
               
               
                 CCTTTCTAAGGAA 
               
            
           
         
       
     
     In alternative embodiments, bacterial strains used in formulations as provided herein, or in methods as provided herein, are identified by their sequence identity to the variable domains of 16S rDNA. 
     For example, in alternative embodiments, a species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to the variable portion of a particular 16S rDNA sequence, wherein the variable portion of the 16S rDNA is: Nucleotides 137-242; Nucleotides 433-497; and/or Nucleotides 986-1043, of the 16S rDNA sequence. 
     For example, in alternative embodiments, a  Enterococcus hirae  species used in formulations as provided herein, or in methods as provided herein, comprises a 16S rDNA sequence having at least about 90%, 95%, 96%, 97% 98% or 99% or complete sequence identity to the variable portions of the 16S rDNA: Nucleotides 137-242; Nucleotides 433-497; and/or Nucleotides 986-1043, of SEQ ID NO:21: 
     In alternative embodiments, for sequence comparison, one sequence acts as a reference sequence, to which another sequence is compared. Methods of alignment of sequences for comparison are well known in the art. See, for example, by the local homology algorithm of Smith and Waterman (1970) Adv. Appl. Math. 2:482c, by the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. (1970) 48:443, by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. USA (1998) 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group. Madison. Wis.), or by manual alignment and visual inspection (see. for example, Brent et al., Current Protocols in Molecular Biology, John Wiley &amp; Sons, Inc. (Ringbou ed., 2003)). Two examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. (1977) 25:3389-3402, and Altschul et al., J. Mol. Biol. (1990) 215:403-410, respectively. 
     In alternative embodiments, align methods comprise use of a BLAST™ analysis employing: (i) a scoring matrix (such as, e.g., BLOSSUM 62™ or PAM 120™) to assign a weighted homology value to each residue and (ii) a filtering program(s) (such as SEG™ or XNU™) that recognizes and eliminates highly repeated sequences from the calculation. In alternative embodiments, align methods comprise use of a BLAST™ analysis employing a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall -p blastp -d “nr pataa”-F F, and all other options are set to default. 
     Any of the above aspects and embodiments can be combined with any other aspect or embodiment as disclosed here in the Summary, Figures and/or Detailed Description sections. 
     As used in this specification and the claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. 
     Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive and covers both “or” and “and”. 
     Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from the context, all numerical values provided herein are modified by the term “about.” 
     Unless specifically stated or obvious from context, as used herein, the terms “substantially all”, “substantially most of”, “substantially all of” or “majority of” encompass at least about 90%, 95%, 97%, 98%, 99% or 99.5%, or more of a referenced amount of a composition. 
     The entirety of each patent, patent application, publication and document referenced herein hereby is incorporated by reference. Citation of the above patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. Incorporation by reference of these documents, standing alone, should not be construed as an assertion or admission that any portion of the contents of any document is considered to be essential material for satisfying any national or regional statutory disclosure requirement for patent applications. Notwithstanding, the right is reserved for relying upon any of such documents, where appropriate, for providing material deemed essential to the claimed subject matter by an examining authority or court. 
     Modifications may be made to the foregoing without departing from the basic aspects of the invention. Although the invention has been described in substantial detail with reference to one or more specific embodiments, those of ordinary skill in the art will recognize that changes may be made to the embodiments specifically disclosed in this application, and yet these modifications and improvements are within the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element(s) not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising”, “consisting essentially of”, and “consisting of” may be replaced with either of the other two terms. Thus, the terms and expressions which have been employed are used as terms of description and not of limitation, equivalents of the features shown and described, or portions thereof, are not excluded, and it is recognized that various modifications are possible within the scope of the invention. Embodiments of the invention are set forth in the following claims. 
     The invention will be further described with reference to the examples described herein; however, it is to be understood that the invention is not limited to such examples. 
     EXAMPLES 
     Unless stated otherwise in the Examples, all recombinant DNA techniques are carried out according to standard protocols, for example, as described in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, NY and in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA. Other references for standard molecular biology techniques include Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, NY, Volumes I and II of Brown (1998) Molecular Biology LabFax, Second Edition, Academic Press (UK). Standard materials and methods for polymerase chain reactions can be found in Dieffenbach and Dveksler (1995) PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, and in McPherson at al. (2000) PCR—Basics: From Background to Bench, First Edition, Springer Verlag, Germany. 
     The following Examples describe methods and compositions for practicing embodiments as provided herein, including methods for making and using compositions comprising non-pathogenic bacteria and non-pathogenic germinable bacterial spores used to practice methods as provide herein. 
     Example 1: Anaerobic Culture Conditions 
     Preparation of Anaerobic Growth Medium 
     Exemplary bacterial strains described herein are obligate anaerobes that require anaerobic conditions for culture. Growth media suitable for culture of anaerobic bacteria include reducing agents such as L-cysteine, sodium thioglycolate, and dithiothreitol, for the purpose of scavenging and removing oxygen. Appropriate commercially available anaerobic growth media include but are not limited to Anaerobe Basal Broth (Oxoid/Thermo Scientific), Reinforced Clostridial Medium (Oxoid/Thermo Scientific), Wilkins-Chalgren Anaerobe Broth (Oxoid/Thermo Scientific), Schaedler Anaerobe Broth (Oxoid/Thermo Scientific), and Brain Heart Infusion Broth (Oxoid/Thermo Scientific). Animal free medium for anaerobic culture include but are not limited to Vegitone  Actinomyces  Broth (Millipore-Sigma), MRS Broth (Millipore-Sigma), Vegitone Infusion Broth (Millipore-Sigma), and Vegitone Casein Soya Broth (Millipore-Sigma). 
     One liter of Anaerobic growth medium is prepared by combining the manufacturer&#39;s recommended amount in grams of dry growth medium powder with 800 ml Reagent Grade Water (NERL™) along with 1 ml 2.5 mg/ml resazurin (ACROS Organics™) in a 2 liter beaker and stirred on a heated stir plate until dissolved. The volume is adjusted to 1 liter by addition of additional Reagent Grade Water, then the volume is brought to a boil while stirring until the red color imbued by the resazurin becomes colorless, indicating removal of oxygen from the solution. The volume is then removed from the stir plate to cool for 10 minutes on the benchtop before further manipulation. 
     From the 1-liter volume, 900 ml is transferred to a 1 liter anaerobic media bottle (Chemglass Life Sciences) and then placed back on the heated stir plate to remove any oxygen introduced in the transfer, as indicated by the color of the added resazurin. The anaerobic media bottle is then stoppered with a butyl rubber bung that is secured by a crimped aluminum collar, and then brought into the anaerobic chamber (Coy Lab Type A Vinyl Anaerobic Chamber, Coy Laboratory Products, Grass Lake, Mich.). The butyl rubber bung is removed to open the bottle within the anaerobic chamber to equilibrate with the anoxic atmosphere while cooling to ambient temperature. The bottle is resealed with a fresh butyl rubber bung and crimped aluminum collar, brought out of the chamber, then sterilized by autoclaving for 20 minutes followed by slow exhaust. 
     Alternatively, the 1-liter volume can be aliquoted into smaller 50 ml volumes in 100 ml serum bottles (Chemglass Life Sciences, Vineland N.J.). The boiled 1-liter volume is transferred to a one-liter screwcap bottle, which is placed back on the heated stir plate to drive off any oxygen introduced by the transfer. The bottle cap is then securely tightened, and the bottle is immediately brought into the anaerobic chamber, where the cap is loosened to allow the volume to equilibrate with the anoxic atmosphere and to cool for 1 hour. The volume is then transferred in 50 ml aliquots to 100 ml serum bottles using a serological pipette, then the liquid contents cooled to ambient temperature. The bottles are sealed with butyl rubber bungs and crimped aluminum collars, brought out of the chamber, then sterilized by autoclaving for 20 minutes followed by slow exhaust. 
     Alternatively, the 1-liter volume can be aliquoted into smaller 10 ml volumes in sealed Hungate tubes (Chemglass Life Sciences, Vineland N.J.) as follows. The boiled 1-liter volume is transferred to a one-liter screwcap bottle, which is placed back on the heated stir plate to drive off any oxygen introduced by the transfer. The bottle cap is then securely tightened, and the bottle is immediately brought into the anaerobic chamber, where the cap is loosened to allow the volume to equilibrate with the anoxic atmosphere and to cool for 1 hour. The volume is then transferred in 10 ml aliquots to fill racked Hungate tubes, then allowed to cool to ambient temperature, followed by securely capping and sealing each tube with screwcaps with butyl rubber septa. The sealed Hungate tube aliquots are removed from the anaerobic chamber and then sterilized by autoclaving for 20 minutes followed by slow exhaust. 
     Alternatively, the 1 liter volume can be combined with 15 grams Agar (Thermo Scientific™) to make solid media in culture plates as follows: The boiled 1 liter volume is poured into a 1 liter screwcap bottle, followed by replacement on a heated stir plate to remove any oxygen introduced by the transfer as indicated by the colorless resazurin oxygen indicator. The bottle is loosely capped and then autoclaved for 20 minutes followed by slow exhaust. Immediately after autoclaving, the cap of the bottle is tightened prior to bringing the bottle into the anaerobic chamber. Once in the anaerobic chamber, the cap is loosened and the contents cooled for 30 minutes, then 25 ml volumes are poured into culture plates and allowed to cool until solidified. The plates are then allowed to dry in the anaerobic chamber for 24 hours prior to use. 
     Live Cryostorage of Anaerobic Microbes 
     Individual microbes of interest are prepared for long-term cryogenic live storage by inoculating a pure colony isolate grown on anaerobic solid medium into a prepared Hungate tube containing liquid anaerobic growth medium previously determined to be optimal for the species. The inoculated Hungate tube is then incubated at 37° C. until turbidity evident of exponential growth is observed. The Hungate culture is brought into the anaerobic chamber, and 1 ml is transferred by pipette into a 2 ml screwcap cryotube containing anoxic 1 ml Biobank Buffer (Phosphate Buffered Saline (PBS) plus 2% trehalose plus 10% dimethyl sulfoxide, filter sterilized and bubbled with nitrogen gas to remove oxygen). The resulting 2 ml volume is thoroughly mixed by pipetting, securely tightened, then placed for long-term storage in the gaseous phase of a liquid nitrogen Dewar or in a −80° C. freezer. 
     Microbes in fecal matter can be cryogenically preserved for later revival and new strain discovery as follows. Freshly obtained fecal material is brought into the anaerobic chamber and 1 gram is weighed and mixed in a 15 ml conical tube with a solution consisting of 5 ml Anaerobe Basal Broth (ABB) and 5 ml Biobank Buffer. The tube is tightly capped, and the fecal matter is thoroughly suspended in the solution by vortexing for 20 minutes, followed by incubation upright on ice to allow large particles to settle. One ml aliquots of the fecal suspension are then transferred by pipette to a 2 ml screwcap cryotube, securely tightened, then placed for long-term storage in the gaseous phase of a liquid nitrogen Dewar or in a −80° C. freezer. 
     Example 2: Fecal Matter Collection from Patients and Processing 
     Fecal matter donations are acquired from healthy volunteers as well as individuals exhibiting disease symptoms. Donors can be patients being administered approved anti-viral therapies or participating in clinical trials testing various anti-viral drug or treatment regimens. Donors can be healthy volunteers that do not exhibit disease symptoms. 
     Donors receive a stool sampling kit by mail sent to the contact address provided or by their physician. Stool samples are collected by the subject at home, or with necessary assistance if hospitalized. Stool sampling kits consist of the following: gloves, instructions for stool collection, welcome card, freezer pack, Styrofoam container, plastic bracket and plastic commode to aid in stool collection, Bristol stool chart, FedEx shipping labels, and stickers to seal kit prior to shipping. Subjects receive a freezer pack for chilling the samples and are instructed to place it in their freezer overnight upon receipt of the sampling kit. The stool sampling kit also includes a plastic commode that can be placed safely and securely on a toilet seat, allowing the subject to defecate directly into a plastic container. The subject is instructed to use the commode to capture a stool sample, then seal the sample container with a provided snap-cap lid. Subjects are instructed to wear the gloves provided in the kit before removing the sample container from the toilet. The subject is instructed to seal the plastic container inside a specimen bag and remove gloves. The subject is then instructed to remove the ice pack from their home freezer and place it inside the Styrofoam cooler box along with the bagged and sealed stool sample, and the graded Bristol Stool card (form indicating stool collection date/time and consistency). The subject is instructed to close the lid on the foam container and then close the box, sealing with the packing sticker. The subject is instructed to schedule a FedEx pickup at their home within 24 hours of stool collection or drop it off at the nearest FedEx location. Under these conditions the stool has been demonstrated to remain chilled during shipment for as long as 48 hours. 
     Once received, the stool sample receptacle is given a unique alphanumeric identifier that is used subsequently for sample tracking. The stool is unpacked from the shipping box in a laboratory setting, homogenized, and divided into enough individual aliquots for all projected analyses prior to freezing and storage at −80° C., as described below. All aliquots also bear an alphanumeric identifier corresponding to the subject donor. Any remaining stool after the aliquots are taken is disposed as biohazardous waste. 
     Preparation of Fecal Matter Samples for Analysis 
     Fecal matter received from donors can be processed using any method known in the art, for example, as described in U.S. Pat. Nos. 10,493,111; 10,471,107; 10,286,012; 10,314,863; 9,623,056. 
     For example, received fecal matter in its receptacle is placed on ice and then brought into the anaerobic chamber. The receptacle is opened and approximately 40 g stool is weighed into a tared specimen cup. 15 ml sterile anoxic PBS is then added, and the mixture is homogenized by a hand-held homogenizer to achieve a smooth consistency. 
     The homogenized fecal matter is then processed and aliquoted for cryo-preservation for several different analyses as follows:
     1) For Genomic and Transcriptomic Analyses: homogenized fecal matter is weighed and then an equal volume to weight amount of RNAlater® (Thermo Fisher Scientific) solution is added. The tube is capped tightly and then vortexed for 20 seconds and then placed on ice. A pipette is used to transfer 1 ml aliquots into 2 ml Eppendorf tubes. Aliquoted samples are frozen on dry ice and then stored at −80° C.   2) Live Cryopreservation for Fecal Microbiome Transfer (FMT) Experiments in Mice: Homogenized fecal matter is combined with FMT Buffer (Phosphate Buffered Saline plus 1% L-Cysteine plus 2% Trehalose plus 30% glycerol). The tube is then vortexed for 20 seconds and then placed on ice. A pipette is used to transfer 1 ml aliquots into 2 ml cryotubes that are then tightly capped. Aliquoted samples are frozen on dry ice and then stored at −80° C.   3) Live Cryopreservation for Isolation and Discovery of Microbes: Homogenized fecal matter is combined in a conical tube with Anaerobe Basal Broth and Biobank Buffer (Phosphate Buffered Saline plus 2% Trehalose plus 10% dimethyl sulfoxide), tightly capped and vortexed for 20 seconds, then put on ice upright and allowed to settle for 10 minutes. Using a pipette, 1 ml aliquots are added to 2 ml cryotubes, which are then tightly capped. Aliquoted samples are frozen on dry ice and then stored at −80° C.
       For Genomic and Metabolomic Analyses: Homogenized fecal matter is added to a plastic bag. About 1 cm of the tip end of the bag is cut off with scissors, then aliquots are made by manually squeezing 1 ml of the bag contents into 2 ml Eppendorf tubes. Aliquoted samples are frozen on dry ice and then stored at −80° C.   
       

     Example 3: Isolation and Characterization of Pure Microbial Strains from Fecal Matter 
     In alternative embodiments, microbes used in compositions as provided herein, or used to practice methods as provided herein, are isolated from fecal matter, and can be used on the form of a pure microbial strain isolated from fecal matter. 
     Individual bacterial strains can be isolated and cultured from fecal matter material for further study and for assembly of therapeutic biologicals, i.e. for manufacturing combinations of microbes as provided herein. The majority of live bacteria that inhabit fecal matter tend to be obligate anaerobes so care must be taken to perform all culture and isolation work in the anaerobic chamber to prevent their exposure to oxygen, and to use various anaerobic growth media that includes reductant compounds as described in Example 1. Growth media that favor growth of target bacteria can be used to improve the ability to find and isolate them as pure living cultures. Different anaerobic growth media are used to enable growth of different subsets of microbes to improve overall ability to isolate and purify an inclusive number of unique bacterial species from each individual fecal material sample. 
     To begin a microbial isolation and characterization campaign, one cryotube containing cryogenically preserved fecal matter is removed from storage in the liquid nitrogen Dewar, brought into the anaerobic chamber, and then allowed to thaw gently on ice. The entire 1 ml contents are added to 10 ml of Anaerobe Basal Broth (ABB) or another suitable anaerobic growth medium to establish a 1/10 dilution. Successive 10-fold serial dilutions are then performed in ABB to establish 1/100, 1/1000, 1/10000, 1/100000, 1/1000000 dilutions of the fecal matter. From each of the 1/10000, 1/100000, and 1,1000000 dilutions, four 0.1 ml volumes are removed and then added to and spread over solid anaerobic growth medium of choice. The platings are incubated at 37° C. for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 days to allow for a wide variety of bacterial colonies to grow. Platings are made from several liquid dilutions of fecal matter to ensure that there will be ones that have numerous yet non-overlapping colonies for efficient colony picking. 
     Colonies are manually picked from plates using sterile pipette tips. Colonies may also be picked by an automated colony picking machine that is enclosed in an anaerobic chamber. Colonies are picked in multiples of 96 to accommodate subsequent 96-well-based genomic DNA isolation steps and large-scale cryogenic storage steps. The individual picked colonies are then struck on solid anaerobic growth medium of choice to isolate single purified colonies from each picked colony, and then incubated at 37° C. for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 days to allow for visible colony growth to arise. After visible colonies are evident on the streak, single colonies are picked and then each inoculated into an individual well of a 2 ml 96-well deep well block, each well with 1 ml liquid anaerobic growth medium of choice. Once all wells of the deep-well block have been inoculated with different picked colonies, the deep well block is covered with an adhesive gas-permeable seal and then incubated at 37° C. in an incubator within the anaerobic chamber for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 days to allow for liquid growth from each isolated colony. 
     After turbid growth is apparent in all wells, the gas-permeable seal is removed from the 96-well deep well block and a viable stock representation is made by transferring 0.1 ml culture from each well to the corresponding wells of a second 96-well deep-well block, each well containing 0.4 ml of the same anaerobic growth medium plus 0.5 ml Biobank Buffer (Phosphate Buffered Saline plus 2% Trehalose plus 10% dimethyl sulfoxide. The volumes in each well are thoroughly mixed by pipetting up and down several times, then the deep-well block is sealed with an impermeable foil seal rated for −80° C. storage, then stored in a −80° C. freezer. 
     Sequence and Computational Characterization of Isolated Fecal Bacteria 
     The remaining 0.9 ml culture in the original 96-well deep-well plate is then used for whole genome sequence determination of the isolated strain as follows: The deep-well block is subjected to centrifugation for 20 minutes at 6000 g to pellet the cells. After centrifugation, 0.8 ml supernatant is carefully removed by pipette, leaving 0.1 ml pellet and medium for gDNA processing. Total genomic DNA is extracted from the cell pellet using the MagAttract PowerMicrobiome DNA/RNA EP kit (Qiagen). Genomic DNA is then prepared for Whole Genome Sequencing analysis using the sparQ DNA Frag &amp; Library Prep kit (Quantabio). Sequencing analysis is conducted on the Illumina platform using paired-end 150 bp reads. 
     Sequencing data is processed to remove low quality reads and adapter contamination using Trim Galore, a wrapper for cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200). 
     The high-quality reads for each isolate are compared against each bacterial or archaeal assembly in NCBI RefSeq using mash (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x). This identifies the most similar organism in the RefSeq database to each isolate at the species and strain level. If the distance reported by mash is below 0.01, the isolate is assumed to be the same strain as the reference strain. If the distance is less than 0.04, the isolate is assumed to be of the same species as the reference strain. If the distance is greater than 0.04, the isolate is assumed to be of a potentially novel species; these isolates are handled on a case-by-case basis. 
     Further analysis is performed on isolates of interest by assembling with SPAdes (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/) and using mummer (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005944) to align the reference genome and isolate genome against each other. 
     Complete genomes are generated for organisms of special interest using long-read sequencing. High molecular weight genomic DNA is prepared from organisms of interest using a commercially available kit for example GENOMIC-TIP™ (Qiagen). Library preparation on genomic DNA is performed using the Ligation Sequencing Kit (Oxford Nanopore) and sequencing is performed on a MINION™ (MinION™) (Oxford Nanopore). Reads are filtered and trimmed for quality and assembly is performed using the assembler Flye (Kolmogorov et al. (2019) Nature Biotechnology 37:540-546). The resulting assembly is polished using multiple rounds of pilon (Walker et al. (2014) PLOS ONE 9:e112963) with short reads to correct for errors inherent in long read sequencing. Genes are predicted on the polished genome using prodigal (Hyatt et al. (2010) BMC Bioinformatics 11:119) or the NCBI Prokaryotic Gene Annotation Pipeline (Tatusova et al. (2016) Nucleic Acids Research 44(14):6614-24). Results of this analysis on isolates collected so far are provided in Table 1. 
     Identification of Viral Genetic Material in Stool or Blood Samples 
     Several approaches well known in the art are used to determine the presence or identity of infective viral material in the stool and blood of patients. For example, specific DNA viruses of interest are detected by PCR or real time PCR (RT-PCR) using primers specific to the virus of interest. An analogous procedure is used for RNA viruses, with reverse transcription followed by RT-PCR. Alternatively, DNA or RNA is extracted from the whole stool or blood sample and sequenced by whole genome sequencing. Total genomic DNA is extracted from the stool using the MagAttract PowerMicrobiome DNA/RNA EP kit (Qiagen), and from blood using the QIAamp DNA Blood Mini Kit (Qiagen). Genomic DNA is then prepared for Whole Genome Sequencing analysis using the sparQ DNA Frag &amp; Library Prep kit (Quantabio). RNA is extracted from the stool or blood sample by binding to an RNeasy™ column (Qiagen) followed by washing and elution using the reagents provided in the RNeasy™ kit (Qiagen). Sequencing libraries are prepared from RNA by fragmentation, ribodepletion, cDNA synthesis, PCR amplification, and barcoding as described in the TRUSEQ® mRNA sample preparation kit (Illumina). Sequencing analysis is conducted on the Illumina platform using paired-end 150 bp reads. Reads not mapping to human or bacterial DNA are then aligned to a viral sequence database, for example the NCBI viral genomes database (https://www.ncbi.nlm.nih.gov/genome/viruses/). This approach has the advantage of detecting any virus, not just those that are targeted by PCR, and the identity of the virus is determined by sequencing. 
                     TABLE 1                  Exemplary bacterial strains isolated from human fecal material that can be used alone to practice methods       as provided herein, or in making or using combinations of microbe compositions as provided herein.                                                         Distance from               NCBI       NCBI   Reference       Strain   Screening   Taxonomy       Infraspecific   Assembly       ID   Medium   ID   NCBI Organism Name a     Name   (mash)                                             1   ABB   742722     Collinsella  sp. 4_8_47FAA   4_8_47FAA   0.0473307       2   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.00558143       3   ABB   1073351     Bacteroides stercoris  CC31F   CC31F   0.0198874       4   ABB   1339345     Parabacteroides distasonis  str. 3999B T(B) 6   3999B T(B) 6   0.00787841       5   ABB   1073351     Bacteroides stercoris  CC31F   CC31F   0.021248       6   ABB   1335613     Gordonibacter urolithinfaciens     DSM 27213T   0.00456858       7   ABB   2292910     Alistipes  sp. AF14-19   AF14-19   0.0168764       8   ABB   742722     Collinsella  sp. 4_8_47FAA   4_8_47FAA   0.0417882       9   ABB   47678     Bacteroides caccae     OM05-21BH   0.05067       10   ABB   47678     Bacteroides caccae     OM05-21BH   0.0121561       11   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.00593905       12   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.00583101       13   ABB   2292316     Collinsella  sp. AM34-10   AM34-10   0.0529596       14   ABB   471875     Ruminococcus lactaris  ATCC 29176   ATCC 29176   0.0131398       15   ABB   28116     Bacteroides ovatus     AM40-4   0.0117158       16   ABB   997891     Bacteroides vulgatus  CL09T03C04   CL09T03C04   0.0141644       17   ABB   742722     Collinsella  sp. 4_8_47FAA   4_8_47FAA   0.0447107       18   ABB   2292316     Collinsella  sp. AM34-10   AM34-10   0.0538719       19   ABB   1680     Bifidobacterium adolescentis     2789STDY5608862   0.0147396       20   ABB   1339345     Parabacteroides distasonis  str. 3999B T(B) 6   3999B T(B) 6   0.00817721       21   ABB   2292236     Odoribacter  sp. AF15-53   AF15-53   0.011787       22   ABB   46503     Parabacteroides merdae     AM48-24BH   0.0113184       23   ABB   88431     Dorea longicatena     AF17-8AC   0.0165507       24   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.00946265       25   ABB   1681     Bifidobacterium bifidum     2789STDY5608877   0.160172       26   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.116478       27   ABB   454154     Paraprevotella clara     AF15-8   0.0236678       28   ABB   742722     Collinsella  sp. 4_8_47FAA   4_8_47FAA   0.0439329       29   ABB   997891     Bacteroides vulgatus  CL09T03C04   CL09T03C04   0.0125382       30   ABB   821     Bacteroides vulgatus     AM39-10   0.0105456       31   ABB   997891     Bacteroides vulgatus  CL09T03C04   CL09T03C04   0.0126174       32   ABB   2292303     Clostridium  sp. AM30-24   AM30-24   0.0326468       33   ABB   2292316     Collinsella  sp. AM34-10   AM34-10   0.0537876       34   ABB   2109334     Blautia  sp. SG-772   SG-772   0.0332125       35   ABB   454154     Paraprevotella clara     AF15-8   0.0238471       36   ABB   2109334     Blautia  sp. SG-772   SG-772   0.0255631       37   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.0114769       38   ABB   33039   [ Ruminococcus ]  torques     2789STDY5608867   0.0279573       39   ABB   1160721     Ruminococcus bicirculans     80/3   0.0243949       40   ABB   2109686     Butyricicoccus  sp. GAM44   GAM44   0.0264344       41   ABB   2109334     Blautia  sp. SG-772   SG-772   0.0246868       42   ABB   2293190     Ruminococcus  sp. AM26-12LB   AM26-12LB   0.0196594       43   ABB   820     Bacteroides uniformis     DSM 6597   0.0115705       44   ABB   411485     Faecalibacterium prausnitzii  M21/2   M21/2   0.0299116       45   ABB   39491   [ Eubacterium ]  rectale     T1-815   0.0237145       46   ABB   28116     Bacteroides ovatus     AF04-46   0.0211933       47   ABB   742722     Collinsella  sp. 4_8_47FAA   4_8_47FAA   0.0448295       48   ABB   39488     Anaerobutyricum hallii         0.0309762       49   ABB   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0259854       50   ABB   88431     Dorea longicatena     2789STDY5608851   0.015968       51   ABB   216816     Bifidobacterium longum     DPC6320   0.0151441       52   ABB   216816     Bifidobacterium longum     DPC6320   0.203899       53   ABB   649756     Anaerostipes hadrus     2789STDY5834860   0.0183835       54   ABB   216816     Bifidobacterium longum     DPC6320   0.0143493       55   ABB   2292976     Blautia  sp. AM42-2   AM42-2   0.0212548       56   ABB   818     Bacteroides thetaiotaomicron     NLAE-zl-C579   0.0111348       57   ABB   2292944     Bacteroides  sp. AM25-34   AM25-34   0.0058836       58   ABB   1504823   bacterium LF-3       0.0156336       59   ABB   1520805     Blautia  sp. SF-50   SF-50   0.0184835       60   ABB   39491   [ Eubacterium ]  rectale     T1-815   0.0231774       61   ABB   28116     Bacteroides ovatus     AF29-12   0.00552489       62   ABB   47678     Bacteroides caccae     OM05-21BH   0.0123645       63   ABB   47678     Bacteroides caccae     OM05-21BH   0.0127433       64   ABB   88431     Dorea longicatena     2789STDY5608851   0.0155486       65   ABB   1547     Erysipelatoclostridium ramosum     OF04-4AC   0.059652       66   ABB   1138888     Enterococcus faecium  EnGen0015   E1007   0.0076997       67   ABB   997891     Bacteroides vulgatus  CL09T03C04   CL09T03C04   0.0126509       68   ABB   1138888     Enterococcus faecium  EnGen0015   E1007   0.00801624       69   ABB   1073351     Bacteroides stercoris  CC31F   CC31F   0.0211864       70   ABB   997891     Bacteroides vulgatus  CL09T03C04   CL09T03C04   0.0132351       71   ABB   820     Bacteroides uniformis     DSM 6597   0.012262       72   ABB   410072     Coprococcus comes     2789STDY5608832   0.0177664       73   YCFACB   39485   [ Eubacterium ]  eligens     AF41-18   0.0460076       74   YCFACB   88431     Dorea longicatena     2789STDY5608851   0.0481542       75   YCFACB   2292357     Faecalibacterium  sp. OM04-11BH   OM04-11BH   0.0598966       76   YCFACB   1350472     Bifidobacterium longum  subsp.  longum  7-1B   7-1B   0.0517639       76   YCFACB   748224     Faecalibacterium  cf.  prausnitzii  KLE1255   KLE1255   0.0426093       77   YCFACB   88431     Dorea longicatena     2789STDY5608851   0.0471561       78   YCFACB   88431     Dorea longicatena     2789STDY5608851   0.0471561       79   YCFACB   1073376     Ruminococcus lactaris  CC59_002D   CC59_002D   0.0436095       80   YCFACB   1917876     Blautia  sp. Marseille-P3087   Marseille-P3087   0.0581289       81   YCFACB   2086273     Subdoligranulum  sp. APC924/74   APC924/74   0.0631331       82   YCFACB   2086273     Subdoligranulum  sp. APC924/74   APC924/74   0.0585937       83   YCFACB   39491   [ Eubacterium ]  rectale     2789STDY5608860   0.0551094       117   ABB+ RF   33039   [ Ruminococcus ]  torques     2789STDY5608867   0.0201569       85   YCFACB   2086273     Subdoligranulum  sp. APC924/74   APC924/74   0.0549626       85   YCFACB   2292357     Faecalibacterium  sp. OM04-11BH   OM04-11BH   0.0625862       86   YCFACB   39485   [ Eubacterium ]  eligens     AF41-18   0.0480639       87   YCFACB   748224     Faecalibacterium  cf.  prausnitzii  KLEI255   KLE1255   0.0647989       88   YCFACB   1073376     Ruminococcus lactaris  CC59_002D   CC59_002D   0.0563141       89   YCFACB   39485   [ Eubacterium ]  eligens     AF41-18   0.0565927       90   YCFACB   515619   [ Eubacterium ]  rectale  ATCC 33656   ATCC 33656   0.0641779       91   ABB + RF   2292969     Blautia  sp. AM16-16B   AM16-16B   0.207695       92   ABB + RF   1907658     Bacteroides ilei     Marseille-P3208   0.168518       95   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.0243467       110   ABB + RF   2153227     Lactobacillus  sp. DS22_6   DS22_6   0.00438886       93   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.0317272       94   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.0445532       96   ABB + RF   820     Bacteroides uniformis     OM07-9   0.0172799       97   ABB + RF   357276     Bacteroides dorei     An16   0.0141874       98   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.015699       99   ABB + RF   2292910     Alistipes  sp. AF14-19   AF14-19   0.0155836       100   ABB + RF   74426     Collinsella aerofaciens     2789STDY5608842   0.0424285       101   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.0116057       102   ABB + RF   28118     Odoribacter splanchnicus     AF36-2   0.00844432       103   ABB + RF   74426     Collinsella aerofaciens     2789STDY5608842   0.0432902       104   ABB + RF   717959     Alistipes shahii  WAL 8301   WAL 8301   0.0166515       105   ABB + RF   2109688   Clostridiales bacterium CCNA10   CCNA10   0.114893       106   ABB + RF   2293194     Ruminococcus  sp. AM28-13   AM28-13   0.0253257       107   ABB + RF   28118     Odoribacter splanchnicus     AF36-2   0.00863912       108   ABB + RF   1871021     Lachnoclostridium phocaeense     Marseille-P3177   0.0176872       109   ABB + RF   411471     Subdoligranulum variabile  DSM 15176   DSM 15176   0.0987184       111   ABB + RF   28116     Bacteroides ovatus     AF20-9LB   0.0209153       112   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.011059       113   ABB + RF   2292910     Alistipes  sp. AF14-19   AF14-19   0.0149744       114   ABB + RF   357276     Bacteroides dorei     An16   0.0129382       115   ABB + RF   28116     Bacteroides ovatus     AF24-28LB   0.00894456       116   ABB + RF   357276     Bacteroides dorei     An16   0.012209       118   ABB + RF   93975     Bacteroides  sp. AR29   AR29   0.00583626       119   ABB + RF   357276     Bacteroides dorei     An16   0.0121318       120   ABB + RF   537012     Bacteroides cellulosilyticus  DSM 14838   DSM 14838   0.0196531       121   ABB + RF   457415     Synergistes  sp. 3_1_synl   3_1_synl   0.0177098       122   ABB + RF   33039   [ Ruminococcus ]  torques     AM22-16   0.0983271       123   ABB + RF   214856     Alistipes finegoldii     2789STDY5608890   0.0109684       124   ABB + RF   1605     Lactobacillus animalis     P38   0.038387       125   ABB + RF   2108523     Lawsonibacter asaccharolyticus     3BBH22   0.0167368       126   ABB + RF   40520     Blautia obeum     2789STDY5834861   0.0656918       127   ABB + RF   40520     Blautia obeum     2789STDY5834861   0.0698723       128   ABB + RF   820     Bacteroides uniformis     OM07-9   0.0156336       129   ABB + RF   46503     Parabacteroides merdae     AM26-6AC   0.0107148       130   ABB + RF   1871021     Lachnoclostridium phocaeense     Marseille-P3177   0.0176477       131   ABB + RF   871324     Bacteroides stercorirosoris     OF03-9BH   0.0133266       132   ABB + RF   1339343     Parabacteroides distasonis  str. 3776 D15 iv   3776 D15 iv   0.0123851       133   ABB + RF   1339343     Parabacteroides distasonis  str. 3776 D15 iv   3776 D15 iv   0.012998       134   ABB + RF   820     Bacteroides uniformis     OM07-9   0.0152174       135   ABB + RF   2153227     Lactobacillus  sp. DS22_6   DS22_6   0.00381963       136   ABB + RF   216816     Bifidobacterium longum     APC1472   0.0129809       137   ABB + RF   216816     Bifidobacterium longum     APC1472   0.0133747       138   ABB + RF   2153227     Lactobacillus  sp. DS22_6   DS22_6   0.0021922       139   ABB + RF   84112     Eggerthella lenta     CC8/6 D5 4   0.051842       141   ABB + RF   46503     Parabacteroides merdae     AF33-34   0.0418058       141   ABB + RF   40520     Blautia obeum     2789STDY5834957   0.0215309       143   ABB + RF   40520     Blautia obeum     2789STDY5834957   0.0421419       146   ABB + RF   40520     Blautia obeum     2789STDY5834957   0.0479964       147   ABB + RF   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0755452       148   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.0311421       151   ABB + RF   2305245   Clostridiaceae bacterium TF01-6   TF01-6   0.0354795       152   ABB + RF   46503     Parabacteroides merdae     AF33-34   0.00811509       153   ABB + RF   47678     Bacteroides caccae     AM16-49B   0.0324692       154   ABB + RF   2292271   Lachnospiraceae bacterium AM48-27BH   AM48-27BH   0.115114       155   ABB + RF   2109334     Blautia  sp. SG-772   SG-772   0.0491926       157   ABB + RF   2109334     Blautia  sp. SG-772   SG-772   0.0500057       158   ABB + RF   2293120     Parabacteroides  sp. AM25-14   AM25-14   0.0330546       160   ABB + RF   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.0320835       161   ABB + RF   40520     Blautia obeum     2789STDY5834957   0.0213648       162   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0616729       163   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.0166462       165   ABB + RF   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0625862       166   ABB + RF   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.0479066       167   ABB + RF   649756     Anaerostipes hadrus     2789STDY5608868   0.0381896       169   ABB + RF   291644     Bacteroides salyersiae     2789STDY5608871   0.0128024       170   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0440096       171   ABB + RF   2292316     Collinsella  sp. AM34-10   AM34-10   0.0316248       172   ABB + RF   2026190     Bacillus mobilis     0711P9-1   0.0365402       173   ABB + RF   47678     Bacteroides caccae     ATCC 43185   0.0133309       174   ABB + RF   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.0604284       175   ABB + RF   47678     Bacteroides caccae     AM16-49B   0.0423206       176   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.031968       177   ABB + RF   47678     Bacteroides caccae     AM16-49B   0.0296094       178   ABB + RF   39486     Dorea formicigenerans     AF36-1BH   0.0394151       179   ABB + RF   291644     Bacteroides salyersiae     2789STDY5608871   0.0250827       180   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0187091       181   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.0179373       182   ABB + RF   40520     Blautia obeum     AM18-2AC   0.0393356       183   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0186138       184   ABB + RF   2292992     Catenibacterium  sp. AM22-6LB   AM22-6LB   0.063331       185   ABB + RF   742738     Flavonifractor plautii  1_3_50AFAA   1_3_50AFAA   0.0462584       186   ABB + RF   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.0312646       187   ABB + RF   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.0644247       188   ABB + RF   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.00299106       189   ABB + RF   1339350     Bacteroides vulgatus  str. 3775 SL(B) 10 (iv)   3775 SL(B) 10 (iv)   0.0288871       190   ABB + RF   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.00287005       191   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.00672075       192   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0189436       193   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0195966       194   ABB + RF   291644     Bacteroides salyersiae     2789STDY5608871   0.0308224       195   ABB + RF   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.0641779       196   ABB + RF   2292271   Lachnospiraceae bacterium AM48-27BH   AM48-27BH   0.0957194       197   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0197225       198   ABB + RF   40520     Blautia obeum     2789STDY5834957   0.0243949       199   ABB + RF   997890     Bacteroides uniformis  CL03T12C37   CL03T12C37   0.0228174       200   ABB + RF   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0741211       201   ABB + RF   292800     Flavonifractor plautii     2789STDY5834932   0.0427185       202   ABB + RF   997890     Bacteroides uniformis  CL03T12C37   CL03T12C37   0.0075679       203   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0182258       204   ABB + RF   40520     Blautia obeum     OM06-11AA   0.0550506       205   ABB + RF   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0194467       206   ABB + RF   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0486105       207   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.0219313       208   ABB + RF   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0388799       209   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.0270028       210   ABB + RF   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0396229       211   ABB + RF   649756     Anaerostipes hadrus     2789STDY5608868   0.0577367       212   ABB + RF   357276     Bacteroides dorei     OF04-10BH   0.00644046       213   ABB + RF   649756     Anaerostipes hadrus     2789STDY5608868   0.0187271       215   ABB + RF   88431     Dorea longicatena     OM02-16   0.041336       216   ABB + RF   28116     Bacteroides ovatus     AM32-14LB   0.0215518       220   ABB + RF   2293220     Ruminococcus  sp. AM46-18   AM46-18   0.0498603       221   ABB + RF   40520     Blautia obeum     APC942/31-1   0.045432       222   ABB + RF   84112     Eggerthella lenta     CC8/6 D5 4   0.0316362       223   ABB + RF   821     Bacteroides vulgatus     AF28-7   0.0382047       227   ABB + RF   40520     Blautia obeum     AF21-24   0.0354526       228   ABB + RF   665950   Lachnospiraceae bacterium 3_1_46FAA   3_1_46FAA   0.0556449       229   ABB + RF   226186     Bacteroides thetaiotaomicron  VPI-5482   VPI-5482   0.0228025       230   ABB + RF   471189     Gordonibacter pamelaeae     3C   0.0276437       231   ABB + RF   84112     Eggerthella lenta     CC8/6 D5 4   0.0280918       232   ABB + RF   665950   Lachnospiraceae bacterium 3146FAA   3146FAA   0.0579648       233   ABB + RF   821     Bacteroides vulgatus     AF28-7   0.0405226       234   ABB + RF   742738     Flavonifractor plautii  1_3_50AFAA   1_3_50AFAA   0.0337178       235   ABB + RF   742738     Flavonifractor plautii  1_3_50AFAA   1_3_50AFAA   0.0297444       236   ABB + RF   74426     Collinsella aerofaciens     2789STDY5608842   0.0768508       237   ABB + RF   74426     Collinsella aerofaciens     2789STDY5608823   0.0661271       238   ABB + RF   1720194     Clostridium  sp. AT4   AT5   0.0475507       239   ABB + RF   471189     Gordonibacter pamelaeae     3C   0.0393992       240   ABB + RF   411462     Dorea longicatena  DSM 13814   DSM 13814   0.0575426       241   RCM   1504823   bacterium LF-3       0.0156336       242   RCM   33038   [ Ruminococcus ]  gnavus     RJX1120   0.022603       243   RCM   33039   [ Ruminococcus ]  torques     2789STDY5608867   0.0235981       244   RCM   33039   [ Ruminococcus ]  torques     2789STDY5608867   0.0273626       245   RCM   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0309541       246   RCM   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0267663       247   RCM   33039   [ Ruminococcus ]  torques     2789STDY5608833   0.0285595       248   RCM   39488     Anaerobutyricum hallii         0.0430304       249   RCM   39488     Anaerobutyricum hallii     AF45-14BH   0.0321067       250   RCM   1532     Blautia coccoides     NCTC11035   0.022559       251   RCM   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.108521       252   RCM   476272     Blautia hydrogenotrophica  DSM 10507   DSM 10507   0.0213993       253   RCM   40520     Blautia obeum     2789STDY5608837   0.0222102       254   RCM   40520     Blautia obeum     AM37-4AC   0.0291893       255   RCM   40520     Blautia obeum     OF03-14   0.0315342       256   RCM   410072     Coprococcus comes     2789STDY5834962   0.0318186       257   RCM   410072     Coprococcus comes     2789STDY5608832   0.0375188       258   RCM   410072     Coprococcus comes     2789STDY5834962   0.0339433       259   RCM   410072     Coprococcus comes     2789STDY5608832   0.0324692       260   RCM   39486     Dorea formicigenerans     AF19-13   0.0283927       261   RCM   39486     Dorea formicigenerans     AF19-13   0.0245322       262   RCM   39486     Dorea formicigenerans     AF19-13   0.0306047       263   RCM   39486     Dorea formicigenerans     TF12-1   0.0844968       264   RCM   39486     Dorea formicigenerans     TF12-1   0.013909       265   RCM   39486     Dorea formicigenerans     TF12-1   0.0367526       266   RCM   88431     Dorea longicatena     2789STDY5608851   0.0210911       267   RCM   88431     Dorea longicatena     2789STDY5608851   0.026948       268   RCM   88431     Dorea longicatena     OM02-16   0.0378742       269   RCM   88431     Dorea longicatena     2789STDY5834914   0.0338178       270   RCM   88431     Dorea longicatena     OM02-16   0.037681       271   RCM   88431     Dorea longicatena     OM02-16   0.0381896       272   RCM   88431     Dorea longicatena     2789STDY5608851   0.0314102       273   RCM   411462     Dorea longicatena  DSM 13814   DSM 13814   0.0304105       274   RCM   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.035887       275   RCM   2292041     Dorea  sp. AF36-15AT   AF36-15AT   0.0313653       276   RCM   28052     Lachnospira pectinoschiza     2789STDY5834886   0.0345299       277   RCM   1160721     Ruminococcus bicirculans     80/3   0.0394469       278   RCM   2293190     Ruminococcus  sp. AM26-12LB   AM26-12LB   0.0238706       279   RCM   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0346335       280   RCM   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0305938       281   RCM   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0353051       282   RCM   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.0292401       283   ActVeg   457422   Erysipelotrichaceae bacterium 2_2_44A   2_2_44A   0.0120469       284   ActVeg   1597     Lactobacillus paracasei     1316.rep1_LPAR   0.0122212       285   ActVeg   573236     Bifidobacterium animalis  subsp.  lactis  V9   V9   0.0122825       286   ActVeg   1522   [ Clostridium ]  innocuum     AF18-35LB   0.0163194       287   ActVeg   457422   Erysipelotrichaceae bacterium 2_2_44A   2_2_44A   0.0170934       288   ActVeg   84112     Eggerthella lenta     CC8/6 D5 4   0.0177777       289   ActVeg   649756     Anaerostipes hadrus     2789STDY5608868   0.0237534       290   ActVeg   39486     Dorea formicigenerans     TF12-1   0.0244433       291   ActVeg   410072     Coprococcus comes     2789STDY5834962   0.0245972       292   ActVeg   410072     Coprococcus comes     2789STDY5834962   0.0252752       293   ActVeg   33035     Blautia producta     DSM 3507   0.0263101       294   ActVeg   2293194     Ruminococcus  sp. AM28-13   AM28-13   0.0269024       295   ActVeg   410072     Coprococcus comes     2789STDY5834962   0.0277667       296   ActVeg   457412     Ruminococcus  sp. 5139BFAA   5139BFAA   0.0293319       297   ActVeg   100884     Coprobacillus cateniformis     OM02-34   0.0320488       298   ActVeg   39486     Dorea formicigenerans     AF36-1BH   0.0344011       299   ActVeg   2293184     Ruminococcus  sp. AM16-34   AM16-34   0.0374015       300   ActVeg   1870991     Massilioclostridium coli     Marseille-P2976   0.0377106       301   ActVeg   665951   Lachnospiraceae bacterium 8_1_57FAA   8_1_57FAA   0.0377551       302   ActVeg   665950   Lachnospiraceae bacterium 3_1_46FAA   3_1_46FAA   0.0381292       303   ActVeg   2302976   Erysipelotrichaceae bacterium AF19-24AC   AF19-24AC   0.0434587       304   ActVeg   649724     Clostridium  sp. ATCC BAA-442   ATCC BAA-442   0.0446515       305   ActVeg   74426     Collinsella aerofaciens     2789STDY5608823   0.0474845       306   ActVeg   74426     Collinsella aerofaciens     2789STDY5608842   0.0479739       307   ActVeg   665950   Lachnospiraceae bacterium 3_1_46FAA   3_1_46FAA   0.0516344       308   ActVeg   649756     Anaerostipes hadrus     2789STDY5608868   0.0525015       309   ActVeg   1965564     Massilimicrobiota  sp. An142   An142   0.0530685       310   ActVeg   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0557352       311   ActVeg   1737424     Blautia massiliensis     GD9   0.0581948       312   ActVeg   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0649247       313   ActVeg   2292330     Collinsella  sp. TF05-9AC   TF05-9AC   0.0649247       314   ActVeg   2292227     Collinsella  sp. AF28-5AC   AF28-5AC   0.0929879       315   ActVeg   552398   Ruminococcaceae bacterium D16   D16   0.0957194       316   ActVeg   208479   [ Clostridium ]  bolteae     AM35-14   0.0989821       317   ActVeg   33039   [ Ruminococcus ]  torques     AM22-16   0.109435       318   ActVeg   2086584     Mordavella  sp. Marseille-P3756   Marseille-P3756   0.112966       319   ActVeg   457412     Ruminococcus  sp. 5_1_39BFAA   5_1_39BFAA   0.114022       320   ActVeg   1121115     Blautia wexlerae  DSM 19850   DSM 19850   0.129179       321   ActVeg   2293156     Ruminococcus  sp. AF18-29   AF18-29   0.130966       322   ActVeg   2292372     Ruminococcus  sp. AM42-11   AM42-11   0.134052       323   ActVeg   552398   Ruminococcaceae bacterium D16   D16   0.13446       324   ActVeg   1965654     Lachnoclostridium  sp. An76   An76   0.13446       325   ActVeg   1965654     Lachnoclostridium  sp. An76   An76   0.138386       326   ActVeg   33039   [ Ruminococcus ]  torques     AM22-16   0.139328       327   ActVeg   552398   Ruminococcaceae bacterium D16   D16   0.139328       328   ActVeg   2292376     Ruminococcus  sp. OM08-7   OM08-7   0.142336       329   ActVeg   116085     Coprococcus catus     AF45-17   0.148079       330   ActVeg   2292970     Blautia  sp. AM22-22LB   AM22-22LB   0.150025       331   ActVeg   2292970     Blautia  sp. AM22-22LB   AM22-22LB   0.163053       332   ActVeg   2293138     Roseburia  sp. AM59-24XD   AM59-24XD   0.164074       333   ActVeg   1235835     Anaerotruncus  sp. G3(2012)   G3   0.166219       334   ActVeg   29348   [ Clostridium ]  spiroforme     OM02-6   0.172308       335   ActVeg   2292376     Ruminococcus  sp. OM08-7   OM08-7   0.176605       336   ActVeg   2293138     Roseburia  sp. AM59-24XD   AM59-24XD   0.183409                 a Listed are the closest genome/species matches for each strain, determined by the analysis described in the text.            
Antibiotic Resistance Characterization of Isolated Strains from Fecal Matter
 
     The complete genome sequence of each organism is screened to ensure it contains no genes or pathogenicity island gene clusters encoding known virulence factors, toxins, or antibiotic resistance functions, using publicly available databases such as DBETH55 (for example, see Chakraborty A, et al. (2012)  Nucleic Acids Res.  40:615-620) and VFDB56 (Chen L, et al. (2005)  Nucleic Acids Res.  33:325-328). Each organism is tested by standard antibiotic sensitivity profile techniques such as broth microdilution susceptibility panels or plate-based methods such as disk diffusion method and antimicrobial gradient method (James H. Jorgensen and Mary Jane Ferraro 2009 Clinical Infectious Diseases 49:1749-1755). Such tests determine the minimal inhibitory concentration (MIC) of an antibiotic on microbial growth. Antibiotics tested include but are not limited to amoxicillin, amoxicillin/clavulanic acid, carbapenem, methicillin, ampicillin, gentamicin, metronidazole, and neomycin. MIC determinations of novel microbes are compared to published values for both sensitive and resistant related strains to make an assessment on sensitivity (CLSI Guideline M45: Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria. Wayne, Pa.; 2015) to type strains of related microbes to determine possible relative increases in antibiotic resistance. 
     Example 4: Isolation and Characterization of Pure Microbial Strains from Endospores Purified from Fecal Matter 
     In alternative embodiments, microbes used in compositions as provided herein, or used to practice methods as provided herein, are derived from, or are cultured as, pure microbial strains derived from endospores purified or derived from fecal matter. 
     Individual spore-forming bacterial strains can be preferentially isolated and cultured from endospores purified from fecal matter using a protocol adapted from Kearney et al 2018 ISME J. 12:2403-2416. Purified endospores are spread on solid anaerobic medium plates and allowed to germinate and form colonies that can be further characterized. Vegetative cells in the fecal matter are rendered non-viable during the endospore purification process, and thus any resulting colonies are restricted to spore-forming bacteria. Endospores are purified from fecal matter as follows: 
     Fecal samples are collected and processed in an anaerobic chamber within 30 minutes of defecation. Samples (5 g) are suspended in 20 mL of 1% sodium hexametaphosphate solution (a flocculant) in order to bring biomass into suspension. The suspension is bump vortexed with glass beads to homogenize and centrifuged at 50×g for 5 min at room temperature to sediment particulate matter and beads. Quadruplicate 1 mL aliquots of the supernatant liquid is transferred into cryovials and stored at −80° C. until processing. 
     The frozen supernatant liquid samples are thawed at 4° C., centrifuged at 4° C. and 10,000×g for 5 minutes, washed and then resuspended in 1 mL Tris-EDTA pH 7.6. The samples are heated at 65° C. for 30 minutes with shaking at 100 rpm and then cooled on ice for 5 minutes. Lysozyme (10 mg/mL) is added to a final concentration of 2 mg/mL and the samples are incubated at 37° C. for 30 minutes with shaking at 100 rpm. At 30 minutes, 50 μL Proteinase K (&gt;600 mAU/ml) (Qiagen) is added and the samples incubated for an additional 30 minutes at 37° C. 200 μL 6% SDS, 0.3 N NaOH solution is added to each sample and incubated for 1 hour at room temperature with shaking at 100 rpm. Samples are then centrifuged at 10,000 rpm for 30 minutes. At this step, a pellet containing resistant endospores is visible, and the pellet is washed three times at 10,000×g with 1 mL chilled sterile ddH2O. The pellet containing endospores is stored at −20° C. until required. 
     To germinate and resuscitate spore-forming bacterial colonies from the purified endospores, the endospore pellet is brought into the anaerobic chamber, thawed and then suspended in 1.0 ml reduced ABB. Successive 10-fold serial dilutions of the suspended spores are then performed in ABB to establish 1/10, 1/100, 1/1000, 1/10000, 1/100000, 1/1000000 dilutions of the endospore preparation. From each 10-fold serial dilution, four 0.1 ml volumes are removed and then added to and spread over Reinforced Clostridial Medium Agar (Oxoid), with 0.1% intestinal bile salts (taurocholate, cholate, glycocholate) to stimulate endospore germination. The platings are incubated at 37° C. for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 days to allow for the endospores to germinate and grow as single colonies. These colonies are then manually picked, individually cultivated, and then subjected to identification by whole genome sequencing analysis as described in Example 3. 
     Example 5: Stability Testing 
     In alternative embodiments, microbes used in compositions as provided herein, or used to practice methods as provided herein, comprise or can be derived from any one of family or genus (or class):  Agathobaculum  (TaxID: 2048137),  Alistipes  (TaxID: 239759),  Anaeromassilibacillus  (TaxID: 1924093),  Anaerostipes  (TaxID: 207244),  Asaccharobacter  (TaxID: 553372),  Bacteroides  (TaxID: 816),  Barnesiella  (TaxID: 397864),  Bifidobacterium  (TaxID: 1678),  Blautia  (TaxID: 572511),  Butyricicoccus  (TaxID: 580596),  Clostridium  (TaxID: 1485),  Collinsella  (TaxID: 102106),  Coprococcus  (TaxID: 33042),  Dorea  (TaxID: 189330),  Eubacterium  (TaxID: 1730),  Faecalibacterium  (TaxID: 216851),  Fusicatenibacter  (TaxID: 1407607),  Gemmiger  (TaxID: 204475),  Gordonibacter  (TaxID: 644652),  Lachnoclostridium  (TaxID: 1506553),  Methanobrevibacter  (TaxID: 2172),  Parabacteroides  (TaxID: 375288), Romboutsia (TaxID: 1501226),  Roseburia  (TaxID: 841),  Ruminococcus  (TaxID: 1263),  Erysipelotrichaceae  (TaxID: 128827),  Coprobacillus  (TaxID: 100883),  Erysipelatoclostridium  sp. SNUG30099 (TaxID: 1982626),  Erysipelatoclostridium  (TaxID: 1505663). 
     In alternative embodiments, any microbe used in a composition as provided herein, or used to practice methods as provided herein, for example, including a microbe as listed above, can be stored in a sealed container, for example, at 25° C. or 4° C. and the container can be placed in an atmosphere having 30%, 40%, 50%, 60%, 70%, 75%, 80%, 90% or 95% relative humidity, or between about 20% and 99% relative humidity. In alternative embodiments, after 1 month, 2 months, 3 months, 6 months, 1 year, 1.5 years, 2 years, 2.5 years or 3 years, at least 50%, 60%, 70%, 80% or 90% of the bacterial strain shall remain as measured in colony forming units determined by standard protocols. 
     Example 6—in Silico Modeling to Discover Microbe-Microbe Interactions 
     Microbe-microbe interactions are determined to exploit and manipulate metabolic reactions present in the gut microbiome using compositions and methods as provided herein for, for example, increase the ability of the immune system to combat viral infections, stimulate activity of specific classes of immune cells, provide essential nutrients that may be depleted or blocked by the virus, produce compounds with antiviral activity, or other direct or indirect effect on cells of the innate or adaptive immune system. 
     Genome scale metabolic modeling is used as a tool to explore the diversity of metabolic reactions present in the gut microbiome, interpret the omics data described here in the framework of cellular metabolism, and evaluate inter-species interactions. A set of 773 different organism-specific metabolic models have been created (Magnusdottir et al. Nature Biotechnology 2017, 35(1):85-89) and are used in this work. Models are used individually to predict the metabolic capabilities of each organism and combined to enable multispecies simulations that predict how these organisms interact when supplied with a nutrient mix mimicking the typical Western human diet or variations thereof. Simulations are performed using the COBRA™ package v2.0™ (Schellenberger et al., Nature Protocols 2011, 6:1290-1307) or updated versions thereof. Commensal relationships among the organisms result when one or more species consume a compound that another species produces and can be detected by an increased maximum predicted growth rate of each species when growing together than when each is grown separately. In the cases where commensalism is not predicted in the live biotherapeutics provided, simulations are used to identify a suitable microbial partner that can be included in the live biotherapeutic product, thus improving the ability of the active microbes to grow in the gut ecosystem. Similarly, simulations are used to identify prebiotic compounds to be supplemented that can be utilized by the active species as a carbon or energy source. 
     Metabolic models are downloaded from the Thiele lab website (https://wwwen.uni.lu/lcsb/research/mol_systems_physiology/in_silico_models) for the following organisms:  Coprococcus comes, Dorea formicigenerans, Anaerostipes hadrus, Dorea longicatena, Coprococcus eutactus, Ruminococcus lactaris, Coprococcus catus, Fusicatenibacter saccharivorans, Lachnoclostridium  sp. SNUG30099,  Clostridium sporogenes, Eubacterium ventriosum, Blautia obeum, Erysipelotrichaceae bacterium  GAM147 , Akkermansia muciniphilia, Faecalibacterium prauznitzii, Ruminococcus torques, Ruminococcus gnavus, Eubacterium hallii, Blautia obeum , and  Clostridium scindens . The models are then used for simulations in the COBRA v2.0™ package (Schellenberger et al., Nature Protocols 2011, 6:1290-1307). Cell metabolism is simulated by defining nutrient uptake rates (mmol/gDCW-hr) and optimizing for growth of each organism (hr −1 ). Oxygen uptake rate is set to zero, to simulate anaerobic conditions. Values for each nutrient uptake rate are obtained from (Magnusdottir et al. Nature Biotechnology 2017, 35(1):85-89, Supplemental Table 12), as estimated for a typical Western diet. To simulate the gut ecosystem comprising of multiple bacterial species, each organism model is treated as a separate compartment, with the extracellular space in the gut considered an additional compartment. Nutrients can enter and exit the extracellular space freely, to simulate food uptake and waste excretion. Nutrients can enter and exit each microbial species based on the specific transporters present in the respective model. The objective function to be maximized is defined to be the total biomass of all species; i.e., the sum of all individual growth rates. The minimum growth rate of each species is set at 0.001 hr −1 . 
     The consortia of gut microbe metabolic models are used as a framework for interpreting genomic, transcriptomic, and metabolomic data obtained from the mouse and human studies. Enriched genes or pathways at the genomic or transcriptomic level are mapped to the source organism model to determine the metabolic functions these represent and how they connect with the rest of metabolism in that organism, as well as in the gut ecosystem. Enrichments also in metabolic intermediates or end products of these pathways provide further evidence for these pathways&#39; contribution to checkpoint inhibitor function. 
     Example 7: In Silico Simulation of Relevant Microbial Species 
     Models were downloaded for the following organisms:  Akkermansia muciniphilia, Faecalibacterium prausnitzii, Ruminococcus torques, Ruminococcus gnavus, Ruminococcus lactaris, Eubacterium hallii, Blautia obeum, Anaerostipes hadrus, Dorea formicigenerans, Coprococcus comes, Coprocuccus catus, Erysipelotrichaceae  sp., and  Clostridium scindens . The models are then used for simulations in the COBRA package v2.0 (Schellenberger et al., Nature Protocols 2011, 6:1290-1307). Cell metabolism was simulated by defining nutrient uptake rates (mmol/gDCW-hr) and optimizing for growth rate of each organism (hr 1 ). Oxygen uptake rate was set to zero, to simulate anaerobic conditions. 
     First, simulations were performed to determine the minimal growth substrate requirements of each organism. Starting with all substrate uptake fluxes open, allowing utilization of any nutrient, simulations were performed as nutrient uptake fluxes are systematically removed. This was continued for each organism until a minimal set of carbon sources remained, the removal of any of which would result in zero predicted growth. Normally, this resulted in a single sugar compound (often glucose) and one or more other nutrients such as amino acids, nucleotides, vitamins, or lipids. These other compounds are considered auxotrophic requirements of the organism. Next, the substrate utilization range of the organism was determined. The uptake flux of the primary growth substrate (generally, a sugar) was set to zero, and growth was evaluated with different carbon sources one at a time. The predicted ability to grow using each carbon source was documented. The ability to co-utilize organic acid carbon sources was also evaluated. These compounds generally cannot be used as a sole growth substrate during anaerobic growth but can be taken up in conjunction with a sugar. Simulations were run with the uptake rate of each compound constrained to a non-zero value, while maintaining the uptake of the primary sugar source. If an increase was observed in the predicted growth rate over the use of the sugar alone, then co-utilization is considered to be feasible. 
     The capability of each strain to produce various fermentation products was evaluated using the models. Some products were predicted to naturally form during the carbon source simulations above, as fermentation products are needed to balance redox in anaerobic conditions. These products were noted. For other compounds, the model was constrained to make each one by setting the output flux to a non-zero value. If the simulation gave a feasible solution, then the organism was considered capable of making this product. 
     Table 2 (illustrated as  FIG.  16   ). Simulation of selected organisms with constraint-based modeling.
 
 a  1 indicates predicted growth on substrate; 0 indicates predicted no growth
 
 b  1 indicates compound is predicted to be used as a supplemental carbon source; 0 indicates it cannot be consumed
 
 c  1 indicates that model predicts production of fermentation product is feasible; 0 indicates it is not feasible
 
 d  Compounds that must be supplied in the growth media are indicated by X
 
     Example 8: Laboratory-Scale Fermentation of Isolated Anaerobic Microorganisms 
     In alternative embodiments, microbes used in compositions as provided herein, or used to practice methods as provided herein, comprise use of isolated anaerobic microorganisms, for example, anaerobic bacteria isolated from a fecal sample, for example, from a donor. 
     A laboratory-scale fermentation is performed using a Sartorius BIOSTAT A™ bioreactor with 2-liter (L) vessel, using the growth media described in Example 1. While still in the anaerobic chamber, 1 L media is transferred to a sterile feed bottle, which has two ports with tubing leading blocked by pinch clamps and covered in foil to maintain sterility. 
     The fermentation vessel is sterilized by autoclaving, then flushed with a continuous purge of sterile nitrogen gas with oxygen catalytically removed. Two inlet ports are fitted with tubing leading to a connector blocked with a pinch clamp, and the sampling port fitted with tubing leading to a syringe. The vessel is also fitted with a dissolved oxygen probe, a pH probe, and a thermowell containing a temperature probe. Once anaerobic conditions are ensured, the media is removed from the anaerobic chamber and connected to one of the inlet ports. The other feed bottle port is connected to sterile nitrogen purge. The pinch clamp is removed, and media transferred into the fermentation vessel by peristaltic pump or just by the nitrogen pressure. Once the transfer is complete, both lines are sealed again by the pinch clamps, the feed bottle removed, and returned to the anaerobic chamber. 
     A 50 mL seed culture of one or more bacteria from the following genera (any one of which are used to practice compositions or methods as provided herein),  Agathobaculum  (TaxID: 2048137),  Alistipes  (TaxID: 239759),  Anaeromassilibacillus  (TaxID: 1924093),  Anaerostipes  (TaxID: 207244),  Asaccharobacter  (TaxID: 553372),  Bacteroides  (TaxID: 816),  Barnesiella  (TaxID: 397864),  Bifidobacterium  (TaxID: 1678),  Blautia  (TaxID: 572511),  Butyricicoccus  (TaxID: 580596),  Clostridium  (TaxID: 1485),  Collinsella  (TaxID: 102106),  Coprococcus  (TaxID: 33042),  Dorea  (TaxID: 189330),  Eubacterium  (TaxID: 1730),  Faecalibacterium  (TaxID: 216851),  Fusicatenibacter  (TaxID: 1407607),  Gemmiger  (TaxID: 204475),  Gordonibacter  (TaxID: 644652),  Lachnoclostridium  (TaxID: 1506553),  Methanobrevibacter  (TaxID: 2172),  Parabacteroides  (TaxID: 375288), Romboutsia (TaxID: 1501226),  Roseburia  (TaxID: 841),  Ruminococcus  (TaxID: 1263),  Erysipelotrichaceae  (TaxID: 128827),  Coprobacillus  (TaxID: 100883),  Erysipelatoclostridium  sp. SNUG30099 (TaxID: 1982626),  Erysipelatoclostridium  (TaxID: 1505663), are grown to mid-exponential phase in a sealed culture bottle using the same media composition as above, and are transferred into the feed bottle in the anaerobic chamber. Repeating the above transfer procedure, this time with the culture, the fermenter is inoculated. 
     5 M ammonium hydroxide is prepared in another feed bottle. One port is connected to sterile nitrogen, and the bottle is purged for 5 minutes to remove all oxygen. The outlet tubing is then blocked by a pinch clamp and attached to the other inlet port in the fermentation vessel. This tubing is then threaded into a peristaltic pump head, and the pinch clamp removed. Using the software built into the Biostat A™ unit, this pump is controlled to maintain pH at 7.0. 
     During growth of the culture, temperature is maintained at 37° C. using a temperature controller and heating blanket on the vessel. Nitrogen purge is set at 0.5 L/min to maintain anaerobic conditions and positive pressure in the vessel, and agitation is set at 500 rpm to keep the culture well mixed. Periodic samples are taken using the syringe attached to the sample port. For each sample, optical density is measured at 600 nm wavelength using a spectrophotometer. 
     Example 9: Patient Data Collection from Clinical Trials and Machine Learning and Data Analysis on the Same 
     The results described here were obtained from a study involving cancer patients undergoing immunotherapy treatment and healthy controls. Microbes, gene functions, and metabolites elucidated as being absent in patients not responding well to treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbes beneficial for immuno-oncology treatment will also be beneficial or even essential for treating or ameliorating a viral infection, or for rapid viral clearance. 
     Eligible patients were selected based on current health condition, cancer status (current or in remission), and treatment program. Prior patient medical history was also collected and analyzed when available. This includes but is not limited to prior cancer history, diabetes, autoimmune disease, neurodegenerative disease, heart disease, metabolic syndrome, digestive disease, psychological disorders, HIV, and allergies. In addition, lifestyle and dietary habits were collected, including diet regimen, exercise routine, alcohol, nicotine, and caffeine intake, medical as well as recreational drug use, recent courses of antibiotics, vitamins, and probiotics. In some cases, information and data collected from wearable devices that monitor but is not limited to heart rate, calories burned, steps walked, blood pressure, biochemical release, time spent exercising and seizures. This data was assembled and used as input to the machine learning algorithms with the goal of determining correlations between patient history, wearable devices and treatment efficacy. In addition, relationships between this data and the results of sample analysis described below were elucidated. 
     In another embodiment, eligible patients testing positive for infection with COVID-19 (SARS-CoV2) or other coronavirus, or influenza virus, as well as age-matched healthy controls. Information is also collected on the severity of disease, symptoms, time of recovery, and response to any treatment, if applicable. Prior patient medical history is also collected and analyzed, including but not limited to cancer, diabetes, autoimmune disease, neurodegenerative disease, heart disease, metabolic syndrome, digestive disease, psychological disorders, coronaviruses, influenza virus, HIV, and allergies. In addition, lifestyle and dietary habits are collected, including diet regimen, exercise routine, alcohol, nicotine, and caffeine intake, medical as well as recreational drug use, recent courses of antibiotics, vitamins, and probiotics. This data is assembled and used as input to the machine learning algorithms with the goal of determining correlations between patient history, course of illness, and results of stool and blood sample analysis 
     For current cancer patients, tumor size and cancer progression are tracked over time and are classified based on radiographic assessment using the Response Criteria in Solid Tumors version 1.1 (Schwartz et al. Eur. J. Cancer 2016, 62:132-137) criteria. This is based on longitudinal measurements of lesions in cancer tissue, given a strict set of guidelines for lesion selection and measurement techniques. Responders to checkpoint inhibitor treatment are defined as patients that were cured or had stable disease lasting at least 6 months, while non-responders are defined as those whose cancer progressed or was stable for less than 6 months. Classification of responders and non-responders implies robust and insufficient immune response, respectively, and thus serves as a proxy for COVID-19, influenza, or other viral disease patients that will effectively clear the virus or have severe symptoms, respectively. 
     Each patient provided stool samples using the procedures as outlined in Example 2 and buccal swabs of the oral biome. In some cases, Urine, Blood and plasma samples were also taken by healthcare personnel within 1-2 days of the stool samples. Stool, urine and buccal samples were kept on ice or at 4° C. until processed. Whole blood was collected into an EDTA tube. Plasma was isolated from the blood by centrifugation at 1000×g for 10 minutes, followed by centrifugation at 2000×g for 10 minutes. At least three timepoints were taken for each patient, roughly every 6 to 8 weeks. 
     Flow Cytometry Analysis of Peripheral Blood 
     Flow cytometry analysis of peripheral blood can provide a non-invasive immune profile of the patients on study (Showe et al. Cancer Res. 2009 Dec. 15; 69(24): 9202-9210). The peripheral blood immuno-profile evaluation was performed on blood samples collected from patients on study. Phenotypic markers of lymphocyte subpopulations and regulatory T cells (Tregs) was evaluated using flow cytometry with populations gated to include CD3, CD4, CD8, CD11b, CD14, CD15, CD25, CD45, CD56, HLA-DR and FoxP3-expressing cells using antibodies to each cell type (BD Biosciences). Peripheral blood cells were stained with Live/Dead violet dye (Invitrogen, Carlsbad, Calif.) to gate on live cells. Data was acquired on an LSR II™ flow cytometer (BD Biosciences) and analyzed with FLOWJO™ software (TreeStar, Ashland, Oreg.). 
     Peripheral Blood Mononuclear Cell (PBMC) Preparation and CyTOF® Analysis 
     Peripheral blood mononuclear cells (PBMC&#39;s) are isolated from subject blood using a standard kit and stored in liquid nitrogen at 1×10{circumflex over ( )}6 cells/mL until use. Prior to storage, PBMC&#39;s may be processed using flow sorting or an antibody spin separation kit to select for a certain purified lymphocyte subpopulation, such as T cells. To characterize the immune profile of the PBMCs, single cell proteomics analysis (CyTOF®) is applied. This work is conducted by the Bioanalytical and Single-Cell Facility at the University of Texas, San Antonio, and entails a comprehensive panel of 29 different immune markers, allowing for deep interrogation of cellular phenotype and function (https://www.fluidigm.com/products/helios). To complement these results, RNA sequencing is applied to the entire population of the PBMCs, sorted populations, and also to single cells. Single cell RNAseq is applied using the method developed by 10×Genomics (https://www.10xgenomics.com/solutions/single-cell/). Finally, cytokine levels are determined using the Human Cytokine 30-Plex Luminex assay (https://www.thermofisher.com/order/catalog/product/LHC6003M). 
     Reassignment of Microbial Genomes into Operational Species Units Because of the limitations of the NCBI taxonomy tree, and the necessity of including proprietary microbial genome assemblies into the reference alignment sequence database, it is necessary to generate a new taxonomy of microbes. Previous work (for example, see Jain et al. (2018) Nature CommunicaGtabletions 9(1):5114) shows that species are a biologically relevant construction, with the average genomic distance (1-average nucleotide identity) between strains of a species being less than 0.04. Using this as an inspiration, all microbial assemblies from the NCBI RefSeq (Pruitt et al. (2006) Nucleic Acids Research 35(suppl_1):D61-D65) were assigned into operational species units (OSUs) based on a clustering in which microbial assemblies within a genomic distance of 0.04 are assigned to the same OSU. 
     All microbial assemblies belonging to bacteria and archaea were acquired from the NCBI RefSeq database. All pairwise distances were calculated between assemblies using mash (Ondov et al. (2016) Genome Biology 17(1):132). Clustering is performed using DBSCAN (Ester et al. (1996) KDD-96 96:226-231) with an epsilon parameter of 0.04. Identified clusters were denoted as operational species units (OSUs). Proprietary microbial assemblies were seamlessly included in this procedure as well. 
     For each OSU, an integer cluster label was created, and a new taxonomic ID created that is unique from any existing NCBI taxonomic identification numbers. The least common ancestor of each OSU was calculated using the original NCBI taxonomy IDs of its member assemblies, and each OSU taxonomic ID was inserted into the NCBI tree under its least common ancestor. Each OSU is also named using its most common species and label number (for example  Bifidobacterium adolescentis  C0001). 
     In  FIG.  1   , the ranks of the least common ancestor of each OSU that contains more than one assembly are displayed. Most OSUs are consistent with pre-existing NCBI taxonomy, with a least common ancestor at the species or genus level. However, for 207 out of 2,112 non-singleton OSUs, the least common ancestor is at the family level or higher. The chart in  FIG.  2    demonstrates that the frequency of OSUs decreases as the cluster size increases in a log-log fashion. 
     The new names, reference sequences, and taxonomy were used to generate a new reference database for the alignment program centrifuge (Kim et al. (2016) Genome Research 26:1721-1729). The centrifuge program classifies sequencing reads from a metagenomic fecal sample to reference sequences and uses an expectation-maximization method to estimate relative abundance of the taxa present in the sample. The estimated relative abundances for each OSU are carried into downstream analyses, such as machine learning or differential abundance analysis. 
     In addition to the method for re-assigning taxonomy described, pre-built databases that use the Genome Taxonomy Database (GTDB) were directly used for centrifuge classification (Parks et al. (2019) bioRxiv 771964, Meric et al. (2019) bioRxiv 712166). 
     Whole Genome Sequencing of Patient Fecal Samples 
     Whole genome sequencing was performed as previously described in Example 3 on a total of 387 fecal samples. Of the 387 samples, 266 samples were from cancer patients, 88 were from control subjects, and 31 were from subjects in remission. The results were classified, and abundance was estimated for each sample using centrifuge, using either a reference database built in-house consisting of operational species units (OSUs) or a publicly available one (Parks et al. (2019) bioRxiv 771964, Meric et al. (2019) bioRxiv 712166). 
     The results were analyzed for differential relative abundance of organisms (classified as OSUs) between cancer and control cohorts, as well as correlations between relative abundance of organisms and immune markers, as measured by flow cytometry. Principal component analysis was performed to visualize the structure of the data ( FIG.  3    and  FIG.  4   ) and exhibited a partial separation between cancer and control samples. This separation is driven by a specific subset of microbes that have differential abundance between the two cohorts ( FIGS.  5 - 7    and Table 3). Microbes were ranked based on the magnitude and significance of this difference. Additionally, machine learning was performed to train a model capable of discriminating between a subject with cancer and a control subject. 
     Identification of Viral Genetic Material in Stool or Blood Samples 
     The DNA extracted from stool samples is also used to determine presence of viral DNA material in the stool. Using the sequencing information obtained above, reads not mapping to human or bacterial DNA are aligned to a viral sequence database, for example the NCBI viral genomes database (https://www.ncbi.nlm.nih.gov/genome/viruses/). To detect RNA viruses, a separate sequencing run is required. RNA is extracted from the stool sample by binding to an RNAEASY™ (RNeasy™) column (Qiagen) followed by washing and elution using the reagents provided in the RNeasy™ kit (Qiagen). Sequencing libraries are prepared from RNA by fragmentation, ribodepletion, cDNA synthesis, PCR amplification, and barcoding as described in the TRUSEQ® mRNA sample preparation kit (Illumina). Sequencing analysis is conducted on the Illumina platform using paired-end 150 bp reads. Reads not mapping to human or bacterial DNA are then aligned to a viral sequence database, for example the NCBI viral genomes database (https://www.ncbi.nlm.nih.gov/genome/viruses/). Both of these approaches will provide the identity and relative quantity (for example, viral reads per total reads) of the virus. An analogous procedure is used to identify viral DNA or RNA in blood samples. 
     Metagenomic sequences are also scanned to identify novel CRISPR sequences using a scoring algorithm such as that described in (Moreno-Mateos et al. (2015) Nat. Met. 12:982-988), and for predicted natural product gene clusters using the ANTISMASH™ (antiSMASH™) routine (Medema et al. (2011) Nuc. Acids Res. 39:W339-W346). 
     Table 3, illustrated as  FIG.  17   . Whole genome sequencing was performed on fecal samples from subjects with and without cancer and the reads were classified and abundance of each operational species unit (OSU) was estimated computationally. The fold change difference and statistical significance (inverse p value, Mann Whitney U test) was calculated for abundances between cancer and control sample cohorts. For OSUs with a mean relative abundance of at least 0.05%, p-values were filtered using an adjusted p-value computed using a two-stage Benjamini-Hochberg procedure. OSUs passing the threshold are reported.
 
Flow Cytometry Analysis of Peripheral Blood from Cancer Patients
 
     Flow cytometry analysis of peripheral blood can provide a non-invasive immune profile of the patients on study (Showe et al. Cancer Res. 2009 Dec. 15; 69(24): 9202-9210). The peripheral blood immuno-profile evaluation was performed on blood samples collected prior to and after the dosing with the immunotherapy. Phenotypic markers of lymphocyte subpopulations and regulatory T cells (Tregs) was evaluated using flow cytometry with populations gated to include CD3, CD4, CD8, CD25, CD45 and FoxP3-expressing cells using antibodies to each cell type (BD Biosciences). Peripheral blood cells are stained with Live/Dead violet dye (Invitrogen, Carlsbad, Calif.) to gate on live cells. Data is acquired on an LSR II™ flow cytometer (BD Biosciences) and analyzed with FLOWJO™ software (TreeStar, Ashland, Oreg.). Exemplary flow cytometry analysis of peripheral blood samples from a patient undergoing immunotherapy are shown in  FIG.  20   . 
     Flow cytometry was performed on 73 blood samples obtained from human subjects with and without cancer. The resulting gated percentages are plotted for different cell markers. For CD8+HLA-DR+, CD4+HLA-DR+, CD11b+, CD3+, CD3+CD56+, Foxp3+, and CD3+HLA-DR+, statistically differences are observed between the cancer and non-cancer populations as shown in  FIG.  21   . CD8+HLA-DR+(activated cytotoxic T cells) and CD4+HLA-DR+(activated T helper cells) are enriched in the cancer population. Similar immune responses have been noted with patients with COVID-19 prior to symptomatic recovery (Thevarajan et al. (2020), Nature Med. https://doi.org/10.1038/s41591-020-0819-2). P values are computed using the Mann-Whitney U test. Principal component analysis was also conducted on the same data set where the gated percentages are mean and standard deviation scaled. The first two principal components are plotted as shown in  FIG.  22   . A statistically significant difference is observed between the cancer and control populations in the scaled data. The P value is computed using permutational multivariate analysis of variance (PERMANOVA). 
       FIG.  23    illustrates metabolomics data on plasma from a third-party provider was processed using a Mann Whitney U test to find significantly different metabolites between cancer and control cohorts. Metabolites enriched in cancer samples appear on the right and those enriched in control samples occur on the left, with higher points on the y-axis corresponding to increased statistical significance. 
       FIG.  24    illustrates the primary principal components for the microbiome sequencing data and immune flow cytometry data are plotted against each, revealing a strong correlation and suggesting that the microbiome may play a role in affecting the immune system and vice versa. Similarly, the interaction between the microbiome and the immune system has been shown to be critical in regulating immune defense against respiratory tract influenza A virus infection (T. Ichinohe et al., Proc. Natl. Acad. Sci. U.S.A 108, 5354-9 (2011) and immunity to vaccines (Hagan et al. (2019) Cell 178 (6): 1313-1328). 
       FIG.  25    illustrates metabolomics data on plasma from a third-party provider was processed using a log transform and PCA to show clear separation between samples from a cancer and control cohort. 
     The empirical distribution between successive longitudinal samples is plotted in  FIG.  26    for both cancer and control cohorts, demonstrating the increased variability of the cancer microbiome. In  FIG.  26   , centered log transformed estimated species abundances were generated for both cancer and control sample cohorts. Distances between successive longitudinal samples in the transformed space were computed for both cancer and control cohorts, and the empirical densities of the distances are displayed, revealing that cancer microbiomes are less stable and move around more over time than control. 
     Spearman correlations were calculated from the peripheral blood flow cytometry analyses and microbiome whole genome sequencing results. Spearman correlations were calculated between each flow gate for humans and each organism in the gut whose mean abundance is greater than or equal to 0.0005. Spearman correlations were calculated between each flow gate (CD11b+, CD3+, CD8-HLADR+ and FoxP3+) for humans and each organism in the gut whose mean abundance is greater than or equal to 0.0005. Results are plotted in a heat map fashion as reported in  FIG.  427   . 
     Metabolomics Analysis of Patient Fecal and Blood 
     Commensal microbiota metabolites have been shown to be critical in suppressing influenza virus as well as the replication of herpes simplex virus (HSV)-2 (N. Li, et. al. Front. Immunol. 10 (2019), p. 1551). The results described here were obtained from a study involving cancer patients undergoing immunotherapy treatment and healthy controls. Metabolites elucidated as being absent in patients not responding well to treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbial metabolites beneficial for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. 
     Metabolomics was performed on fecal samples taken from eight cancer patients and two healthy individuals. A total of 856 metabolites could be identified in one or more ofthese samples. 
     Here we look at all metabolites that were significantly increased in the cancer patients relative to the healthy controls, based on Welch&#39;s two-sample t-test with p&lt;0.05, see Tables 11 and 12: 
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 List of metabolites increased in the cancer population relative 
               
               
                 to the control group, given as the ratio of the mean peak 
               
               
                 areas for the specified metabolites. Significance was evaluated 
               
               
                 based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
            
               
                 Compound 
                 Ratio cancer/control 
                 P value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 tyramine 
                 566 
                 0.00415 
               
               
                 Taurine 
                 278 
                 0.00390 
               
               
                 creatinine 
                 274 
                 0.0230 
               
               
                 Indolelactate 
                 97.6 
                 0.0537 
               
               
                 OAHSA (T8:1/OH-18:0) 
                 92.5 
                 0.00853 
               
               
                 Arachidonic acid (20:4n6) 
                 86.5 
                 0.00836 
               
               
                 LAHSA (18:2/OH-18:0)* 
                 73.9 
                 0.00797 
               
               
                 Alpha-hydroxyisovalerate 
                 55.0 
                 0.0182 
               
               
                 docosahexaenoate (DHA; 22:6n3) 
                 47.2 
                 0.0176 
               
               
                 docosahexaenoate (DHA; 22:6n3) 
                 41.0 
                 0.0359 
               
               
                 sulfate 
                 30.7 
                 0.0113 
               
               
                 2-hydroxypalmitate 
                 30.4 
                 0.0429 
               
               
                 stachydrine 
                 25.4 
                 9.56E−5 
               
               
                 Cholate sulfate 
                 25.2 
                 0.0317 
               
               
                 Palmitoylcarnitine (C16) 
                 24.6 
                 0.0139 
               
               
                 phenethyl amine 
                 21.5 
                 0.0223 
               
               
                 N-propionylmethionine 
                 20.6 
                 0.00669 
               
               
                 dihydroferulate 
                 20.0 
                 0.0120 
               
               
                 Beta-alanine 
                 19.6 
                 0.0145 
               
               
                 tryptamine 
                 19.5 
                 0.0289 
               
               
                 3-ureidopropionate 
                 18.7 
                 0.00232 
               
               
                 Stearoylcarnitine (C18) 
                 17.7 
                 0.00365 
               
               
                 2-hydroxybutyrate 
                 17.5 
                 0.00802 
               
               
                 3-methylhistidine 
                 15.5 
                 0.0331 
               
               
                 Nervonate (24:1n9) 
                 14.8 
                 0.0278 
               
               
                 1-palmitoyl-2-oleoyl-GPE (16:0/18:1) 
                 14.5 
                 0.0281 
               
               
                 5,6-dihydrothymine 
                 11.8 
                 0.0294 
               
               
                 octadecadienedioate (C18:2-DC) 
                 11.2 
                 0.0299 
               
               
                 agmatine 
                 10.8 
                 0.0428 
               
               
                 caffeine 
                 10.0 
                 0.0268 
               
               
                 N-methylhydantoin 
                 9.8 
                 0.0405 
               
               
                 gentisate 
                 9.6 
                 0.0121 
               
               
                 ceramide (d18:2/24:1, d18:1/24:2) 
                 8.9 
                 0.0292 
               
               
                 homostachydrine 
                 8.3 
                 0.00739 
               
               
                 N-acetylvaline 
                 8.3 
                 0.00242 
               
               
                 xanthurenate 
                 7.9 
                 0.0141 
               
               
                 N-acetylalanine 
                 7.4 
                 0.0304 
               
               
                 Margaroylcamitine (C17) 
                 7.3 
                 0.0256 
               
               
                 S-methylcysteine 
                 6.5 
                 0.0449 
               
               
                 Hydatoin-5-propionate 
                 6.3 
                 0.0238 
               
               
                 N-acetylphenylalanine 
                 6.3 
                 0.0079 
               
               
                 N-acetylleucine 
                 6.0 
                 0.00918 
               
               
                 Adrenate (22:4n6) 
                 4.9 
                 0.0212 
               
               
                 diaminopimelate 
                 4.3 
                 0.0268 
               
               
                 pristanate 
                 4.0 
                 0.0331 
               
               
                 2-aminoheptanoate 
                 3.9 
                 0.0296 
               
               
                 sarcosine 
                 3.8 
                 0.0380 
               
               
                 2-hydroxyheptanoate 
                 3.6 
                 0.0163 
               
               
                 Gamma-glutamylglutamate 
                 3.6 
                 0.0466 
               
               
                 lysine 
                 3.2 
                 0.0109 
               
               
                 4-oxovalerate 
                 3.2 
                 0.00970 
               
               
                 3-methyl-2-oxovalerate 
                 3.2 
                 0.0122 
               
               
                 Eicosenoylcamitine (C20:1) 
                 3.1 
                 0.0414 
               
               
                 1-methylguanidine 
                 3.0 
                 0.00760 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 12 
               
             
            
               
                   
               
               
                 List of metabolites decreased in the cancer population relative 
               
               
                 to the control group, given as the ratio of the mean peak 
               
               
                 areas for the specified metabolites. Significance was evaluated 
               
               
                 based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
            
               
                 Compound 
                 Ratio cancer/control 
                 P value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 L-urobilin 
                 0.07 
                 0.00466 
               
               
                 Linolenate (18:3n3 or 18:3n6) 
                 0.11 
                 0.0192 
               
               
                 Linoleoyl-linolenoyl-glycerol 
                 0.12 
                 0.000537 
               
               
                 (18:2/18:3) 
               
               
                 Heptadecatrienoate (17:3) 
                 0.13 
                 0.00224 
               
               
                 Heptadecatrienoate (17:3) 
                 0.13 
                 0.00224 
               
               
                 Azelate (C9-DC) 
                 0.13 
                 0.0151 
               
               
                 Undecanedioate (C11-DC) 
                 0.14 
                 0.0203 
               
               
                 Linoleoyl-linolenoyl-glycerol 
                 0.15 
                 0.0348 
               
               
                 (18:3/18:3) 
               
               
                 Suberate (C8-DC) 
                 0.29 
                 0.00177 
               
               
                 Octadecanedioate (C18-DC) 
                 0.35 
                 0.00999 
               
               
                 N-acetylglutamate 
                 0.43 
                 0.0178 
               
               
                 Oleoyl-linolenoyl-glycerol (18:1/18:3) 
                 0.59 
                 0.0214 
               
               
                 pyridoxamine 
                 0.60 
                 0.0446 
               
               
                 2-oxo-1-pyrrolindinepropionate 
                 0.75 
                 0.0314 
               
               
                   
               
            
           
         
       
     
     In a separate study, metabolomics was performed on a total of 55 samples obtained from 22 healthy subjects and 18 cancer patients. In some cases, two or more samples were from the same individual, spaced 6 weeks apart; in such a case they are referred to as timepoints T1 and T2. In general, T1 samples were prior to immunotherapy treatment while T2 samples were during treatment. Approximately 1 gram of raw fecal material stored at −80 deg. C. was processed for metabolite extraction by methanol as described above. 
     Metabolomics was also performed on plasma extracted from blood obtained from some of the same subjects as the fecal samples. There was a total of 44 plasma samples obtained from 18 healthy subjects and 10 cancer patients. To obtain plasma, 1 mL whole blood was centrifuged at 2800×g for 10 minutes, creating two phases with the plasma on top. 0.5 mL of plasma was removed using a pipette and transferred to a clean tube which was then stored at −80 deg. C. until processing. 0.1 mL of the plasma was used for metabolite extraction, with methanol under vigorous shaking for 2 min (Glen Mills GENOGRINDER 2000™) to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation to recover chemically diverse metabolites. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods using positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS using negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS using negative ion mode ESI, and one reserved for backup. Samples are placed briefly on a TURBOVAP® (Zymark) to remove the organic solvent. The sample extracts are stored overnight under nitrogen before preparation for analysis. 
     Three types of controls were analyzed in concert with the experimental samples: a pooled sample generated from a small portion of each experimental sample of interest served as a technical replicate throughout the platform run; extracted water samples served as process blanks; and a cocktail of standards spiked into every analyzed sample allowed for instrument performance monitoring. Instrument variability was determined by calculation of the median relative s.d. (RSD) for the standards that were added to each sample before injection into the mass spectrometers (median RSDs were determined to be 3% for plasma and 4% for fecal extracts). Overall process variability was determined by calculating the median RSD for all endogenous metabolites (i.e., non-instrument standards) present in 90% or more of the pooled technical-replicate samples (median RSD of 7% for plasma and 10% for fecal). 
     Compounds are identified by comparison to library entries of purified standards maintained by Metabolon, that contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data) on all molecules present in the library. Furthermore, biochemical identifications are based on three criteria: retention index within a narrow RI window of the proposed identification, accurate mass match to the library+/−10 ppm, and the MS/MS forward and reverse scores. MS/MS scores are based on a comparison of the ions present in the experimental spectrum to ions present in the library entry spectrum. While there may be similarities between these molecules based on one of these factors, the use of all three data points can be utilized to distinguish and differentiate biochemicals. Peaks are quantified as area-under-the-curve detector ion counts. 
     A total of 992 known compounds were identified in at least one of the plasma samples, and 1049 were identified in at least one of the fecal samples. 734 of these compounds were common between the two sample types. 
     The overall metabolic profiles were represented as two principal components. Principal components analysis is an unsupervised statistical method that compresses the number of dimensions of the data to provide a high-level view of the data over an entire set of samples. Each principal component is a linear combination of every metabolite and the principal components are uncorrelated. Principal components analysis exhibited a reasonable ability to separate the cancer and healthy groups, especially in plasma. When considering two principal components, there was a notable separation of healthy controls from cancer samples collected at T1 or T2 in plasma ( FIG.  57   , left panel). Interestingly, four samples from three cancer group subjects whose fecal whole metagenomic sequencing data clustered with healthy rather than cancer subjects also clustered on PCAs with healthy subject based on metabolic profiles in plasma. Points corresponding to these samples are indicated in the plots by arrows. In fecal samples, there was much greater overlap of healthy and cancer groups on PCA, though samples from these same cancer patients (labeled 95798, 96218, and PN4) were centered among the greatest concentration of healthy samples ( FIG.  57   , right panel). 
       FIG.  28    is a table of the top 100 differential metabolites, ranked by p value (Mann Whitney U test). Metabolomics data on plasma from a third-party provider was processed using a Mann Whitney U test to find significantly different metabolites between cancer and control cohorts. The top 100 metabolites ranked by p value are reported. 
     Examination of the results demonstrated potential differences between the plasma metabolic phenotype in healthy versus cancer T1 and cancer T2 groups (Table 13). Specifically, compounds connected to pathways of protein degradation (i.e., modified amino acids), chromatin packing in the nucleus (i.e., polyamines), nucleotide metabolism (i.e., pentose phosphate and nucleotide pathways), and extracellular matrix metabolism (i.e., aminosugars) were prioritized for their connection to activities prominent in cancer including proliferation and DNA synthesis, cell division, and invasion. Potential markers of protein post-translational modification and proteolysis (for example, N-acetyl amino acids) were elevated in plasma from both cancer T1 and T2 relative to the healthy group, respectively. Elevated proteinase expression and activity are associated with metastatic cancers (extracellular matrix invasion, autophagy, etc.) and signs of proteinase activity can be registered in the metabolome by the appearance of post-translationally modified amino acids. Likewise, polyamines and nucleic acids are required for the synthesis and packaging of DNA in proliferating cells, and these metabolites tended to be higher at both cancer T1 and T2 with respect to the healthy control group. Glycosaminoglycan degradation and oxidation products (for example, N-acetylneuraminate, the isobar N-acetylglucosamine/N-acetylgalactosamine, erythronate) were moderately elevated in cancer T1 and T2 compared to healthy controls. Reductions in various progestin steroids were noticeable in cancer T1 and T2 compared to the healthy group. Together, these biomarker patterns could reflect a persistent cancer phenotype related to protein degradation, nucleic acid synthesis, turnover, and packaging, extracellular matrix glycan turnover, and altered hormonal regulatory cues. 
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Compounds in plasma possibly representative of a cancer phenotype 
               
               
                 with statistically significant elevations in either cancer T1, cancer 
               
               
                 T2 or both relative to the healthy control group. Values given are 
               
               
                 ratios of the mean peak areas for the specified metabolites between 
               
               
                 the two groups indicated. Up or down arrows indicate whether the 
               
               
                 increase or decrease in the treatment relative to the control is 
               
               
                 significant based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 N-acetylserine 
                 1.41 ↑ 
                 1.31 
                 0.93 
               
               
                 N-acetylalanine 
                 1.24 ↑ 
                 1.21 
                 0.98 
               
               
                 Hydroxyasparagine 
                 1.4 ↑ 
                 1.32 
                 0.94 
               
               
                 5-galactosylhydroxy-L-lysine 
                 2.3 ↑ 
                 1.73 ↑ 
                 0.75 
               
               
                 C-glycosyltryptophan 
                 1.44 ↑ 
                 1.41 ↑ 
                 0.98 
               
               
                 N-acetylputrescine 
                 1.65 
                 1.22 ↑ 
                 0.74 
               
               
                 N-acetyl-isoputreanine 
                 1.2 
                 1.19 ↑ 
                 0.98 
               
               
                 (N(1) + N(8))-acetylspermidine 
                 1.9 ↑ 
                 1.89 ↑ 
                 1 
               
               
                 Acisoga 
                 1.43 ↑ 
                 1.35 ↑ 
                 0.94 
               
               
                 5-methylthioadenosine 
                 2.01 ↑ 
                 1.95 ↑ 
                 0.97 
               
               
                 Ribitol 
                 1.82 ↑ 
                 1.29 
                 0.71 
               
               
                 Ribonate 
                 1.37 ↑ 
                 1.11 
                 0.81 
               
               
                 Arabitol/xylitol 
                 1.48 ↑ 
                 1.08 
                 0.73 
               
               
                 Glucuronate 
                 2.2 ↑ 
                 1.07 
                 0.48 
               
               
                 N-acetylneuraminate 
                 1.47 ↑ 
                 1.5 ↑ 
                 1.02 
               
               
                 Erythronate 
                 1.2 ↑ 
                 1.26 
                 1.05 
               
               
                 N-acetylglucosamine/N- 
                 1.52 ↑ 
                 1.57 ↑ 
                 1.03 
               
               
                 acetylgalactosamine 
               
               
                 5-alpha-pregnan-3beta,20beta-diol 
                 0.18 ↓ 
                 0.24 ↓ 
                 1.3 
               
               
                 monosulfate (1) 
               
               
                 5-alpha-pregnan-3beta,20beta-diol 
                 0.11 ↓ 
                 0.14 ↓ 
                 1.24 
               
               
                 monosulfate (2) 
               
               
                 5-alpha-pregnan-3beta,20beta-diol 
                 0.24 ↓ 
                 0.38 ↓ 
                 1.19 
               
               
                 disulfate 
               
               
                 5-alpha-pregnan-diol disulfate 
                 0.25 ↓ 
                 0.3 
                 1.21 
               
               
                 Pregnanediol-3-glucuronide 
                 0.25 ↓ 
                 0.23 ↓ 
                 0.92 
               
               
                 Adenine 
                 1.55 ↑ 
                 1.5 
                 0.97 
               
               
                 N1-methyladenosine 
                 1.29 ↑ 
                 1.41 ↑ 
                 1.1 
               
               
                 N6-carbamoylthreonyladenosine 
                 1.5 ↑ 
                 1.31 
                 0.87 
               
               
                 N6-succinyladenosine 
                 1.88 ↑ 
                 1.82 ↑ 
                 0.97 
               
               
                 7-methylguanine 
                 1.29 ↑ 
                 1.02 
                 0.8 ↓ 
               
               
                 N2,N2-dimethylguanosine 
                 1.55 ↑ 
                 1.45 ↑ 
                 0.94 
               
               
                 Orotidine 
                 1.62 ↑ 
                 1.54 ↑ 
                 0.95 
               
               
                 Pseudouridine 
                 1.45 ↑ 
                 1.38 ↑ 
                 0.95 
               
               
                   
                 1.46 ↑ 
                 1.43 ↑ 
                 0.98 
               
               
                 2′-O-methyluridine 
                 2.81 ↑ 
                 0.46 
                 0.16 
               
               
                 Cytidine 
                 2.41 ↑ 
                 2.25 ↑ 
                 0.93 
               
               
                 N4-acetylcytidine 
                 2.38 ↑ 
                 2.1 ↑ 
                 0.88 
               
               
                 2′-O-methylcytidine 
                 1.92 ↑ 
                 1.58 
                 0.82 
               
               
                   
               
            
           
         
       
     
     The tricarboxylic acid (TCA) cycle and glycolysis pathways connected to energy production from glucose were enriched with connected metabolites that differed significantly between the plasma cancer T1 and cancer T2 groups (Table 14). In cancer the TCA cycle has been noted to serve as both a source of energy production and as a central metabolic node in the utilization and production of key metabolite classes including free fatty acid synthesis from citrate, heme from fumarate, nucleotides and proteins from oxaloacetate and alpha-ketoglutarate [3]. Mutations affecting dysregulation of oncogenes and tumor suppressors have direct impact on TCA cycle metabolism and transport of substrates into the mitochondria and direct mutations of TCA cycle enzymes also occur with some cancers [4]. Although carbon from glucose is presented as the canonical substrate for citrate production, carbons from both fatty acids and amino acids readily enter the cycle at specific points. Glutamine, via glutaminolysis to glutamate, is noted as a highly utilized fuel and carbon source for many cancers [5; 6]. The shifting profile of glutamate, pyruvate, and TCA cycle metabolites in the cancer T2 group relative to the cancer T1 group suggest that anticancer treatment has a disruptive effect on energy or mitochondrial carbon repurposing. 
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 The tricarboxylic acid (TCA) cycle profile in plasma shifted 
               
               
                 in cancer T2 compared to cancer T1 as a possible sign of response 
               
               
                 to anticancer treatment. Values given are ratios of the mean 
               
               
                 peak areas for the specified metabolites between the two groups 
               
               
                 indicated. Up or down arrows indicate whether the increase or 
               
               
                 decrease in the treatment relative to the control is significant 
               
               
                 based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                   
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 Glutamate 
                 1.29 ↑ 
                 1.31 
                 1.01 
               
               
                   
                 Pyruvate 
                 0.93 
                 0.68 
                 0.73 ↓ 
               
               
                   
                 Lactate 
                 1.12 
                 0.81 
                 0.72 ↓ 
               
               
                   
                 Citrate 
                 1 
                 1.1 
                 1.09 ↑ 
               
               
                   
                 Isocitric lactone 
                 1.37 
                 2.01 
                 1.47 ↑ 
               
               
                   
                 Alpha-ketoglutarate 
                 1.11 
                 1.21 
                 1.09 ↑ 
               
               
                   
                 Succinate 
                 1.08 
                 0.93 
                 0.86 ↓ 
               
               
                   
                 Fumarate 
                 0.91 
                 0.85 
                 0.93 ↓ 
               
               
                   
                 Malate 
                 0.97 
                 0.91 
                 0.94 ↓ 
               
               
                   
                   
               
            
           
         
       
     
     Plasma metabolites connected to glutathione metabolism and oxidative stress differed in the cancer T2 group with respect to the cancer T1 group (Table 15). Oxidized forms of glutathione and cysteine were reduced in the cancer T2 group relative to the cancer T1 group and may suggest a relative decrease in oxidative stress in the cancer T2 plasma samples. Oxidized ascorbic acid derivatives showed significant reductions in the cancer T2 group compared to the healthy control group. Tumors operate with a high level of incidental oxidative stress through the production of free radicals, reactive oxygen and nitrogen species, and hydrogen peroxide and thus depend on antioxidants such as glutathione and ascorbate to neutralize oxidative species and repair oxidative damage [7; 8]. The decreasing level of oxidative intermediates of glutathione, cysteine, and ascorbate in the cancer T2 group may be a sign of overall reduced metabolic activity and oxidative species production in response to anticancer treatment. 
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Most oxidized forms of cysteine, glutathione, and ascorbate in plasma 
               
               
                 decreased during anticancer treatment in the cancer T2 group. Values 
               
               
                 given are ratios of the mean peak areas for the specified metabolites 
               
               
                 between the two groups indicated. Up or down arrows indicate whether 
               
               
                 the increase or decrease in the treatment relative to the control is 
               
               
                 significant based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Glycine 
                 0.79 ↓ 
                 0.72 ↓ 
                 0.9 
               
               
                 Glutamate 
                 1.29 ↑ 
                 1.31 
                 1.01 
               
               
                 Methionine 
                 0.79 
                 0.8 
                 1.02 
               
               
                 cysteine 
                 1.04 
                 0.97 
                 0.93 ↓ 
               
               
                 Cystine 
                 1.25 
                 1.63 ↑ 
                 1.31 
               
               
                 Cysteine sulfinic acid 
                 1.04 
                 0.81 
                 0.78 ↓ 
               
               
                 Cysteine-glutathione disulfide 
                 1.03 
                 0.66 
                 0.64 
               
               
                 Cysteinylglycine 
                 1.21 
                 0.62 
                 0.51 ↓ 
               
               
                 Cysteinylglycine disulfide 
                 1.14 
                 0.89 
                 0.78 ↓ 
               
               
                 Cys-Gly, oxidized 
                 1.15 
                 0.56 
                 0.49 ↓ 
               
               
                 Ascorbic acid 3-sulfate 
                 1.55 
                 0.5 ↓ 
                 0.32 
               
               
                 Threonate 
                 0.79 
                 0.46 ↓ 
                 0.58 
               
               
                 Oxalate 
                 0.76 
                 0.56 ↓ 
                 0.74 
               
               
                 Gul onate 
                 2.17 ↑ 
                 1.28 
                 0.59 
               
               
                   
               
            
           
         
       
     
     Some statistically significant differences in fecal primary and secondary acids were observed for the cancer T2 group with respect to the cancer T1 group (Table 16). Most bile acids in the cancer T1 and cancer T2 groups showed large fold-change differences with respect to the healthy control group but the combination of low statistical power and large within-group variation prevented many of these differences from reaching statistical significance. Primary bile acids produced in the liver serve as emulsifiers to aid nutrient absorption from the digestive tract and are transformed into secondary bile acids by members of the gut microbiota. The significantly altered levels of some primary and secondary bile acids in the cancer T2 group relative to the baseline cancer T1 could reflect altered liver synthesis of primary bile acids, modified systemic transport, or changes in gut microflora composition and bile acid metabolism secondary to the anticancer treatment. 
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Altered levels of primary and secondary bile acids in feces 
               
               
                 among the sample groups. Values given are ratios of the mean 
               
               
                 peak areas for the specified metabolites between the two groups 
               
               
                 indicated. Up or down arrows indicate whether the increase 
               
               
                 or decrease in the treatment relative to the control is significant 
               
               
                 based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Cholate 
                 1.07 
                 3.28 
                 3.07 
               
               
                 Glycocholate 
                 4.5 
                 1.52 
                 0.34 
               
               
                 Taurocholate 
                 15.98 
                 11.5 
                 0.72 
               
               
                 Chenodeoxycholate 
                 1.83 
                 4.47 
                 2.45 
               
               
                 Chenodeoxycholic acid (1) 
                 3.44 ↑ 
                 2.72 
                 0.79 
               
               
                 Chenodeoxycholic acid (1) 
                 1.55 
                 5.62 
                 3.63 
               
               
                 Glycochenodeoxycholate 
                 3.41 
                 1.29 
                 0.38 
               
               
                 Taurochenodeoxycholate 
                 8.62 
                 3.54 
                 0.41 ↓ 
               
               
                 Cholate sulfate 
                 2 
                 5.74 
                 2.86 ↑ 
               
               
                 Glycochenodeoxycholate 3-sulfate 
                 17.41 
                 1.29 
                 0.07 
               
               
                 Glycocholate sulfate 
                 2.85 
                 1 
                 0.35 ↓ 
               
               
                 Deoxycholate 
                 1.27 
                 1.56 
                 1.23 
               
               
                 Deoxycholic acid 3-sulfate 
                 3.83 
                 6.56 
                 1.71 
               
               
                 Deoxycholic acid (12 or 24)-sulfate 
                 8.23 ↑ 
                 4.25 
                 0.52 
               
               
                 Deoxycholic acid glucuronide 
                 0.48 
                 0.33 
                 0.69 ↓ 
               
               
                 Taurodeoxycholate 
                 15.78 ↑ 
                 16.4 
                 1.04 
               
               
                 Lithocholate 
                 1.17 
                 1.03 
                 0.88 ↓ 
               
               
                 Lithocholate sulfate (1) 
                 3.58 ↑ 
                 1.74 
                 0.48 
               
               
                 Lithocholate sulfate (2) 
                 4.33 
                 6.12 
                 1.41 
               
               
                 Glycolithocholate sulfate 
                 2.23 
                 1.86 
                 0.83 
               
               
                 Taurolithocholate 3-sulfate 
                 2.5 
                 2.54 ↑ 
                 1.01 
               
               
                 Ursodeoxycholate 
                 1.48 ↑ 
                 2.72 
                 1.84 
               
               
                 Isoursodeoxycholate 
                 2.13 
                 2.1 
                 0.98 
               
               
                 Isoursodeoxycholate sulfate (1) 
                 3.89 ↑ 
                 5.62 
                 1.45 
               
               
                 Glycoursodeoxycholate 
                 2.59 
                 1.12 
                 0.43 
               
               
                 Tauroursodeoxycholate 
                 2.84 
                 1.26 
                 0.44 ↓ 
               
               
                 Taurochenodeoxycholic acid 3-sulfate 
                 10.04 
                 1.13 
                 0.11 
               
               
                 Ursodeoxycholate sulfate (1) 
                 2.76 
                 11.72 
                 4.24 
               
               
                   
               
            
           
         
       
     
     Several fecal metabolites with metabolic origins possibly connected to the microbiome were altered in either the cancer T1 or cancer T2 groups compared to the healthy control group (Table 17). These included polyamine compounds such as cadaverine and putrescine, derivatives of the aromatic amino acids—phenylalanine, tyrosine, and tryptophan, benzoates, and compounds related to the microbial-aided breakdown of complex polymers such as lignin present in plant foodstuffs. Many differential changes were apparent between cancer T1 and the healthy group relative to the cancer T2 and healthy group comparison, and other compounds differed in the baseline cancer T1 to cancer T2 treatment groups. The differential pattern of microbiome-associated metabolites in the cancer T1 and cancer T2 groups could reflect compositional changes in the microflora both driven by cancer (i.e., cancer T1 differences) as well as anticancer treatment (i.e., cancer T2 distinctions). A healthy microflora maintains an intestinal barrier that keeps out genotoxic and inflammatory bacteria and their toxins [9]. An increasing number of publications point to likely contributions of dysbiosis and toxins to carcinogenesis and the role of a healthy microflora supported by lifestyle, diet, prebiotics, and probiotics to prevent and serve as anticancer adjuvants are being explored [10]. 
     
       
         
           
               
             
               
                 TABLE 17 
               
             
            
               
                   
               
               
                 Microbiome-associated compounds displayed differential patterns in 
               
               
                 the fecal metabolome of the cancer T1 and cancer T2 groups. Values 
               
               
                 given are ratios of the mean peak areas for the specified metabolites 
               
               
                 between the two groups indicated. Up or down arrows indicate whether 
               
               
                 the increase or decrease in the treatment relative to the control 
               
               
                 is significant based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Cadaverine 
                 1.85 
                 3.91 ↑ 
                 2.11 
               
               
                 N-acetyl-cadaverine 
                 5.06 
                 5.56 ↑ 
                 1.1 
               
               
                 Phenethylamine 
                 0.73 
                 1.42 ↑ 
                 1.95 
               
               
                 Tyramine 
                 2.26 ↑ 
                 12.82 
                 5.69 
               
               
                 Phenol sulfate 
                 6.03 ↑ 
                 2.12 
                 0.35 
               
               
                 p-cresol glucuronide 
                 2.56 
                 1 
                 0.39 ↓ 
               
               
                 Vanillic alcohol sulfate 
                 1 
                 35.29 
                 35.29 ↑ 
               
               
                 Tryptamine 
                 4.79 ↑ 
                 12.5 
                 2.61 
               
               
                 Skatol 
                 1.41 
                 0.13 ↓ 
                 0.09 
               
               
                 Indole 
                 2.63 
                 0.89 ↓ 
                 0.34 
               
               
                 Indole-3-carboxylate 
                 0.83 
                 0.26 ↓ 
                 0.31 
               
               
                 2-aminophenol 
                 2.82 ↑ 
                 0.95 
                 0.34 
               
               
                 Agmatine 
                 2.67 
                 1.92 
                 0.72 ↓ 
               
               
                 Putrescine 
                 2.18 
                 4.89 ↑ 
                 2.24 
               
               
                 N-acetylputrescine 
                 2.39 
                 2.67 
                 1.12 
               
               
                 Spermidine 
                 1.16 
                 2.37 
                 2.04 
               
               
                 N(′1)-acetylspermidine 
                 1.46 
                 1.42 ↑ 
                 0.97 
               
               
                 Acisoga 
                 2.26 ↑ 
                 1.46 
                 0.64 
               
               
                 Alpha-CEHC sulfate 
                 4.5 ↑ 
                 6.95 
                 1.54 
               
               
                 Delta-CEHC 
                 0.78 
                 0.56 
                 0.73 
               
               
                 Gamma-CEHC sulfate 
                 1.53 ↑ 
                 3.58 
                 2.34 
               
               
                 3-hydroxyhippurate 
                 0.49 
                 0.15 ↓ 
                 0.31 
               
               
                 2-(4-hydroxyphenyl)propionate 
                 1.52 
                 0.23 ↓ 
                 0.15 
               
               
                 4-hydroxycyclohexylcarboxylic acid 
                 0.5 ↓ 
                 0.94 
                 1.89 
               
               
                 Caffeate 
                 0.54 
                 0.57 
                 1.05 
               
               
                 Coumaroylquinate (1) 
                 0.35 
                 0.42 
                 1.2 ↑ 
               
               
                 Coumaroylquinate (3) 
                 0.54 
                 0.58 
                 1.08 ↑ 
               
               
                 Genistein sulfate 
                 15.6 
                 2.23 
                 0.14 ↓ 
               
               
                 Enterolactone 
                 1.1 ↑ 
                 0.47 
                 0.43 
               
               
                   
               
            
           
         
       
     
     Hemne degradation markers, including bilirubin and L-urobilinogen, showed changes across the cancer T1 and cancer T2 compared to the healthy group in feces and in the cancer T1 group of plasma compared to the healthy controls (Tables 18 and 19). Urobilinogen and urobilin are downstream products connected to the microbiome. An interesting recent metabolomic publication found increasing fecal levels of urobilinogen with increasing radiation dose and cross-omic analysis showed that the increase was positively correlated to microbes of the Lachnospiraceae, Ruminococcaceae, and Rikenellacea taxa [11]. This work shows how cross-omic integration can lead to a greater understanding and provide needed specificity to changes in distinct metabolites. 
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                 Heme degradation markers with altered levels in feces. Values given 
               
               
                 are ratios of the mean peak areas for the specified metabolites between 
               
               
                 the two groups indicated. Up or down arrows indicate whether the 
               
               
                 increase or decrease in the treatment relative to the control is 
               
               
                 significant based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                   
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 Protoporphyrin IX 
                 1.32 
                 0.86 
                 0.65 ↓ 
               
               
                   
                 Bilirubin (Z,Z) 
                 4.39 ↑ 
                 2.95 
                 0.67 
               
               
                   
                 Bilirubin (E,E) 
                 3.54 
                 1.81 
                 0.51 
               
               
                   
                 Biliverdin 
                 1.8 
                 0.86 
                 0.48 
               
               
                   
                 Urobilinogen 
                 3.74 
                 5.02 ↑ 
                 1.34 
               
               
                   
                 D-urobilin 
                 0.99 
                 0.73 
                 0.74 
               
               
                   
                 L-urobilin 
                 0.37 ↓ 
                 0.7 
                 1.9 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 19 
               
             
            
               
                   
               
               
                 Heme degradation markers with altered levels in plasma. Values given 
               
               
                 are ratios of the mean peak areas for the specified metabolites between 
               
               
                 the two groups indicated. Up or down arrows indicate whether the 
               
               
                 increase or decrease in the treatment relative to the control is 
               
               
                 significant based on Welch&#39;s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Cancer 
                 Cancer 
                   
               
               
                   
                   
                 T1/All 
                 T2/All 
                 Cancer T2/ 
               
               
                   
                 Compound 
                 Healthy 
                 Healthy 
                 Cancer T1 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 Heme 
                 1.15 
                 1.98 
                 1.72 
               
               
                   
                 Bilirubin (Z,Z) 
                 0.68 ↓ 
                 0.71 
                 1.05 
               
               
                   
                 Bilirubin (E,Z) or (Z,E) 
                 0.66 ↓ 
                 0.66 
                 1 
               
               
                   
                 Biliverdin 
                 0.77 
                 0.87 
                 1.12 
               
               
                   
                 Urobilinogen 
                 1.72 ↑ 
                 1.3 
                 0.75 
               
               
                   
                   
               
            
           
         
       
     
     Example 10: Data Driven and Machine Learning Approaches for Therapeutic Design 
     Whole genome sequencing and flow cytometry analysis were performed on human fecal and blood samples, respectively, as described in Example 9. A machine learning model was fit to discriminate cancer and control samples, using all fecal data collected to date. The model was validated using leave-one-out cross-validation, and performance evaluated using a receiver operating characteristic curve ( FIG.  8    and Table 4). Organisms were then scored based on a composite score accounting for their correlations to immune markers ( FIG.  9    and Tables 5 and 6) and fold change between cancer and control cohorts. The organisms were also ranked according to differential abundance between responder and non-responder patients ( FIG.  10    and Table 7). As a healthy immune response characterized by an increase in CD8+ and NK-like T cells is important for rapid viral clearance (Apt et al. (2012), Immunity 37:158-170; Thevarajan et al. (2020), Nature Med. https://doi.org/10.1038/s41591-020-0819-2), microbes identified this way are predicted to be beneficial for recovery from viral infections such as influenza or COVID-19. Indeed, similar immune marker correlations are seen with the data from the cancer patient study (Table 5). Classification of responders and non-responders also implies robust and insufficient immune response, respectively, and thus serves as a proxy for response to viral infections. 
                     TABLE 4                  A random forest classifier was trained to classify operational species unit abundances for       a sample as corresponding to cancer or control. A ROC curve was generated on 145 cancer       samples and 88 control samples using leave-one-out cross validation. Following validation,       the model was trained on all the samples and feature importance values are reported.                         Feature Importance   log 10 of Fold Change   Organism Name       (Random Forest)   (Control vs Cancer)   (Operational Species Unit)                                 0.016501858   −0.415683892     Blautia  sp. AF19-10LB C2906       0.013518985   −0.764382216   Erysipelotrichaceae bacterium GAM147 C2844       0.010943304   0.280259145     Flavonifractor plautii  C2284       0.009899023   −0.565340143   Firmicutes bacterium AF12-30 C2644       0.009291084   −0.557690435     Ruminococcus  sp. OF03-6AA C2904       0.008763332   −0.52436559     Coprobacillus  sp. 8_1_38FAA C2606       0.008543128   −0.370730577     Eubacterium ramulus  C2852       0.008185491   0.314786908   [ Clostridium ]  symbiosum  C2238       0.00777239   −0.449283525     Coprococcus comes  C2152       0.007387547   −0.432405099     Dorea  sp. AM58-8 C2913       0.007370147   0.386220508     Streptococcus vestibularis  C7338       0.00712668   −0.436129729     Dorea longicatena  C2413       0.006857525   0.266781049     Catenibacterium  sp. AM22-15 C2888       0.00606504   0.249321416   [ Clostridium ]  bolteae  C2137       0.006038427   0.629434999   [ Clostridium ]  scindens  C2143       0.005741584   0.559795019     Blautia  sp. N6H1-15 C2865       0.005164589   −0.516206872     Dorea longicatena  C2131       0.005038218   0.440453628   Clostridiales bacterium TF09-2AC C2150       0.004962784   0.089210304     Parabacteroides merdae  C0130       0.00488605   −0.442770588     Dorea  sp. OM07-5 C2890       0.00482885   −0.353929055     Anaerostipes hadrus  C2144       0.004801012   0.531527103     Blautia hansenii  C3044       0.004709165   0.446480902     Anaerostipes caccae  C2134       0.004700494   0.204253574     Alistipes senegalensis  C0284       0.004668466   0.189644361     Hungatella hathewayi  C2175       0.004549795   0.246863312     Alistipes  sp. An66 C0846       0.004488856   −0.201826507     Fusicatenibacter saccharivorans  C2643       0.004384083   −0.504914016     Blautia obeum  C2129       0.004369678   0.341085636     Lactobacillus fermentum  C3433       0.004361877   0.198581902     Oscillibacter  sp. PEA192 C2443       0.00430547   −0.486272557     Phascolarctobacterium succinatutens  YIT 12067 C2237       0.00427777   −0.490502377     Bifidobacterium catenulatum  C0014       0.004249632   0.185525714     Angelakisella massiliensis  C3120       0.004222488   −0.352856347     Ruminococcus callidus  C2440       0.004185622   0.324033352     Bifidobacterium dentium  C0003       0.004155963   0.253779907     Extibacter muris  C2915       0.004044015   0.507281373   [ Clostridium ]  clostridioforme  AGR2157 C2412       0.004017688   0.47474479   [ Clostridium ]  lavalense  C2843       0.004004597   −0.163492912     Clostridium  sp. AM18-55 C2845       0.003953855   0.181627961   Clostridia bacterium UC5.1-1D1 C2633       0.003917395   0.231236234     Streptococcus parasanguinis  C4037       0.003901166   0.40868596     Streptococcus mutans  C3345       0.003875451   −0.421426117     Anaerobutyricum hallii  C2206       0.003867169   0.259650758     Erysipelatoclostridium ramosum  C2142       0.003761301   0.375605827     Paraprevotella clara  C0224       0.003659752   0.400215198   Eubacteriaceae bacterium CHKCI004 C2759       0.003549486   −0.727951095     Collinsella  sp. AM34-10 C1986       0.003509696   0.195100824     Flavonifractor  sp. An9 C2755       0.003494686   −0.348031554     Ruminococcus  sp. AF46-10NS C2926       0.003477621   −0.206071101     Clostridium  sp. OM02-18AC C2931       0.003447056   0.457446985     Dorea  sp. Marseille-P4003 C3269       0.003386838   0.440006771     Blautia producta  C2356       0.00337533   −0.305064647   Firmicutes bacterium TM09-10 C2909       0.003362471   0.273578745     Phocea massiliensis  C2631       0.003322609   0.009697135     Merdibacter massiliensis  C3221       0.003256256   −0.247491324     Oscillibacter  sp. ER4 C2580       0.003236909   0.547982486   Clostridiales bacterium VE202-09 C2460       0.003178005   0.309883036     Harryflintia acetispora  C2880       0.003172428   0.224781595     Flavonifractor  sp. An82 C2757       0.00315518   0.405385756     Streptococcus  sp. HSISS2 C4629       0.003153913   0.185518308     Eisenbergiella massiliensis  C2435       0.003099824   0.309145503     Clostridium  sp. SN20 C3256       0.003032509   0.190748088     Butyricicoccus porcorum  C2752       0.002974263   0.21217243     Bifidobacterium scardovii  C0042       0.002943309   −0.183114283   Firmicutes bacterium AM10-47 C2889       0.002906076   −0.344627962     Blautia  sp. TF11-31AT C2841       0.0029012   0.069794378     Bacteroides clarus  C0195       0.0028804   0.218206762     Lachnoclostridium  sp. An14 C2775       0.00287576   −0.103576385     Bacteroides uniformis  C0132       0.002848749   −0.167126002   Firmicutes bacterium AF36-3BH C2905       0.002824076   0.309520673   Clostridiales bacterium CCNA10 C2953       0.002809724   0.314889985     Dorea  sp. 5-2 C2378       0.002808948   0.251398969     Clostridium  sp. AT4 C2666       0.002808102   −0.399757353     Christensenella minuta  C2682       0.002796624   0.40212407     Acidaminococcus intestini  C2208       0.00277314   −0.349179114     Massilioclostridium coli  C3076       0.002759323   0.447842365     Streptococcus gordonii  C3645       0.002718198   −0.312636412     Ruminococcus  sp. AF14-10 C2897       0.00270911   −0.304912298     Odoribacter  sp. AF21-41 C0847       0.002652152   0.136177714     Anaeromassilibacillus  sp. An200 C2765       0.002620021   0.243049812     Blautia hansenii  C2161       0.002615116   0.233225815     Lachnoclostridium  sp. An298 C2760       0.002611426   −0.032159744     Roseburia faecis  C2648       0.002606658   −0.304525941   [ Ruminococcus ]  torques  C2636       0.002587424   0.352092737     Dialister pneumosintes  C2708       0.002576223   0.155095629     Bacteroides caccae  C0156       0.002573354   0.192538373     Butyricimonas  sp. Marseille-P4593 C1362       0.002552093   −0.244156505   Clostridiales bacterium VE202-01 C2458       0.002548102   0.361035514     Blautia  sp. An249 C2761       0.002517171   −0.394453097     Turicibacter sanguinis  C2220       0.002506636   0.277784722     Enorma massiliensis  C1943       0.002501752   0.275045721     Streptococcus  sp. HSISM1 C4627       0.00249105   −0.534927741     Raoultibacter massiliensis  C2013       0.002478591   0.165198022   Ruminococcaceae bacterium AM07-15 C2928       0.002471317   −0.392581823     Clostridium  sp. AF36-4 C2893       0.002468113   0.175364006     Eubacterium  sp. 3_1_31 C2186       0.002461251   −0.215314373   Clostridiales bacterium AM23-16LB C2886       0.002456084   0.016078272     Tyzzerella nexilis  C2155       0.002443061   0.267120144     Sellimonas intestinalis  C2461       0.002440381   −0.295779942     Butyricicoccus  sp. AM29-23AC C2943       0.002429933   −0.160088535     Alistipes putredinis  DSM 17216 C0133       0.002403414   −0.34579043   Firmicutes bacterium AF25-13AC C2695       0.002389793   0.233921669   [ Clostridium ]  citroniae  C2272       0.002388663   −0.287905997     Faecalibacterium prausnitzii  C2809       0.002377287   0.265105676     Collinsella intestinalis  C1929       0.002371557   0.325006666     Lachnoclostridium  sp. An196 C2766       0.002331412   0.161011335     Ruthenibacterium lactatiformans  C2282       0.00232152   −0.257009611     Ruminococcus  sp. AF21-42 C2938       0.002321468   −0.069789147     Butyrivibrio crossotus  DSM 2876 C2154       0.002319772   0.003128369     Bacteroides vulgatus  C0099       0.00229641   0.091890638     Bacteroides acidifaciens  C0604       0.002277453   0.195676439     Flavonifractor  sp. An10 C2786       0.002276704   −0.046379748     Drancourtella  sp. An177 C2763       0.002272041   0.160264471     Anaerotruncus colihominis  C2145       0.00225912   −0.120363782     Pseudoflavonifractor capillosus  ATCC 29799 C2198       0.002256141   −0.517722756     Bifidobacterium bifidum  C0005       0.002250462   −0.094755491     Anaeromassilibacillus  sp. Marseille-P3876 C2925       0.002249251   0.292298556     Coprobacter fastidiosus  C0231       0.002245262   0.338335356     Bariatricus massiliensis  C3067       0.002237507   0.162776529     Coprococcus  sp. AF21-14LB C2900       0.002226962   −0.408971832   Clostridiaceae bacterium OM08-6BH C2949       0.002218309   −0.002771039   [ Bacteroides ]  pectinophilus  ATCC 43243 C2151       0.002217958   0.25729072     Pseudoflavonifractor  sp. An184 C2770       0.002200796   −0.200989635     Eubacterium  sp. AM18-26 C2923       0.00218927   −0.081898577     Parabacteroides  sp. AF18-52 C1227       0.002187486   −0.123209619     Coprococcus eutactus  C2642       0.002161484   0.30195464     Phascolarctobacterium faecium  C2862       0.002158572   −0.087502084   Lachnospiraceae bacterium OM04-12BH C2952       0.002148262   0.047074352     Parabacteroides distasonis  C0100       0.002142893   −0.255666512     Faecalibacterium  sp. AF28-13AC C2810       0.002134925   −0.158568078     Bacteroides stercoris  C0134       0.002114346   −0.355662173   Firmicutes bacterium AM41-11 C2946       0.002110017   −0.165551333   [ Clostridium ]  amygdalinum  C2887       0.00210878   0.250557414     Anaerotignum lactatifermentans  C2790       0.002107104   0.436062031   [ Clostridium ]  aldenense  C2884       0.002095506   0.084877313     Intestinimonas timonensis  C3301       0.002094298   0.256448208     Alistipes finegoldii  C0177       0.002084535   0.058630203     Mordavella  sp. Marseille-P3756 C3280       0.002082758   0.128186268     Streptococcus oralis  subsp.  tigurinus  C6034       0.002078318   0.085608213     Prevotella  sp. P3-92 C0874       0.002078069   0.213972847     Alterileibacterium massiliense  C3118       0.002056041   −0.041470873     Coprococcus eutactus  C2140       0.00205311   0.306957134     Fusobacterium nucleatum  C2028       0.002052465   −0.248224092     Massilimaliae massiliensis  C3228       0.00204697   −0.360378609     Clostridium  sp. AM33-3 C2947       0.00204635   −0.169578698   Firmicutes bacterium AM29-6AC C2940       0.002030614   0.14595452     Hungatella hathewayi  C2351       0.00202297   −0.251539605     Blautia luti  C2436       0.001993254   −0.189503492     Holdemanella biformis  C2160       0.001989672   −0.240687636     Anaerobutyricum hallii  C3263       0.001971269   0.089118345     Alistipes shahii  C0199       0.001965797   0.274298289     Odoribacter laneus  YIT 12061 C0239       0.001965483   0.078208985     Peptoniphilus lacrimalis  C2213       0.00194357   0.120085576     Streptococcus constellatus  C4635       0.001936923   −0.130171095     Eubacterium  sp. AF15-50 C2941       0.001934746   0.058661303   Clostridiales bacterium CHKCI006 C3057       0.00193182   0.157031233     Alistipes onderdonkii  C0322       0.001930949   0.599613718     Lactobacillus salivarius  C3392       0.001892559   0.121653741     Neglecta timonensis  C3059       0.001887608   0.232534892     Clostridium  sp. 1001271st1 H5 C3046       0.001866112   0.045627845     Prevotellamassilia timonensis  C1705       0.001865236   0.16241841     Slackia exigua  C1932       0.001854461   −0.219463054     Bacteroides finegoldii  C0138       0.001852121   −0.224535064     Barnesiella intestinihominis  C0275       0.001841628   −0.224153342     Eubacterium ventriosum  C2128       0.001839575   0.14243286     Streptococcus anginosus  C4636       0.001839422   0.049603186     Prevotella  sp. BCRC 81118 C1221       0.001838081   0.080289666     Akkermansia  sp. aa_0143 C1922       0.001836116   0.387030309     Blautia  sp. Marseille-P3201T C3179       0.001832526   −0.319221468     Ruminococcus lactaris  C2149       0.001830134   −0.187587381     Eubacterium  sp. AF34-35BH C2902       0.001829468   0.227277401     Paraprevotella xylaniphila  C0198       0.001821326   −0.005377338     Alistipes  sp. 5CPEGH6 C1580       0.001819158   −0.045467144     Eubacterium  sp. TM06-47 C2917       0.001812327   −0.36246911     Faecalibacterium prausnitzii  C2651       0.001807702   0.407496562     Lachnoclostridium  sp. An118 C2782       0.001804296   0.162945863     Bacteroides  sp. AM10-21B C1214       0.001801377   −0.612948492     Collinsella aerofaciens  C1977       0.001799781   0.200783717   Ruminococcaceae bacterium D16 C2214       0.001795815   −0.230812001     Dorea formicigenerans  C2197       0.001782118   0.050805612   [ Clostridium ]  leptum  C2136       0.001769616   0.255735482     Parabacteroides johnsonii  C0139       0.001757969   0.335044837   [ Clostridium ]  methylpentosum  DSM 5476 C2167       0.001748845   0.137798554     Parabacteroides  sp. SN4 C1840       0.001732845   −0.088799912     Clostridium  sp. YH-panp20 C2971       0.001730465   0.187542345   [ Ruminococcus ]  gnavus  C2199       0.001721291   0.245585432     Holdemania  sp. Marseille-P2844 C3176       0.001711469   0.326189698   [ Clostridium ]  asparagiforme  C2165       0.001709265   −0.32340108     Ruminococcus  sp. AM42-11 C2945       0.001708751   −0.211956107     Blautia  sp. OF03-15BH C2912       0.001705071   −0.326716726     Subdoligranulum  sp. APC924/74 C2870       0.001704797   −0.391815999     Romboutsia timonensis  C3123       0.001697621   0.114228311     Streptococcus oralis  C5466       0.0016965   −0.048932599     Clostridium  sp. AF34-13 C2653       0.001691772   0.20344874     Dialister invisus  DSM 15470 C2174       0.001689134   0.095511852     Olsenella uli  C1928       0.001673536   −0.100055999   [ Eubacterium ]  siraeum  C2135       0.001662325   0.122632002     Akkermansia muciniphila  C1917       0.001656155   0.214252057     Faecalimonas umbilicata  C2244       0.001642083   0.182409993   Clostridiales bacterium Marseille-P5551 C3291       0.001637493   0.004280452   Ruminococcaceae bacterium C2861       0.001634056   0.134322164     Lactonifactor longoviformis  C2830       0.00162656   0.485421565     Lactobacillus rhamnosus  C3457       0.001625673   0.273598423   Coriobacteriaceae bacterium CHKCI002 C1973       0.001624111   −0.011206269     Anaerofilum  sp. An201 C2764       0.001623073   0.072560155     Bacteroides stercorirosoris  C0463       0.001622251   −0.202159024     Alistipes  sp. CHKCI003 C1653       0.001620599   0.174483602     Anaeromassilibacillus  sp. Marseille-P3371 C2632       0.001619706   0.30918881     Bacteroides  sp. HF-5092 C1596       0.001619395   0.147450868     Bacteroides coprocola  C0136       0.001617633   −0.087543931     Blautia obeum  C2901       0.001614518   0.34599988     Evtepia gabavorous  C2876       0.001613136   −0.161787704     Ruminococcus  sp. AF31-8BH C2903       0.001603563   0.123138967     Anaerococcus  sp. HMSC068A02 C2185       0.001598053   0.202218832     Lactobacillus plantarum  C3798       0.001594311   −0.488328224     Allisonella histaminiformans  C3105       0.001586576   −0.098634411     Roseburia intestinalis  C2158       0.001584302   −0.452532206     Bifidobacterium pseudocatenulatum  C0013       0.001572828   −0.061735341     Alistipes  sp. 5CBH24 C0283       0.001570429   0.116445939     Streptococcus salivarius  C4352       0.001563761   −0.1456938     Gordonibacter pamelaeae  C1937       0.001552982   −0.476696467     Collinsella aerofaciens  C1933       0.001550017   0.146736525     Flavonifractor  sp. An92 C2753       0.001546685   −0.312675608     Clostridium  sp. OF10-22XD C2132       0.001544022   0.143206979     Haemophilus parainfiuenzae  T3T1 C4194       0.001541656   0.177526741     Streptococcus gallolyticus  C3902       0.001538447   −0.306056064     Bacteroides heparinolyticus  C1005       0.00153663   −0.11819143     Eubacterium  sp. OM08-24 C2896       0.001535096   −0.242001524     Faecalibacterium prausnitzii  C2863       0.001532366   −0.074691634     Bacteroides nordii  C0263       0.00153067   −0.077986369     Marvinbryantia formalexigens  C2205       0.00152307   0.128955058   Lachnospiraceae bacterium 1_4_56FAA C2258       0.001515629   0.100560583     Roseburia  sp. OF03-24 C2911       0.001515375   −0.070429456   Lachnospiraceae bacterium AM48-27BH C2935       0.00151401   0.209874419     Fusobacterium nucleatum  C2027       0.001504779   −0.142905059     Clostridium  sp. OF09-36 C2944       0.001497974   0.032287603     Peptostreptococcus anaerobius  C2217       0.00149702   −0.090219746     Leuconostoc mesenteroides  C3570       0.001495408   0.419154573     Blautia producta  C2581       0.001489385   0.10891937     Bacteroides cellulosilylicus  C0143       0.001487732   −0.474788291     Faecalibacterium prausnitzii  C2184       0.00147645   0.378916316     Lachnoclostridium  sp. An181 C2771       0.001467508   −0.26283664     Clostridium  sp. AM49-4BH C2934       0.001467098   0.000605824     Clostridium  sp. ATCC 29733 C2438       0.0014621   −0.322415354     Blautia  sp. KGMB01111 C3003       0.001454853   0.095997825     Clostridioides difficile  C2074       0.001447136   −0.061440984     Parvimonas micra  C2139       0.001444928   0.212594053     Megasphaera  sp. DISK 18 C2433       0.001443122   0.285426008     Bacteroides salyersiae  C0264       0.001438622   −0.046750403     Lactobacillus paracasei  C3573       0.00143852   −0.082129699     Eggerthella timonensis  C2011       0.001425959   −0.114661776     Bifidobacterium animalis  C0002       0.001416675   0.280368137     Klebsiella variicola  C3709       0.001414944   −0.246601387     Agathobaculum butyriciproducens  C2850       0.001405704   0.074907434     Anaeromassilibacillus  sp. An250 C2762       0.001402711   −0.081852178     Ruminococcus  sp. AF24-32LB C2894       0.001385668   −0.358288898     Faecalibacterium prausnitzii  C2138       0.001385102   −0.035320328     Streptococcus mitis  NCTC 12261 C4004       0.001379637   0.168782631     Prevotella  sp. AM23-5 C0872       0.001378158   0.138984788     Collinsella tanakaei  C1938       0.001375186   0.128316545     Intestinimonas butyriciproducens  C2577       0.001357814   −0.130545436     Gemmiger formicilis  C3234       0.001356921   0.099487524     Culturomica massiliensis  C1230       0.001349152   −0.028077053     Roseburia  sp. AM51-8 C2924       0.001346043   0.172383478     Eubacterium  sp. An11 C2784       0.001345379   0.067714209     Hungatella hathewayi  C2462       0.001342127   0.190693108     Bacteroides rodentium  JCM 16496 C0461       0.001325512   −0.073609518     Clostridium  sp. TM06-18 C2922       0.001314021   −0.14364999     Clostridium  sp. AF27-2AA C2937       0.001303967   −0.118957311     Parabacteroides  sp. TM07-1AC C1229       0.001301855   0.049387119     Butyricimonas  sp. Marseille-P2440 C0330       0.001297003   −0.022569114     Neobitarella massiliensis  C3275       0.001291043   −0.159405658     Clostridium  sp. AM30-24 C2942       0.001276208   −0.060522193     Prevotella  sp. Marseille-P4119 C1902       0.001268369   0.116021978     Clostridium perfringens  C2078       0.001264612   −0.0200892     Bacteroides  sp. An19 C0842       0.001263236   0.301353216     Klebsiella pneumoniae  C3423       0.001260612   −0.160766973     Alistipes timonensis  C0271       0.001256742   0.252094618     Salmonella enterica  C3329       0.001253605   0.178630171     Intestinimonas massiliensis  C2614       0.001252735   0.470799178     Cuneatibacter caecimuris  C3008       0.001241543   0.105626404     Eubacterium brachy  ATCC 33089 C2452       0.001233195   −0.111096287     Eisenbergiella tayi  C2259       0.001231803   0.203084745     Akkermansia muciniphila  C1923       0.001229663   0.07528375     Akkermansia muciniphila  C1921       0.001227806   0.316271739     Metaprevotella massiliensis  C1901       0.001223817   0.103266649     Streptococcus intermedius  C4476       0.001223003   −0.009215998     Desulfovibrio piger  C7227       0.001210017   −0.103823837     Eubacterium ramulus  C2442       0.001208958   −0.066912759     Clostridium  sp. OM07-10AC C2948       0.001208297   −0.011533879     Faecalicatena fissicatena  C2241       0.001206301   −0.14769711     Clostridium  sp. AF23-8 C2908       0.001201907   0.087391156     Klebsiella michiganensis  C4315       0.001201625   0.090163662     Collinsella  sp. AF08-23 C1987       0.001199225   0.047629461     Megasphaera cerevisiae  C2604       0.00119489   0.157003749     Lachnoclostridium  sp. An138 C2776       0.001192374   0.346071847     Eubacterium limosum  C2659       0.001183998   0.163715553     Streptococcus pneumoniae  C3327       0.001173126   0.161269394     Eubacterium callanderi  C2127       0.001161929   −0.321742198     Ruminococcus champanellensis  C2249       0.001157051   −0.04739511     Catenibacterium mitsuokai  DSM 15897 C2204       0.001154034   0.069882758     Streptococcus sanguinis  C3561       0.001152159   −0.229970619   Firmicutes bacterium AF22-6AC C2933       0.001149193   −0.093698754     Roseburia  sp. OM04-15AA C2892       0.001148872   −0.136898288     Holdemania massiliensis  AP2 C2339       0.00114848   −0.143597792     Olsenella  sp. AF21-51 C1985       0.001145605   0.041391195     Bacteroides ovatus  C0131       0.001144548   0.310613625     Eggerthella  sp. YY7918 C1941       0.001142328   0.294636274   Lachnospiraceae bacterium 2_1_46FAA C2247       0.001139964   −0.109907027     Anaerostipes  sp. 992a C2729       0.001136248   0.071917201     Eggerthella lenta  C1927       0.001127673   −0.035851608     Streptococcus  sp. ChDC B345 C6537       0.00112536   0.235371201     Ruminococcus  sp. AF18-22 C2662       0.001124558   0.22935135     Blautia  sp. An81 C2788       0.001120621   −0.502954606     Ruminococcus  sp. KGMB03662 C2557       0.001117895   −0.016216198     Bacteroides  sp. OF04-15BH C1226       0.001117113   −0.317608637     Eubacterium  sp. AF22-8LB C2898       0.001116776   −0.13214399     Candidatus Borkfalkia ceftriaxoniphila  C3005       0.001115975   −0.245958899     Gordonibacter urolithinfaciens  C1971       0.001114616   −0.335185925     Bifidobacterium adolescentis  C0001       0.001114192   0.083292114     Eubacterium pyruvativorans  C3098       0.001113405   −0.113942218     Massilimaliae timonensis  C3250       0.001111358   −0.321124776     Clostridium disporicum  C2479       0.001108373   0.416260181     Bacteroides zoogleoformans  C1004       0.001099862   0.103183512     Bacteroides sartorii  C0346       0.001096801   0.127258668     Finegoldia magna  C2170       0.001096565   0.053902093   Burkholderiales bacterium YL45 C5482       0.001090767   −0.25222383     Bacteroides mediterraneensis  C1791       0.001089194   −0.192935162     Clostridium  sp. AF46-9NS C2891       0.001085672   −0.022510129     Bacteroides faecis  C0221       0.001084937   0.183744827     Enteroscipio rubneri  C1978       0.001080288   0.217242623     Streptococcus agalactiae  C3342       0.001077696   0.014956563     Oscillibacter ruminantium  GH1 C2321       0.001071923   0.226961129     Bacteroides coprophilus  C0141       0.001070282   −0.085202725     Prevotella  sp. 885 C0883       0.001068757   0.41779361     Blautia hominis  C2806       0.00106737   0.227560508     Fusobacterium nucleatum  C2023       0.001063571   −0.005996163     Alistipes  sp. Marseille-P2431 C1656       0.001046414   −0.131247999     Christensenella  sp. Marseille-P3954 C3290       0.001046021   0.073482048     Blautia hydrogenotrophica  C2163       0.001034582   0.033741303     Escherichia coli  C6189       0.001034232   0.000419447     Bacteroides plebeius  C0183       0.001033161   0.037947008     Eubacterium limosum  C2585       0.001031559   0.231894983     Bacteroides  sp. NM69_E16B C1512       0.00102259   −0.332512425     Olsenella  sp. Marseille-P4518 C1983       0.001019694   −0.164199636     Lachnoanaerobaculum saburreum  C2233       0.001017125   −0.206044424     Clostridium  sp. AF20-17LB C2921       0.001013385   −0.159145062     Bifidobacterium angulatum  C0006       0.001011242   −0.124685694     Coprococcus  sp. OM04-5BH C2951       0.001010502   0.199924075     Bacteroides caecimuris  C0768       0.001005476   −0.054514013     Paramuribaculum intestinale  C1027       0.001002001   0.065282268     Bacteroides eggerthii  C0137       0.001001469   −0.069431173     Pseudoflavonifractor  sp. An44 C2769       0.00100062   0.224179803     Bacteroides togonis  C1815       0.000998879   −0.079349954     Enterorhabdus caecimuris  C1946       0.000996811   −0.035659589     Butyricicoccus pullicaecorum  C2367       0.000996394   0.119454752   Lachnospiraceae bacterium KGMB03038 C3054       0.000988689   −0.095646493     Clostridium  sp. SY8519 C2300       0.00098773   −0.244190108     Bifidobacterium ruminantium  C0033       0.000983787   0.167974308     Veillonella dispar  C2172       0.000981089   0.009434997     Faecalibacterium  sp. An122 C2768       0.000971714   −0.078320362     Paraeggerthella hongkongensis  C1991       0.000970657   −0.061838315     Bacteroides faecichinchillae  C0462       0.000970589   −0.100958093     Veillonella seminalis  C2333       0.000966201   −0.203389419     Anaerofustis stercorihominis  C3043       0.000965329   −0.127606155     Gabonia massiliensis  C0573       0.000958921   0.097531327   Lachnospiraceae bacterium C7401       0.000955835   0.220644706   Clostridia bacterium UC5.1-1D10 C2630       0.000946293   −0.119032203     Parabacteroides acidifaciens  C1178       0.000939111   −0.491867958     Collinsella  sp. TM05-38 C1984       0.000937568   0.238492033     Veillonella parvula  C2108       0.000932801   0.088210302     Gemmiger  sp. An50 C2791       0.000932461   0.080276705     Bacteroides pyogenes  C0391       0.000932048   0.20638792     Lachnoclostridium  sp. An76 C2789       0.000931273   −0.417870861     Faecalibacterium prausnitzii  C2650       0.00093091   0.034378724     Drancourtella  sp. An57 C2780       0.000930578   −0.057174001     Desulfovibrio  sp. G11 C3781       0.000927044   0.214918452     Faecalicatena orotica  C2855       0.000926301   0.080750766   [ Ruminococcus ]  torques  C2130       0.000924352   −0.052296196     Coprobacillus cateniformis  C2235       0.000924235   −0.30548312     Prevotella stercorea  C0227       0.000922776   0.214718723     Enterobacter asburiae  C4744       0.000921102   0.275685331     Streptococcus lutetiensis  C4617       0.000908652   −0.209498347     Bacteroides massiliensis  C0310       0.000902209   0.024387818     Anaerofustis stercorihominis  C2147       0.000897276   −0.417096051     Senegalimassilia anaerobia  C1940       0.000895988   0.122269666     Clostridium cadaveris  C2409       0.000894405   −0.129710456     Eubacterium coprostanoligenes  C3232       0.000892552   0.092455818     Streptococcus infantarius  subsp.  infantarius  CJ18 C4334       0.000889081   −0.157473973   Clostridiales bacteriumMarseille-P2846 C3254       0.000885777   0.084144866     Lachnoclostridium  sp. An169 C2774       0.000885709   −0.011837149     Bacteroides fragilis  C0096       0.000885092   −0.096838499     Intestinibacter bartlettii  C2141       0.000884226   0.102943242     Absiella dolichum  C2133       0.000879993   0.276721768     Bacteroides intestinalis  C1222       0.000874022   −0.176033978   Lachnospiraceae bacterium OF09-6 C2885       0.000871852   0.11799681     Lachnoclostridium edouardi  C3267       0.000867157   0.03000888     Bacteroides timonensis  C0434       0.000859738   −0.191448288   [ Clostridium ]  spiroforme  C2146       0.000854106   0.032964866     Streptococcus  sp. I-G2 C4650       0.000852642   0.193752289   [ Clostridium ]  clostridioforme  C2275       0.000850375   −0.107533876     Alistipes ihumii  AP11 C0292       0.00084566   0.029668283   [ Clostridium ]  innocuum  C2230       0.000841331   −0.182746209     Leuconostoc lactis  C5492       0.000837107   −0.148687377     Lactococcus lactis  C3409       0.000833791   0.075233896     Bifidobacterium gallinarum  C0040       0.000832892   −0.052348168     Lachnospira pectinoschiza  C2649       0.000819471   0.044124824     Clostridium tertium  C2166       0.000818078   0.013262705     Bacteroides gallinarum  C0320       0.000816004   −0.007624252     Gardnerella vaginalis  C0077       0.000814064   0.124276378     Candidatus Stoquefichus  sp. KLE1796 C2685       0.000810143   −0.077567242     Megamonas funiformis  C2294       0.000806911   −0.216211462     Eubacterium  sp. TM05-53 C2895       0.000805937   −0.10501558     Roseburia hominis  C2266       0.00080548   0.160289033     Actinomyces naeslundii  C5308       0.00080031   −0.040410654     Clostridium  sp. M62/1 C2168       0.000794225   0.016679858   Lachnospiraceae bacterium OF09-33XD C2950       0.000784244   0.025757522     Mediterranea massiliensis  C1792       0.000783028   −0.473565196     Collinsella bouchesdurhonensis  C1956       0.000780365   0.18073776     Parabacteroides distasonis  C1282       0.000776777   −0.066719417     Alistipes  sp. cv1 C1225       0.000775056   0.215608385     Lactobacillus paragasseri  C5843       0.000774821   0.106290282     Enterococcus faecalis  C3356       0.000770822   0.044316403     Emergencia timonensis  C2919       0.000770705   0.007621492     Muribaculum  sp. An287 C0841       0.000765772   −0.039039051     Candidatus Stoquefichus  sp. SB1 C2613       0.000764151   0.149737605     Haemophilus parainfluenzae  C6724       0.000758758   −0.139580633     Acidaminococcus fermentans  C2110       0.000758604   0.014886565     Streptococcus  sp. A12 C5358       0.000757928   0.103430739     Ruminococcus  sp. JE7A12 C3041       0.000757477   0.124922464     Anaeroglobus geminatus  F0357 C2283       0.000752717   0.201105928     Bacteroides  sp. An322 C0849       0.000750886   0.092991853     Klebsiella aerogenes  C4223       0.00074905   −0.151453151   Firmicutes bacterium AM43-11BH C2910       0.00074725   0.319641701     Citrobacter freundii  C4862       0.000746863   0.019294667   Lachnospiraceae bacterium C2825       0.000744408   0.024367545     Collinsella stercoris  DSM 13279 C1930       0.000742398   −0.069413745     Alistipes inops  C0554       0.000740749   0.074724867     Staphylococcus aureus  C3394       0.000737647   0.166740913     Pseudoflavonifractor  sp. AF19-9AC C2939       0.000734243   0.047494987     Bifidobacterium breve  C0007       0.000733278   −0.106066732     Asaccharobacter celatus  C1952       0.000733193   0.200658318     Bacteroides thetaiotaomicron  C0098       0.000732128   0.006225001     Streptococcus mitis  C5142       0.000731863   −0.123724955     Lactobacillus acidophilus  C3484       0.000727884   −0.197342794     Subdoligranulum variabile  DSM 15176 C2162       0.000725883   −0.32980633     Turicibacter sanguinis  C2647       0.000724945   0.024395901     Lactobacillus curvatus  C5454       0.000721941   −0.116696596     Roseburia inulinivorans  C2207       0.000719454   0.14576632     Agathobaculum desmolans  ATCC 43058 C2531       0.000719137   0.061521208     Eisenbergiella  sp. OF01-20 C2932       0.000717609   −0.008006904     Lawsonibacter asaccharolyticus  C2612       0.000716353   −0.27637531     Coprococcus catus  C2881       0.000714658   −0.235792289     Faecalibacterium prausnitzii  C2864       0.000713496   0.044440911     Bacteroides fluxus  YIT 12057 C0196       0.000709063   0.057843542   Ruminococcaceae bacterium Marseille-P2935 C3117       0.000708861   0.132034289     Lactobacillus casei  C4934       0.000706391   −0.223572419     Faecalibacterium prausnitzii  C2191       0.00070492   0.178244024     Escherichia coli  C3313       0.000702873   −0.053059381     Prevotella lascolaii  C1655       0.000699434   −0.068127523     Christensenella timonensis  C3068       0.000695606   −0.191454148     Streptococcus thermophilus  C3480       0.00068995   −0.007031037     Dielma fastidiosa  C2331       0.000689289   0.054494897     Faecalitalea  sp. Marseille-P3755 C3257       0.000689111   −0.231345103     Dialister succinatiphilus  YIT 11850 C2287       0.000687764   −0.101689367     Chitinophaga  sp. K20C18050901 C1205       0.000683105   −0.18109626     Bifidobacterium longum  C0000       0.000681336   0.121849135     Streptococcus australis  C7313       0.000680574   −0.255797065     Clostridium cuniculi  C3022       0.000675816   −0.101093017   Clostridiales bacterium KA00274 C2670       0.0006733   0.066007328     Erysipelatoclostridium  sp. An173 C2772       0.000667452   0.055143325     Pseudoflavonifractor  sp. Marseille-P3106 C3237       0.000666343   0.27979269     Lachnoclostridium  sp. An131 C2777       0.000663042   −0.127290782     Ruminococcus  sp. AF41-9 C2929       0.000659973   0.094285428     Shuttleworthia  sp. MSX8B C2176       0.00065507   0.110634228     Methanobrevibacter smithii  C3636       0.000649624   −0.078446486     Butyricimonas faecihominis  C1324       0.000647276   0.05887023     Massilimicrobiota timonensis  C2778       0.000646901   0.137638451     Bacteroides barnesiae  C0323       0.0006433   −0.134246508   Victivallales bacterium CCUG 44730 C6246       0.000640184   0.122380223     Haemophilus parainfluenzae  C6455       0.000636883   0.064289399     Akkermansia muciniphila  C1920       0.000632492   −0.308227618     Catabacter hongkongensis  C2600       0.000630493   −0.363573867     Bacteroides bouchesdurhonensis  C1842       0.000622319   −0.014535125     Prevotella  sp. P3-122 C0877       0.000619871   0.0165477     Roseburia  sp. 831b C2726       0.000615916   −0.163514198     Sutterella megalosphaeroides  C6522       0.000614283   −0.082835345   Erysipelotrichaceae bacterium 3_1_53 C2188       0.000614281   0.013021903     Holdemania filiformis  C2164       0.000613954   0.059841271     Alistipes  sp. Marseille-P5997 C0839       0.00060878   0.148711311     Blautia coccoides  C2701       0.000597168   −0.02417881     Clostridium  sp. BSD2780061688st1 E8 C3045       0.000594817   −0.17197938     Mogibacterium diversum  C2838       0.000591669   0.038151561     Fusobacterium ulcerans  C2030       0.000588198   0.24254803     Enterobacter cloacae  C3869       0.000587106   0.027112536     Monoglobus pectinilyticus  C2823       0.000581387   0.090800994     Prevotella oris  C0118       0.000576756   0.144277974     Veillonella tobetsuensis  C2607       0.000574411   −0.155129298     Kandleria vitulina  C2503       0.00057406   0.021398815     Negativibacillus massiliensis  C3220       0.0005648   −0.270611264   [ Eubacterium ]  eligens  C2123       0.000561479   −0.00147982     Fournierella massiliensis  C2661       0.000557105   0.017814008     Agathobacter ruminis  C2528       0.000554427   0.126947262     Acetitomaculum ruminis  DSM 5522 C3147       0.000551557   −0.119643009     Parolsenella catena  C1992       0.000546323   0.093101738     Alistipes  sp. An31A C0840       0.000544823   0.100984449     Slackia piriformis  YIT 12062 C1942       0.000542329   0.084136379     Pseudoflavonifractor  sp. An85 C2787       0.000541822   0.150927143     Enterococcus faecium  C4060       0.000536091   −0.257161011     Faecalitalea cylindroides  C2250       0.000528743   −0.065393049     Lactobacillus sanfranciscensis  TMW 1.1304 C4264       0.000525582   −0.129615434     Absiella  sp. AM22-9 C2879       0.000524183   0.15556154     Streptococcus mitis  C5322       0.00052379   −0.131464448     Streptococcus mitis  C3901       0.000521696   −0.005526656     Butyricimonas virosa  C0441       0.000521234   0.161136825     Agathobaculum  sp. Marseille-P7918 C3297       0.000520468   0.079408986     Bacteroides intestinalis  C0161       0.000517736   −0.007357649     Senegalimassilia  sp. KGMB04484 C1994       0.000515789   0.116997696     Anaeromassilibacillus  sp. An172 C2773       0.000513282   −0.22188977     Anaeromassilibacillus  sp. Marseille-P4683 C3061       0.000507316   −0.160416981     Clostridium  sp. Marseille-P3244 C3177       0.00050396   0.078131194     Rothia mucilaginosa  C3456       0.000501417   0.027192943     Candidatus Methanomassiliicoccus intestinalis  Issoire-               Mx1 C4599       0.000499738   0.0174744     Anaerostipes  sp. 494a C2731       0.000498341   −0.029178099     Paraeggerthella hongkongensis  C1982       0.000496569   −0.032045271     Lactococcus garvieae  C6016       0.000494032   0.057726242     Eubacterium  sp. AF19-12LB C2907       0.000491168   0.033329345   Lachnospiraceae bacterium oral taxon 096 C2846       0.000491138   −0.14106364     Prevotella intermedia  C0255       0.000483914   0.076399152     Bacteroides  sp. OM05-12 C1216       0.000478931   −0.12999452     Propionibacterium freudenreichii  C3941       0.000478583   −0.216633597     Oxalobacter formigenes  C5820       0.000473254   0.13675923     Eubacterium  sp. ER2 C2579       0.000472977   −0.15732306     Alistipes indistinctus  C0222       0.00047013   −0.01796799     Traorella massiliensis  C3119       0.000463894   −0.134877322     Weissella cibaria  C5172       0.000461977   0.043780038     Prevotella pleuritidis  C0414       0.000461965   0.379126295     Citrobacter  sp. FDAARGOS_156 C5320       0.000458829   −0.103085248   [ Collinsella ]  massiliensis  C1944       0.000455848   −0.216482839     Alloscardovia omnicolens  C0021       0.000454098   −0.101700886     Bacteroides ilei  C1793       0.000452132   0.27056853     Dialister  sp. Marseille-P5638 C3282       0.000447852   0.21438821     Christensenella massiliensis  C3223       0.000446473   0.089598965     Bacteroides cutis  C1215       0.000442533   −0.125406142     Prevotella  sp. P4-51 C0876       0.0004413   0.013913335     Bacteroides coprosuis  DSM 18011 C0203       0.000440392   0.228587525     Lachnoclostridium phocaeense  C3180       0.000438656   0.057515059     Ruminococcus bromii  C2818       0.000435684   0.170474597     Prevotella copri  C0142       0.000434472   0.278015777     Enterobacter kobei  C4431       0.000430769   0.15735214     Clostridioides difficile  C2586       0.000429829   0.275828056     Collinsella phocaeensis  C2002       0.000427367   0.069690121   Muribaculaceae bacterium Isolate-102 (HZI) C1306       0.000425447   0.254830162   [ Clostridium ]  scindens  C2446       0.000425124   0.07985737     Enterobacter roggenkampii  C4889       0.000424989   0.039030901     Erysipelatoclostridium  sp. AM42-17 C2927       0.000422993   −0.009708183     Weissella confusa  C6837       0.000421896   −0.083440639     Bacteroides fragilis  C0140       0.000421212   0.151608309     Anaerotruncus massiliensis  C2969       0.00041345   −0.066234762     Parabacteroides goldsteinii  C0282       0.000409746   −0.008970984     Anaerotruncus  sp. AF02-27 C2916       0.000408594   −0.076490222     Akkermansia  sp. KLE1605 C1918       0.000408035   −0.013734886     Butyricimonas  sp. Marseille-P3923 C1885       0.000404935   −0.12049091     Prevotella buccalis  C0169       0.00040246   0.105160049     Merdimonas faecis  C2715       0.000402431   −0.118683458     Streptococcus suis  C3679       0.000399456   0.167898284     Klebsiella oxytoca  C5296       0.00039537   0.140861068     Colibacter massiliensis  C3075       0.000394389   −0.099002939     Leclercia  sp. W6 C6193       0.000389717   −0.047195465     Bifidobacterium pseudolongum  C0023       0.000385746   0.137224213   Clostridiaceae bacterium OM02-2AC C2883       0.000376658   −0.006154069     Odoribacter splanchnicus  C0185       0.000376547   0.132471129     Lactobacillus crispatus  C3942       0.000372155   0.077170538     Clostridium liquoris  C2835       0.000371344   −0.013289801     Prevotella shahii  C0456       0.000369066   0.058668971     Prevotella buccae  C0148       0.000368916   −0.151810317     Carnobacterium divergens  C5502       0.000365348   0.037280739     Intestinimonas massiliensis  C3302       0.000362723   0.096694087     Megasphaera  sp. MJR8396C C2669       0.000362664   −0.209757142     Lactococcus lactis  C3326       0.000359275   0.013743499     Ruminococcus gauvreauii  DSM 19829 C2421       0.000354446   −0.067786957     Megasphaera  sp. NM10 C2382       0.000354236   −0.101587608     Lactobacillus sakei  C3886       0.000349708   0.052923252     Fusobacterium varium  C2031       0.000349377   0.12801912     Raoultella ornithinolytica  C4582       0.000342204   −0.224210946     Clostridium  sp. CL-2 C2570       0.000339415   −0.018984193     Schaalia odontolytica  C6913       0.000336634   0.085134208   [ Clostridium ]  aminophilum  C2554       0.000318155   0.079087407     Escherichia  sp. E4742 C6917       0.000317742   −0.111845972     Porphyromonas  sp. COT-290 OH860 C0549       0.000316438   −0.129465239     Criibacterium bergeronii  C2703       0.00031524   −0.151761323     Gardnerella vaginalis  C0008       0.000313466   0.093860399     Citrobacter freundii  complex sp. CFNIH3 C5883       0.00031154   −0.030174898     Veillonella  sp. S13053-19 C2226       0.000305314   −0.019154943     Enterococcus casseliflavus  C4021       0.000301412   −0.028685455     Clostridium paraputrificum  C2404       0.000301347   0.135067509     Citrobacter amalonaticus  C5315       0.000299201   0.056396549     Peptoniphilus harei  C2229       0.000295876   0.105606587     Lactobacillus reuteri  C3427       0.00029558   −0.087470002     Prevotella bivia  C0170       0.00029533   0.2944697     Massilimicrobiota  sp. An134 C2756       0.000292461   −0.16360222     Clostridium celatum  DSM 1785 C2336       0.000290231   −0.107393237     Eubacterium saphenum  ATCC 49989 C2183       0.000289466   0.098825501     Caproiciproducens galactitolivorans  C3034       0.000283388   0.088913554     Peptococcus niger  C3096       0.000281338   −0.199624188     Bacteroides  sp. Marseille-P3684 C1903       0.000280597   −0.35259961   [ Eubacterium ]  rectale  C2102       0.000278229   −0.123327354     Hungatella hathewayi  C2277       0.000275274   0.032280996     Raoultibacter timonensis  C2015       0.000274761   0.026049476     Bifidobacterium minimum  C0024       0.000274208   −0.250305123     Slackia isoflavoniconvertens  C1981       0.000272806   −0.148295608     Prevotella  sp. 109 C0642       0.000271138   0.085385438     Bacteroides ndongoniae  C1721       0.000270351   0.096334331     Sanguibacteroides justesenii  C0594       0.000268105   −0.092100556     Enterococcus  sp. M190262 C4628       0.000264389   0.028275689     Candidatus Soleaferrea massiliensis  AP7 C2589       0.000258394   0.095952069     Fusobacterium mortiferum  C2024       0.000257776   −0.123638868     Mitsuokella jalaludinii  C2546       0.000256938   −0.044689114     Haemophilus pittmaniae  C7263       0.000256376   0.057471563     Citrobacter koseri  C3675       0.000255931   0.098498867     Staphylococcus epidermidis  C3349       0.000255753   −0.157103426     Lachnotalea  sp. AF33-28 C2930       0.000249354   0.103829306     Streptococcus troglodytae  C6006       0.000247989   −0.04348123     Eubacterium nodatum  ATCC 33099 C2463       0.000237849   0.136436955     Bacteroides acidifaciens  C0454       0.000235895   0.025076982     Cloacibacillus porcorum  C5498       0.000234449   0.207586523     Desulfovibrio fairfieldensis  C5303       0.000232439   0.06389105     Citrobacter amalonaticus  Y19 C5026       0.000231523   0.21351164     Frisingicoccus caecimuris  C3012       0.000229189   0.116831596     Streptococcus equinus  C4630       0.000224376   −0.071274749     Enterobacter ludwigii  C4314       0.000223221   −0.001425117     Lachnospira multipara  C2406       0.000219577   −0.252448758     Comamonas kerstersii  C5760       0.000215028   −0.201289125     Odoribacter  sp. AF15-53 C1228       0.000212884   0.129978944     Clostridium ventriculi  C2645       0.000212879   0.012267554     Prevotella denticola  C0190       0.00021254   −0.090029408     Acidaminococcus timonensis  C3121       0.000209014   0.081821172     Pediococcus acidilactici  C5564       0.00020599   −0.091958501     Parabacteroides gordonii  C0394       0.000204627   −0.03219179     Salmonella bongori  C4344       0.000201044   0.046058989     Corynebacterium argentoratense  DSM 44202 C4728       0.000195048   −0.148177716     Ruminococcus  sp. Marseille-P6503 C3293       0.000193863   0.115675916     Veillonella atypica  C2224       0.000191688   0.075560921     Clostridium neonatale  C2656       0.000191566   0.059627079     Hafnia paralvei  C5321       0.000187799   0.004958554     Ruminococcus bromii  C3091       0.000187592   0.108114105     Megasphaera micronuciformis  F0359 C2190       0.000185989   0.049809679     Hafnia alvei  C4732       0.000184299   0.072305952     Clostridium  sp. Marseille-P8228 C3298       0.000182455   0.081144244     Salmonella enterica  C3691       0.000182401   0.040354086     Prevotella maculosa  C0236       0.000180958   0.045550681     Tetragenococcus halophilus  C4414       0.000180446   0.155453018   [ Clostridium ]  cocleatum  C2817       0.000175141   0.003197966     Ruminococcus flavefaciens  C3174       0.000175125   0.088990805     Clostridium  sp. CL-6 C2568       0.000173291   −0.017099749     Prevotella  sp. P5-125 C0597       0.000169963   −0.057233209     Pseudomonas fragi  C5503       0.00016916   −0.248823705     Leuconostoc gelidum  JB7 C4451       0.00016589   0.065183802     Cronobacter sakazakii  C3665       0.00016331   −0.208923621     Megasphaera elsdenii  C2304       0.000161384   0.067558754     Klebsiella oxytoca  C5056       0.000161379   0.13837813     Lactobacillus helveticus  C3606       0.000159676   −0.003463017     Pediococcus pentosaceus  C3572       0.000157298   0.144136167     Enterobacter hormaechei  C4773       0.000155828   −0.260724092     Roseburia  sp. AM59-24XD C2936       0.000151336   −0.292938975     Lactobacillus delbrueckii  C3568       0.000141557   0.076327611     Prevotella salivae  C0180       0.000131281   0.143665959     Lactobacillus amylovorus  C4089       0.000130941   −0.047422488     Lactobacillus ruminis  ATCC 27782 C4263       0.000130595   −0.04481037     Paraclostridium bifermentans  C2432       0.000129911   0.167682779     Escherichia albertii  C4681       0.000127495   0.04633969     Enterococcus durans  C5114       0.000127484   0.072529092     Cellulosilyticum  sp. WCF-2 C2221       0.000123473   0.173686087   Clostridiales bacterium S5-A14a C2574       0.000122727   −0.074297589     Blautia wexlerae  C2171       0.000121299   −0.053122344     Methanosphaera stadtmanae  DSM 3091 C3505       0.000120188   0.119050783     Clostridium  sp. MSTE9 C2303       0.000120039   −0.052843577     Clostridium disporicum  C2646       0.000116659   0.080030593     Lactobacillus johnsonii  C3366       0.000113997   0.104093107     Serratia marcescens  C4687       0.000113245   −0.00308721     Prevotella amnii  C0171       0.000107199   −0.022568473     Cronobacter condimenti  1330 C5129       0.000104701   0.000252647   Ruminococcaceae bacterium CPB6 C2750       0.000104084   0.066800683     Veillonella ratti  C2991       0.000102394   0.152599321     Bacteroides paurosaccharolyticus  JCM15092 C0457       9.37347E−05   0.174241239     Lactobacillus gasseri  C3569       8.56015E−05   0.059945469   [ Clostridium ]  hylemonae  C2157       7.75294E−05   0.1191171     Citrobacter amalonaticus  C5318       7.55257E−05   0.068345197     Bacteroides  sp. KCTC15687 C1337       6.75319E−05   0.006391049     Lactococcus garvieae  C4388       6.59076E−05   0.120223702     Faecalicoccus pleomorphus  C2383       6.45031E−05   0.097753343     Lactobacillus animalis  C6895       5.21062E−05   0.149698537     Anaerostipes rhamnosivorans  C3039       4.42633E−05   −0.007497948     Enterobacter bugandensis  C5325       4.37847E−05   0.032643624     Lactobacillus mucosae  LM1 C4338       4.32409E−05   0.065872962     Bacteroides propionicifaciens  C0324       0   0.078372213     Streptococcus sobrinus  C6344       0   −0.064034551   Ruminococcaceae bacterium D5 C3161       0   0.015908673     Ruminococcus albus  C3136       0   0.070235779     Selenomonas noxia  C2179       0   0.102015151     Citrobacter werkmanii  C4750       0   0.106931981     Providencia rettgeri  C6875       0   −0.08278651     Anaerococcus lactolyticus  C2159       0   0.026978526     Ruminococcus  sp. FC2018 C2499       0   0.040473615     Robinsoniella peoriensis  C2512       0   −0.153859627     Megasphaera hexanoica  C2664       0   0.005437415     Atlantibacter hermannii  C7332       0   −0.050219427     Megasphaera  sp. AM44-1BH C2918       0   0.013360056     Clostridium  sp. 12(A) C2475       0   −0.075062059     Eggerthella sinensis  C1979       0   0.029503909     Proteus vulgaris  C6084       0   0.020972769   Plautia stall symbiont C4087       0   −0.009219528     Bacteroides graminisolvens  C0392       0   0.034902834     Providencia rettgeri  C4489       0   −0.072959896     Candidatus Ishikawaella capsulata  Mpkobe C4922       0   −0.060674729   secondary endosymbiont of  Ctenarytaina eucalypti  C4438       0   0.000740595     Shimwellia blattae  C4368       0   0.042068637     Bacteroides reticulotermitis  JCM 10512 C0437       0   0.134402606     Proteus mirabilis  C3929       0   0.085291723     Peptoclostridium  sp. AF21-18 C2156       0   0.071303376   Bacteroidales bacterium KA00251 C0708       0   0.044896419     Klebsiella  sp. PO552 C5864       0   −0.020350527     Cronobacter universalis  NCTC 9529 C5126       0   0.042060758     Lelliottia jeotgali  C5960       0   0.010010498     Pseudomonas balearica  DSM 6083 C4912       0   0.069859304     Fusobacterium nucleatum  C2036       0   −0.098855648     Mitsuokella  sp. AF21-1AC C2899                    
Table 5, illustrated as  FIG.  18   . Flow cytometry was performed on 38 cancer blood samples and 38 control blood samples, along with corresponding whole genome sequencing and classification. All operational species unit (OSU) abundances were correlated against a suite of immune markers (CD11b+, CD14+CD15−, CD14-CD15+, CD15+CD14−, CD15-CD14+, CD3+, CD3+CD56+, CD3+HLADR+, CD3-CD56+, CD3-HLA-DR+, CD3-HLA-DRlow, CD4+, CD4+HLA-DR+, CD8+, CD8+HLA-DR+, Foxp3+). Correlations and p values were computed on all the samples, or on a subset of samples consisting of just control samples or just cancer samples. The p values obtained from all the samples were filtered using a two-stage Benjamini-Hochberg procedure and correlated with an adjusted p value below 0.15 are reported.
 
Table 6, illustrated in  FIG.  19   . Flow cytometry was performed on 38 cancer blood samples and 38 control blood samples, along with corresponding whole genome sequencing and classification. All operational species units (OSUs) were correlated against the CD3+ and CD3+CD56+ immune markers (as a subset of CD45+) using a Spearman rank correlation. Adjusted p values were computed using a two-stage Benjamini-Hochberg procedure for each immune marker, and correlations with an adjusted p value below 0.2 are retained. The retained correlations were further vetted using a linear mixed model that accounts for a random effect induced by group (cancer vs. control). The logarithm of the OSU abundance was used as the input to the model. For CD3+CD56+, the logarithm of the immune marker proportion was used as the output of the mixed model. The mixed model p values and coefficients are reported.
 
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Whole genome sequencing was performed on the initial time point fecal samples from subjects undergoing 
               
               
                 cancer immunotherapy and the reads were classified and abundance of each operational species unit 
               
               
                 was estimated computationally. Operational species unit abundances were correlated to response 
               
               
                 to therapy using a score of 2 for complete response, 1 for partial response, 0 for no response, 
               
               
                 using the Spearman rank correlation. Correlations with a p value below 0.15 are reported. 
               
            
           
           
               
               
               
               
               
            
               
                 Mean Abundance 
                 p value 
                 Spearman 
                 Organism 
                 Adjusted p value 
               
               
                 (All Samples) 
                 (Spearman rank) 
                 Correlation 
                 (Operational Species Unit) 
                 (Two Stage BH) 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 0.004824863 
                 0.009065354 
                 −0.460919277 
                   Bacteroides barnesiae  C0323 
                 0.50270646 
               
               
                 0.001854242 
                 0.011550331 
                 −0.447714196 
                   Streptococcus mutans  C3345 
                 0.50270646 
               
               
                 0.002592642 
                 0.013008588 
                 −0.441044685 
                   Lactobacillus fermentum  C3433 
                 0.50270646 
               
               
                 0.003900899 
                 0.01697159 
                 −0.425648294 
                   Bacteroides heparinolyticus  C1005 
                 0.50270646 
               
               
                 0.011114361 
                 0.020991328 
                 0.412834447 
                   Bacteroides coprosuis  DSM 18011 C0203 
                 0.50270646 
               
               
                 0.001347612 
                 0.021974899 
                 −0.410011686 
                   Blautia obeum  C2901 
                 0.50270646 
               
               
                 0.005138808 
                 0.022206972 
                 −0.409360874 
                   Streptococcus vestibularis  C7338 
                 0.50270646 
               
               
                 0.004109069 
                 0.028915901 
                 −0.392598094 
                   Streptococcus thermophilus  C3480 
                 0.50270646 
               
               
                 0.002625559 
                 0.029553117 
                 0.391177567 
                   Bacteroides eggerthii  C0137 
                 0.50270646 
               
               
                 0.00180933 
                 0.029570968 
                 −0.391138132 
                   Streptococcus  sp. HSISS2 C4629 
                 0.50270646 
               
               
                 0.006421035 
                 0.045485127 
                 −0.361828833 
                   Bacteroides coprocola  C0136 
                 0.702951961 
               
               
                 0.00479161 
                 0.066985005 
                 −0.333215846 
                   Lachnospira pectinoschiza  C2649 
                 0.884186581 
               
               
                 0.001357573 
                 0.067614268 
                 −0.332494913 
                   Lactobacillus paragasseri  C5843 
                 0.884186581 
               
               
                 0.002942156 
                 0.074018907 
                 −0.325438908 
                   Escherichia coli  C3313 
                 0.894382098 
               
               
                 0.001499661 
                 0.089187848 
                 −0.310437419 
                   Intestinibacter bartlettii  C2141 
                 0.894382098 
               
               
                 0.001315245 
                 0.090931568 
                 −0.308841524 
                   Lactococcus lactis  C3409 
                 0.894382098 
               
               
                 0.000593797 
                 0.093500218 
                 0.306532546 
                   Anaerotignum lactatifermentans  C2790 
                 0.894382098 
               
               
                 0.001096895 
                 0.100936329 
                 −0.300108932 
                   Bifidobacterium dentium  C0003 
                 0.894382098 
               
               
                 0.001297862 
                 0.101670448 
                 0.2994944 
                   Odoribacter splanchnicus  C0185 
                 0.894382098 
               
               
                 0.002123253 
                 0.113189533 
                 −0.290262241 
                   Faecalimonas umbilicata  C2244 
                 0.894382098 
               
               
                 0.014086171 
                 0.120986249 
                 0.284404931 
                   Faecalibacterium prausnitzii  C2138 
                 0.894382098 
               
               
                 0.001420926 
                 0.123671567 
                 0.282452495 
                   Tyzzerella nexilis  C2155 
                 0.894382098 
               
               
                 0.000841219 
                 0.131047516 
                 0.277245997 
                   Clostridiales bacterium  CCNA10 C2953 
                 0.894382098 
               
               
                 0.001049951 
                 0.132465355 
                 −0.276270029 
                   Clostridium disporicum  C2479 
                 0.894382098 
               
               
                 0.000534773 
                 0.1330099 
                 0.275897229 
                   Gordonibacter pamelaeae  C1937 
                 0.894382098 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Operational species units (OSUs) with a mean abundance of at least 0.05% with significant differences between cancer and 
               
               
                 control cohorts for inclusion into the therapeutic. For each OSU, CD3+ and CD3+ CD56+ correlations are 
               
               
                 included in the table as per the linear mixed model analysis or set to zero if the mixed model correlation is negative 
               
               
                 or if the Spearman correlation was not significant enough to necessitate mixed model analysis. The cancer and control 
               
               
                 fold change, CD3+ correlation, and CD3+ CD56+ correlation for each OSU were converted to percentile scores, 
               
               
                 and a combined score for each OSU was generated as the geometric mean of each of the three percentiles. 
               
               
                 Table 8 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                 CD3+ 
                 CD3+ CD56+ 
                   
               
               
                 p value 
                   
                   
                 Correlation 
                 Correlation 
                   
               
               
                 Control vs Cancer 
                 log10 Fold Change 
                 Organism Name 
                 (Spearman, if 
                 (Spearman, if 
                   
               
               
                 (Mann Whitney U) 
                 (Cancer/ Control) 
                 (Operational Species Unit) 
                 significant) 
                 significant) 
                 Total Score 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 1.13356E−08 
                 −0.764382216 
                 Erysipelotrichaceae bacterium GAM147 C2844 
                 0.417881066 
                 0.481640465 
                 99.3759725 
               
               
                 0.000236114 
                 −0.432405099 
                   Dorea  sp. AM58-8 C2913 
                 0.395242652 
                 0.415256323 
                 94.53854775 
               
               
                 0.000111496 
                 −0.304525941 
                 [ Ruminococcus ]  torques  C2636 
                 0.282433356 
                 0.290799727 
                 81.68743735 
               
               
                 4.96202E−05 
                 −0.504914016 
                   Blautia obeum  C2129 
                 0.441968558 
                 0 
                 75.35264806 
               
               
                 1.19211E−05 
                 −0.565340143 
                 Firmicutes bacterium AF12-30 C2644 
                 0.279890636 
                 0 
                 73.10872098 
               
               
                  3.1747E−07 
                 −0.415683892 
                   Blautia  sp. AF19-10LB C2906 
                 0.3738098 
                 0 
                 71.5962122 
               
               
                 0.016231058 
                 −0.392581823 
                   Clostridium  sp. AF36-4 C2893 
                 0.39447635 
                 0 
                 71.56015136 
               
               
                 3.36506E−05 
                 −0.474788291 
                   Faecalibacterium prausnitzii  C2184 
                 0.277732589 
                 0 
                 71.19231957 
               
               
                 3.45381E−06 
                 −0.557690435 
                   Ruminococcus  sp. OF03-6AA C2904 
                 0.246561859 
                 0 
                 69.34836951 
               
               
                  1.9624E−05 
                 −0.436129729 
                   Dorea longicatena  C2413 
                 0.268680793 
                 0 
                 69.18884624 
               
               
                 0.013509112 
                 −0.452532206 
                   Bifidobacterium pseudocatenulatum  C0013 
                 0.256499594 
                 0 
                 69.12262094 
               
               
                 0.008426878 
                 −0.517722756 
                   Bifidobacterium bifidum  C0005 
                 0.239694858 
                 0 
                 68.55170178 
               
               
                 1.77058E−05 
                 −0.449283525 
                   Coprococcus comes  C2152 
                 0.245550239 
                 0 
                 67.24353586 
               
               
                 0.006074794 
                 −0.502954606 
                   Ruminococcus  sp. KGMB03662 C2557 
                 0.219878468 
                 0 
                 66.11567283 
               
               
                 0.00457584 
                 −0.312675608 
                   Clostridium  sp. OF10-22XD C2132 
                 0.320929597 
                 0 
                 65.97044298 
               
               
                 0.003783812 
                 −0.358288898 
                   Faecalibacterium prausnitzii  C2138 
                 0.249514696 
                 0 
                 65.6229349 
               
               
                 0.015331343 
                 −0.34579043 
                 Firmicutes bacterium AF25-13AC C2695 
                 0.257170198 
                 0 
                 65.61067466 
               
               
                 0.01271148 
                 −0.27637531 
                   Coprococcus catus  C2881 
                 0.35595352 
                 0 
                 65.4138845 
               
               
                 0.000860995 
                 −0.417870861 
                   Faecalibacterium prausnitzii  C2650 
                 0.237566644 
                 0 
                 65.21900583 
               
               
                 0.51444269 
                 −0.130545436 
                   Gemmiger formicilis  C3234 
                 0.27442242 
                 0.283691046 
                 64.00839092 
               
               
                 0.014929144 
                 −0.247491324 
                   Oscillibacter  sp. ER4 C2580 
                 0.362077922 
                 0 
                 63.36416394 
               
               
                 0.001048844 
                 −0.353929055 
                   Anaerostipes hadrus  C2144 
                 0.224716336 
                 0 
                 63.19608844 
               
               
                 0.019540986 
                 −0.319221468 
                   Ruminococcus lactaris  C2149 
                 0 
                 0.37621326 
                 61.28393922 
               
               
                 0.013186687 
                 −0.224153342 
                   Eubacterium ventriosum  C2128 
                 0.32683527 
                 0 
                 59.96015726 
               
               
                 0.002439804 
                 −0.251539605 
                   Blautia luti  C2436 
                 0.251838688 
                 0 
                 59.70580459 
               
               
                 0.039249769 
                 −0.240687636 
                   Anaerobutyricum hallii  C3263 
                 0.255775803 
                 0 
                 58.66605169 
               
               
                 0.018826044 
                 −0.257161011 
                   Faecalitalea cylindroides  C2250 
                 0 
                 0.322093794 
                 58.53674188 
               
               
                 0.03257254 
                 −0.230812001 
                   Dorea formicigenerans  C2197 
                 0 
                 0.383267259 
                 56.61344825 
               
               
                 0.29746277 
                 −0.106066732 
                   Asaccharobacter celatus  C1952 
                 0.219961719 
                 0.298085866 
                 55.95335448 
               
               
                 0.386245537 
                 −0.224535064 
                   Barnesiella intestinihominis  C0275 
                 0.239107807 
                 0 
                 55.71314544 
               
               
                 0.717556152 
                 −0.160088535 
                   Alistipes putredinis  DSM 17216 C0133 
                 0.306064417 
                 0 
                 53.10583588 
               
               
                 3.44484E−05 
                 −0.516206872 
                   Dorea longicatena  C2131 
                 0 
                 0 
                 52.8235779 
               
               
                 0.005503739 
                 −0.476696467 
                   Collinsella aerofaciens  C1933 
                 0 
                 0 
                 52.30053782 
               
               
                  7.0925E−05 
                 −0.442770588 
                   Dorea  sp. OM07-5 C2890 
                 0 
                 0 
                 51.58644796 
               
               
                 0.08814635 
                 −0.14769711 
                   Clostridium  sp. AF23-8 C2908 
                 0.272672591 
                 0 
                 51.08317009 
               
               
                 0.00646676 
                 −0.421426117 
                   Anaerobutyricum hallii  C2206 
                 0 
                 0 
                 51.03761433 
               
               
                 0.026898361 
                 −0.165551333 
                 [ Clostridium ]  amygdalinum  C2887 
                 0 
                 0.37771702 
                 50.67666817 
               
               
                 0.577485114 
                 −0.11819143 
                   Eubacterium  sp. OM08-24 C2896 
                 0.285831465 
                 0 
                 50.55687075 
               
               
                 0.009817398 
                 −0.391815999 
                   Romboutsia timonensis  C3123 
                 0 
                 0 
                 50.28695213 
               
               
                 0.011792583 
                 −0.36246911 
                   Faecalibacterium prausnitzii  C2651 
                 0 
                 0 
                 50.09574515 
               
               
                 0.004344805 
                 −0.352856347 
                   Ruminococcus callidus  C2440 
                 0 
                 0 
                 49.51318366 
               
               
                 0.016312939 
                 −0.35259961 
                 [ Eubacterium ]  rectale  C2102 
                 0 
                 0 
                 49.31591789 
               
               
                 0.001239483 
                 −0.344627962 
                   Blautia  sp. TF11-31AT C2841 
                 0 
                 0 
                 48.91658119 
               
               
                 0.233152423 
                 −0.335185925 
                   Bifidobacterium adolescentis  C0001 
                 0 
                 0 
                 48.71444425 
               
               
                 0.019421399 
                 −0.326716726 
                   Subdoligranulum  sp. APC924/74 C2870 
                 0 
                 0 
                 48.51061574 
               
               
                 0.035937114 
                 −0.32340108 
                   Ruminococcus  sp. AM42-11 C2945 
                 0 
                 0 
                 48.30505982 
               
               
                 0.00812493 
                 −0.322415354 
                   Blautia  sp. KGMB01111 C3003 
                 0 
                 0 
                 48.09773941 
               
               
                 0.097361497 
                 −0.321124776 
                   Clostridium disporicum  C2479 
                 0 
                 0 
                 47.88861616 
               
               
                 0.117266616 
                 −0.306056064 
                   Bacteroides heparinolyticus  C1005 
                 0 
                 0 
                 47.25002508 
               
               
                 0.038561827 
                 −0.305064647 
                 Firmicutes bacterium TM09-10 C2909 
                 0 
                 0 
                 47.0332788 
               
               
                 0.269625863 
                 −0.114661776 
                   Bifidobacterium animalis  C0002 
                 0.248008991 
                 0 
                 47.00940403 
               
               
                 0.188811422 
                 −0.270611264 
                 [ Eubacterium ]  eligens  C2123 
                 0 
                 0 
                 46.37075 
               
               
                 0.023532312 
                 −0.26283664 
                   Clostridium  sp. AM49-4BH C2934 
                 0 
                 0 
                 46.14564573 
               
               
                 0.555562154 
                 −0.10501558 
                   Roseburia hominis  C2266 
                 0.267204375 
                 0 
                 46.03382224 
               
               
                 0.187155428 
                 −0.260724092 
                   Roseburia  sp. AM59-24XD C2936 
                 0 
                 0 
                 45.91832359 
               
               
                 0.326490078 
                 −0.116696596 
                   Roseburia inulinivorans  C2207 
                 0 
                 0.286753247 
                 45.8451976 
               
               
                 0.001936194 
                 −0.255666512 
                   Faecalibacterium  sp. AF28-13AC C2810 
                 0 
                 0 
                 45.45680166 
               
               
                 0.005147868 
                 −0.246601387 
                   Agathobaculum butyriciproducens  C2850 
                 0 
                 0 
                 44.74642259 
               
               
                 0.009668016 
                 −0.242001524 
                   Faecalibacterium prausnitzii  C2863 
                 0 
                 0 
                 44.50454531 
               
               
                 0.23748252 
                 −0.094755491 
                   Anaeromassilibacillus  sp. Marseille-P3876 C2925 
                 0.353693881 
                 0 
                 44.32727446 
               
               
                 0.553126103 
                 −0.098634411 
                   Roseburia intestinalis  C2158 
                 0.270102529 
                 0 
                 44.05697948 
               
               
                 0.028683688 
                 −0.235792289 
                   Faecalibacterium prausnitzii  C2864 
                 0 
                 0 
                 44.01274212 
               
               
                 0.01512723 
                 −0.229970619 
                 Firmicutes bacterium AF22-6AC C2933 
                 0 
                 0 
                 43.5096953 
               
               
                 0.299408337 
                 −0.223572419 
                   Faecalibacterium prausnitzii  C2191 
                 0 
                 0 
                 42.73256973 
               
               
                 0.230520123 
                 −0.219463054 
                   Bacteroides finegoldii  C0138 
                 0 
                 0 
                 42.46714319 
               
               
                 0.07671217 
                 −0.209757142 
                   Lactococcus lactis  C3326 
                 0 
                 0 
                 42.1983566 
               
               
                 0.412393028 
                 −0.209498347 
                   Bacteroides massiliensis  C0310 
                 0 
                 0 
                 41.92610156 
               
               
                 0.004324117 
                 −0.206044424 
                   Clostridium  sp. AF20-17LB C2921 
                 0 
                 0 
                 41.65026396 
               
               
                 0.000839149 
                 −0.201826507 
                   Fusicatenibacter saccharivorans  C2643 
                 0 
                 0 
                 41.37072356 
               
               
                 0.171446365 
                 −0.192935162 
                   Clostridium  sp. AF46-9NS C2891 
                 0 
                 0 
                 41.08735355 
               
               
                 0.190921078 
                 −0.191454148 
                   Streptococcus thermophilus  C3480 
                 0 
                 0 
                 40.80002 
               
               
                 0.24012289 
                 −0.191448288 
                 [ Clostridium ]  spiroforme  C2146 
                 0 
                 0 
                 40.50858134 
               
               
                 0.238875443 
                 −0.189503492 
                   Holdemanella biformis  C2160 
                 0 
                 0 
                 40.21288772 
               
               
                 0.350722809 
                 −0.18109626 
                   Bifidobacterium longum  C0000 
                 0 
                 0 
                 39.91278036 
               
               
                 0.092953142 
                 −0.093698754 
                   Roseburia  sp. OM04-15AA C2892 
                 0.232754614 
                 0 
                 39.82976685 
               
               
                 0.511730372 
                 −0.167126002 
                 Firmicutes bacterium AF36-3BH C2905 
                 0 
                 0 
                 39.60809076 
               
               
                 0.002091197 
                 −0.163492912 
                   Clostridium  sp. AM18-55 C2845 
                 0 
                 0 
                 38.98423732 
               
               
                 0.044817697 
                 −0.161787704 
                   Ruminococcus  sp. AF31-8BH C2903 
                 0 
                 0 
                 38.66468002 
               
               
                 0.163286482 
                 −0.158568078 
                   Bacteroides stercoris  C0134 
                 0 
                 0 
                 38.00921984 
               
               
                 0.196410058 
                 −0.123209619 
                   Coprococcus eutactus  C2642 
                 0 
                 0 
                 36.98143604 
               
               
                 0.645760506 
                 −0.111096287 
                   Eisenbergiella tayi  C2259 
                 0 
                 0 
                 35.51525914 
               
               
                 0.247286492 
                 −0.107393237 
                   Eubacterium saphenum  ATCC 49989 C2183 
                 0 
                 0 
                 35.12919314 
               
               
                 0.194954789 
                 −0.103823837 
                   Eubacterium ramulus  C2442 
                 0 
                 0 
                 33.91686307 
               
               
                 0.072831555 
                 −0.103576385 
                   Bacteroides uniformis  C0132 
                 0 
                 0 
                 33.49285783 
               
               
                 0.568492801 
                 −0.100055999 
                 [ Eubacterium ]  siraeum  C2135 
                 0 
                 0 
                 33.05783641 
               
               
                 0.505564788 
                 −0.096838499 
                   Intestinibacter bartlettii  C2141 
                 0 
                 0 
                 32.15168231 
               
               
                 0.083226778 
                 −0.087543931 
                   Blautia obeum  C2901 
                 0 
                 0 
                 30.68817687 
               
               
                 0.025598358 
                 −0.081852178 
                   Ruminococcus  sp. AF24-32LB C2894 
                 0 
                 0 
                 30.16793778 
               
               
                 0.992080795 
                 −0.077567242 
                   Megamonas funiformis  C2294 
                 0 
                 0 
                 29.629109 
               
               
                 0.933770138 
                 −0.076490222 
                   Akkermansia  sp. KLE1605 C1918 
                 0 
                 0 
                 29.06993521 
               
               
                 0.386824312 
                 −0.074691634 
                   Bacteroides nordii  C0263 
                 0 
                 0 
                 28.48837982 
               
               
                 0.085278665 
                 −0.074297589 
                   Blautia wexlerae  C2171 
                 0 
                 0 
                 27.88205907 
               
               
                 0.330051192 
                 −0.073609518 
                   Clostridium  sp. TM06-18 C2922 
                 0 
                 0 
                 27.24815505 
               
               
                 0.083262321 
                 −0.072959896 
                   Candidatus Ishikawaella capsulata  Mpkobe C4922 
                 0 
                 0 
                 26.58329888 
               
               
                 0.683600356 
                 −0.066234762 
                   Parabacteroides goldsteinii  C0282 
                 0 
                 0 
                 25.88341081 
               
               
                 0.643910037 
                 −0.061735341 
                   Alistipes  sp. 5CBH24 C0283 
                 0 
                 0 
                 25.14347607 
               
               
                 0.242773051 
                 −0.052348168 
                   Lachnospira pectinoschiza  C2649 
                 0 
                 0 
                 24.35722212 
               
               
                 0.283452611 
                 −0.048932599 
                   Clostridium  sp. AF34-13 C2653 
                 0 
                 0 
                 23.5166394 
               
               
                 0.792065697 
                 −0.04739511 
                   Catenibacterium mitsuokai  DSM 15897 C2204 
                 0 
                 0 
                 22.61124205 
               
               
                 0.75605445 
                 −0.045467144 
                   Eubacterium  sp. TM06-47 C2917 
                 0 
                 0 
                 21.626875 
               
               
                 0.47084588 
                 −0.041470873 
                   Coprococcus eutactus  C2140 
                 0 
                 0 
                 20.54367678 
               
               
                 0.903395164 
                 −0.032159744 
                   Roseburia faecis  C2648 
                 0 
                 0 
                 19.33234001 
               
               
                 0.776663172 
                 −0.022510129 
                   Bacteroides faecis  C0221 
                 0 
                 0 
                 17.94655471 
               
               
                 0.686897002 
                 −0.016216198 
                   Bacteroides  sp. OF04-15BH C1226 
                 0 
                 0 
                 16.30552706 
               
               
                 0.77256713 
                 −0.008006904 
                   Lawsonibacter asaccharolyticus  C2612 
                 0 
                 0.303877071 
                 14.43735499 
               
               
                 0.226827239 
                 −0.011837149 
                   Bacteroides fragilis  C0096 
                 0 
                 0 
                 14.24418991 
               
               
                 0.804445324 
                 −0.006154069 
                   Odoribacter splanchnicus  C0185 
                 0 
                 0 
                 0 
               
               
                   
               
            
           
         
       
     
     Machine Learning for Live Biotherapeutic Design 
     The top 32 scoring organisms from Example 9 (Table 6) is selected for screening in simulated microbial mixes. Each combination of 4 organisms from the 32 is evaluated in silico using the trained machine learning model. For the cancer samples in the model, relative species abundances for the four organisms in the putative mix are increased in silico by a certain amount (here 0.5%). This simulates in silico the physical action of adding microbes to the gut microbiome. Classification is then performed using the machine learning model to estimate the probability that each augmented sample is a cancer sample. The hypothesis is that combinations of microbes that make cancer samples appear more like control samples according to the model are better candidates for therapeutic mixes. Each putative mix is scored by its mean predicted cancer probability across all the augmented cancer samples, with lower mean predicted cancer probabilities corresponding to notionally better therapeutic candidates. The top 30 exemplary live biotherapeutic compositions (exemplary microbial combinations) are then validated experimentally as described in Examples 11, and 15 to 21 as described below. 
     In another embodiment, inputs to the model are organisms identified as significantly more abundant in COVID-19 patients with rapid viral clearance and recovery from disease than in those patients with prolonged disease or severe symptoms. Combinations of organisms with top scores for relative abundance and immune correlation are inputs to the model, simulating in silico the physical action of adding microbes to the gut of patients with severe viral disease. Classification is then performed using the machine learning model to estimate the probability that each augmented sample becomes that of a patient with rapid recovery. The hypothesis is that combinations of microbes that enable rapid recovery from viral infection according to the model are better candidates for therapeutic mixes. Each putative mix is scored by its mean predicted probability across all the augmented severe disease samples, with lower mean predicted severe disease probabilities corresponding to notionally better therapeutic candidates to improve viral clearance and lessen disease symptoms. 
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 List of exemplary live biotherapeutic compositions, 
               
               
                 i.e., list of exemplary microbial combinations. 
               
            
           
           
               
               
            
               
                 Microbial 
                   
               
               
                 Mix 
                 Organism 
               
               
                   
               
            
           
           
               
               
            
               
                 1 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                 2 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Enterococcus hirae 
                 
               
               
                 3 
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                 4 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                 5 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Bacteroides thetaiotamicron 
                 
               
               
                   
                 
                   Bacteroides caccae 
                 
               
               
                   
                 
                   Gemmiger formicilis 
                 
               
               
                 6 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Alistipes indistinctus 
                 
               
               
                   
                 
                   Dorea formicigenerans 
                 
               
               
                 7 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Bifidobacterium longum 
                 
               
               
                   
                 
                   Bifidobacterium breve 
                 
               
               
                 8 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                 9 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                 10 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 11 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 12 
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 13 
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                 14 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                 15 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Adlercreutzia equolifaciens 
                 
               
               
                   
                 
                   Senegalimassilia anaerobia 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 16 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 17 
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Ellagibacter isourolithinifaciens 
                 
               
               
                 18 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Paraeggerthella hongkongensis 
                 
               
               
                 19 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Paraeggerthella hongkongensis 
                 
               
               
                   
                 
                   Slackia isoflavoniconvertens 
                 
               
               
                   
                 
                   Slackia equolifaciens 
                 
               
               
                 20 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                 21 
                 
                   Eubacterium hallii 
                 
               
               
                 22 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 23 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 24 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Enterococcus hirae 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 25 
                 
                   Blautia massiliensis 
                 
               
               
                 26 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                 27 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                 28 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Enterococcus hirae 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                 29 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Eggerthella lenta 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 30 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Enterococcus hirae 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 31 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                 32 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Clostridium coccoides 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Clostridium scindens 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                   
                 
                   Eubacterium hallii 
                 
               
               
                   
                 
                   Blautia massiliensis 
                 
               
               
                 33 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                 34 
                 
                   Eubacterium Hallii 
                 
               
               
                   
                 
                   Dorea Longicatena 
                 
               
               
                   
                   Blautia  sp. SG-772 
               
               
                 35 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Eubacterium Hallii 
                 
               
               
                   
                 
                   Dorea Longicatena 
                 
               
               
                   
                   Blautia  sp. SG-772 
               
               
                 36 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                 37 
                 
                   Dorea Longicatena 
                 
               
               
                   
                 
                   Dorea formicigenerans 
                 
               
               
                   
                   Blautia  sp. SG-772 
               
               
                   
                 
                   Eubacterium Hallii 
                 
               
               
                   
                 
                   Ruminococcus faecis 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                 38 
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                 39 
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Eubacterium ramulus 
                 
               
               
                   
                 
                   Gemmiger formicilis 
                 
               
               
                 40 
                 
                   Anaerostipes hadrus 
                 
               
               
                   
                 
                   Dorea formicigenerans 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Ruminococcus faecis 
                 
               
               
                 41 
                 
                   Anaerostipes hadrus 
                 
               
               
                   
                 
                   Dorea formicigenerans 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Ruminococcus faecis 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                 42 
                 
                   Anaerostipes hadrus 
                 
               
               
                   
                 
                   Dorea formicigenerans 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Ruminococcus faecis 
                 
               
               
                   
                 
                   Akkermansia muciniphila 
                 
               
               
                 43 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Eubacterium ramulus 
                 
               
               
                   
                 
                   Gemmiger formicilis 
                 
               
               
                 44 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Ruminococcus torques 
                 
               
               
                   
                 
                   Bifidobacterium bifidum 
                 
               
               
                 45 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Ruminococcus torques 
                 
               
               
                 46 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Ruminococcus torques 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Anaerostipes hadrus 
                 
               
               
                 47 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Roseburia inulivorans 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Anaerostipes hadrus 
                 
               
               
                 48 
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Anaerostipes hadrus 
                 
               
               
                   
                 
                   Eubacterium Hallii 
                 
               
               
                   
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                 49 
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Anaerostipes hadrus 
                 
               
               
                   
                 
                   Eubacterium Hallii 
                 
               
               
                   
                 
                   Faecalibacterium prausnitzii 
                 
               
               
                   
                 
                   Blautia obeum 
                 
               
               
                 50 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                   
                 
                   Coprococcus comes 
                 
               
               
                   
                 
                   Anaerostipes hadrus 
                 
               
               
                 51 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Gemmiger formicilis 
                 
               
               
                   
                 
                   Asacharobacter celatus 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                   
                 
                   Alistipes putredinis 
                 
               
               
                   
                 
                   Gordonibacter urolithinfaciens 
                 
               
               
                 52 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Monoglobus pectinilyticus 
                 
               
               
                   
                 
                   Bacteroides galacturonicus 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                   
                 
                   Ruminococcus gnavus 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                 53 
                 
                   Akkermansia muciniphila 
                 
               
               
                   
                 
                   Monoglobus pectinilyticus 
                 
               
               
                   
                 
                   Bacteroides galacturonicus 
                 
               
               
                   
                 
                   Collinsella aerofaciens 
                 
               
               
                   
                 
                   Ruminococcus torques 
                 
               
               
                   
                 
                   Dorea longicatena 
                 
               
               
                 54 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 55 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 56 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 57 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 58 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 59 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 60 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 61 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 62 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 63 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 64 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 65 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 66 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 67 
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 68 
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 69 
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 70 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 71 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 72 
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 73 
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 74 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 75 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 76 
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 77 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 78 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 79 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 80 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 81 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 82 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 83 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 84 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 85 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 86 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 87 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 88 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 89 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 90 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 91 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 92 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 93 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 94 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 95 
                   Bifidobacterium bifidu m C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 96 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 97 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 98 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 99 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 100 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 101 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 102 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 103 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 104 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 105 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 106 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 107 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 108 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 109 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 110 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 111 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 112 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 113 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 114 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 115 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 116 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 117 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 118 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 119 
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM 147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 120 
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 121 
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 122 
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 123 
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 124 
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 125 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 126 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 127 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 128 
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 129 
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 130 
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 131 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 132 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 133 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 134 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 135 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 136 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 137 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 138 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 139 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 140 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 141 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 142 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 143 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 144 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 145 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 146 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 147 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 148 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM 147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 149 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 150 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 151 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 152 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 153 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 
               
               
                   
                 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 154 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 155 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 156 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 157 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 158 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 159 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 160 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 161 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 162 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 163 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 164 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 165 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 166 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 167 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 168 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 169 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 170 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 171 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 172 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 173 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 174 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 175 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 176 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 177 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 178 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 179 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 180 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 181 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 182 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 183 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 184 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 185 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 186 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 187 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 188 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 189 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 190 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 191 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 192 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 193 
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 194 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 195 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 196 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 197 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 198 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 199 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 200 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 201 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 202 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 203 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 204 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 205 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 206 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 207 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 208 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 209 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 210 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 211 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 212 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 213 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 214 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 215 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 216 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 217 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 218 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 219 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 220 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 221 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 222 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 223 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 224 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 225 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 226 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 227 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 228 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 229 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 230 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 231 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 232 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 233 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 234 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 235 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 236 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 237 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 238 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 239 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 240 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 241 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 242 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 243 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 244 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                 Erysipelotrichaceae bacterium GAM 147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 245 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 246 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 247 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 248 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 249 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 250 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 251 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 252 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 253 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 254 
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 255 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 256 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 257 
                   Blautia obeum  C2129 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 258 
                   Blautia obeum  C2129 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 259 
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 260 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 261 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 262 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 263 
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 264 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Bifidobacterium catenulatum  C0014 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                 265 
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Bifidobacterium catenulatum  C0014 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                 266 
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Bifidobacterium catenulatum  C0014 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                 267 
                   Dorea  sp. OM07-5 C2890 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                   Anaerobutyricum hallii  C2206 
               
               
                   
                   Faecalibacterium prausnitzii  C2650 
               
               
                   
                   Faecalibacterium prausnitzii  C2651 
               
               
                   
                   Anaerostipes hadrus  C2144 
               
               
                   
                   Dorea formicigenerans  C2197 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                   
                   Coprococcus catus  C2881 
               
               
                   
                   Faecalibacterium  sp. AF28-13AC C2810 
               
               
                   
                 [ Clostridium ]  amygdalinum  C2887 
               
               
                   
                   Roseburia inulinivorans  C2207 
               
               
                   
                   Asaccharobacter celatus  Cl952 
               
               
                 268 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Bifidobacterium catenulatum  COO 14 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                   Dorea formicigenerans  C2197 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                   
                   Coprococcus catus  C2881 
               
               
                 269 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Bifidobacterium catenulatum  COO 14 
               
               
                   
                   Dorea formicigenerans  C2197 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Coprococcus catus  C2881 
               
               
                 270 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Dorea  sp. OM07-5 C2890 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                   Faecalibacterium prausnitzii  C2650 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                 271 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 272 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Dorea formicigenerans  C2197 
               
               
                   
                 [ Clostridium ]  amygdalinum  C2887 
               
               
                   
                   Roseburia inulinivorans  C2207 
               
               
                   
                   Asaccharobacter celatus  C1952 
               
               
                 273 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Dorea formicigenerans  C2197 
               
               
                   
                 [ Clostridium ]  amygdalinum  C2887 
               
               
                   
                   Roseburia inulinivorans  C2207 
               
               
                   
                   Asaccharobacter celatus  C1952 
               
               
                 274 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                 275 
                   Bifidobacterium bifidum  C0005 
               
               
                   
                   Bifidobacterium catenulatum  C0014 
               
               
                   
                   Bifidobacterium pseudocatenulatum  C0013 
               
               
                 276 
                   Blautia luti  C2436 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Blautia obeum  C2901 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                 277 
                   Blautia luti  C2436 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Blautia obeum  C2901 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                   Blautia  sp. KGMB01111 C3003 
               
               
                   
                   Blautia  sp. TF11-31AT C2841 
               
               
                   
                   Blautia wexlerae  C2171 
               
               
                 278 
                   Clostridium  sp. AF20-17LB C2921 
               
               
                   
                   Clostridium  sp. AF23-8 C2908 
               
               
                   
                   Clostridium  sp. AF34-13 C2653 
               
               
                   
                   Clostridium  sp. AF36-4 C2893 
               
               
                   
                   Clostridium  sp. AM18-55 C2845 
               
               
                   
                   Clostridium  sp. AM49-4BH C2934 
               
               
                   
                   Clostridium  sp. OF10-22XD C2132 
               
               
                 279 
                   Collinsella aerofaciens  C1933 
               
               
                   
                   Collinsella bouchesdurhonensis  C1956 
               
               
                   
                   Collinsella  sp. TM05-38 C1984 
               
               
                 280 
                   Coprococcus catus  C2881 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Coprococcus eutactus  C2642 
               
               
                 281 
                   Dorea formicigenerans  C2197 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                   Dorea  sp. AM58-8 C2913 
               
               
                   
                   Dorea  sp. OM07-5 C2890 
               
               
                 282 
                   Eubacterium ramulus  C2442 
               
               
                   
                   Eubacterium ramulus  C2852 
               
               
                   
                   Eubacterium saphenum  ATCC 49989 C2183 
               
               
                   
                   Eubacterium ventriosum  C2128 
               
               
                 283 
                   Faecalibacterium prausnitzii  C2138 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Faecalibacterium prausnitzii  C2650 
               
               
                   
                   Faecalibacterium prausnitzii  C2651 
               
               
                   
                   Faecalibacterium prausnitzii  C2863 
               
               
                   
                   Faecalibacterium prausnitzii  C2864 
               
               
                   
                   Faecalibacterium  sp. AF28-13AC C2810 
               
               
                 284 
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                 Firmicutes bacterium AF22-6AC C2933 
               
               
                   
                 Firmicutes bacterium AF25-13AC C2695 
               
               
                   
                 Firmicutes bacterium AM41-11 C2946 
               
               
                   
                 Firmicutes bacterium TM09-10 C2909 
               
               
                 284 
                   Roseburia inulinivorans  C2207 
               
               
                   
                   Roseburia  sp. AM59-24XD C2936 
               
               
                   
                   Roseburia  sp. OM04-15AA C2892 
               
               
                 285 
                   Ruminococcus callidus  C2440 
               
               
                   
                   Ruminococcus lactaris  C2149 
               
               
                   
                   Ruminococcus  sp. AF31-8BH C2903 
               
               
                   
                   Ruminococcus  sp. AM42-11 C2945 
               
               
                   
                   Ruminococcus  sp. KGMB03662 C2557 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                 286 
                   Flavonifractor plautii  C2284 
               
               
                   
                 [ Clostridium ]  scindens  C2143 
               
               
                   
                 [ Clostridium ]  bolteae  C2137 
               
               
                 287 
                   Flavonifractor plautii  C2284 
               
               
                   
                 [ Clostridium ]  scindens  C2143 
               
               
                   
                 [ Clostridium ]  bolteae  C2137 
               
               
                   
                   Blautia hansenii  C3044 
               
               
                   
                 [ Clostridium ]  clostridioforme  C2275 
               
               
                 288 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                 289 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                 290 
                   Dorea longicatena  C2131 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                 291 
                   Dorea longicatena  C2131 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                 292 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                 293 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Ruminococcus  sp. OF03-6AA C2904 
               
               
                   
                   Blautia  sp. AF19-10LB C2906 
               
               
                   
                 Firmicutes bacterium AF12-30 C2644 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                 294 
                 Erysipelotrichaceae bacterium GAM147 C2844 
               
               
                   
                   Dorea longicatena  C2131 
               
               
                   
                   Coprococcus comes  C2152 
               
               
                   
                   Blautia obeum  C2129 
               
               
                   
                   Faecalibacterium prausnitzii  C2184 
               
               
                   
                   Dorea longicatena  C2413 
               
               
                   
                 [ Ruminococcus ]  torques  C2636 
               
               
                   
               
            
           
         
       
     
     Example 11: Gene Expression Analysis of Microbial Treatment in Co-Culture 
     Live biotherapeutic compositions as provided herein, including the exemplary combinations of microbes 1 to 294, as described in Table 9, Example 10 and Table 42, Example 25, are evaluated in co-culture for immunomodulatory effects. Live biotherapeutics are co-cultured with human colonic cells (CaCo2) to investigate the effects of the bacteria on the host. Live biotherapeutic compositions are also co-cultured on CaCo2 cells that were stimulated with Interleukin 1 (IL1) to mimic the effect of the bacteria in an inflammatory environment. The effects in both scenarios are evaluated through gene expression analysis either by PCR or by next generation sequencing approaches. 
     Cytokine Production in THP-1 Cells Induced by Live Biotherapeutics 
     Live biotherapeutic compositions as provided herein, including for example the exemplary combinations of microbes 1 to 294, Table 9, Example 10 and Table 42, Example 25, and single bacterial strains are evaluated alone and in combination with lipopolysaccharide (LPS) on cytokine production in THP-1 cells, a model cell line for monocytes and macrophages. 
     THF-1 cells are differentiated into M0 medium for 48 h with 5 ng/mL phorbol-12-myristate-13-acetate (PMA). These cells are subsequently incubated with the live biotherapeutic composition at a final concentration of 10 8 /ml, with or without the addition of LPS at a final concentration of 100 ng/ml. Alternatively, the bacterial cells are centrifuged, and the resulting supernatant is added to the THF-1 cell preparation. The bacteria are then washed off and the cells allowed to incubate under normal growing conditions for 24 h. The cells are then spun down and the resulting supernatant is analyzed for cytokine content using a Luminex 200 analyzer or equivalent method. 
     Cytokine Production in Immature Dendritic Cells Induced by Live Biotherapeutic Compositions 
     Live biotherapeutic compositions as provided herein, including the exemplary combinations of microbes 1 to 294, as described in Table 9, Example 10, and Table 42, Example 25 and single bacterial strains are evaluated alone and in combination with LPS on cytokine production in immature dendritic cells. A monocyte population is isolated from peripheral blood mononuclear cells (PBMCs). The monocyte cells are subsequently differentiated into immature dendritic cells. The immature dendritic cells are plated out at 200,000 cells/well and incubated with the live biotherapeutic composition at a final concentration of 10 7 /ml in RPMI media, with the optional addition of LPS at a final concentration of 100 ng/ml. Alternatively, the bacterial cells are centrifuged, and the resulting supernatant is added to the dendritic cell preparation. The negative control involves incubating the cells with RPMI media alone and positive controls incubating the cells with LPS at a final concentration of 100 ng/ml. The cytokine content of the cells is then analyzed. 
     Cytokine Production and Analysis in PBMCs 
     Peripheral blood mononuclear cells (PBMC&#39;s) are isolated from subject blood using a standard kit and stored in liquid nitrogen at 1×10 6  cells per mL until use. Prior to storage, PBMC&#39;s may be processed using flow sorting or an antibody spin separation kit to select for a certain purified lymphocyte subpopulation, such as T cells. 
     PBMCs are thawed at 37° C. and then transferred to a growth medium consisting of RPMI-1640 (Lonza, Switzerland), with 10% heat inactivated FCS added, as well as 0.1% penicillin-streptavidin, 1% L-glutamine, and DNase at 10 mg/mL to inhibit aggregation. Cells are centrifuged at 200×g for 15 minutes and then counted using trypan blue and spread into 24 well plates at 1×10 6  cells per well (1 mL per well) (Kechaou et al. (2013) Applied and Environmental Microbiology 79:1491-1499; Martin et al. (2017) Frontiers in Microbiology 8:1226). 
     An overnight bacterial culture is inoculated using a pre-stocked isolated bacterial strain. This strain is grown at 37° C. for 10 to 20 hours in a YBHI medium with added cellobiose (1 mg/mL), maltose (1 mg/mL) and cysteine (0.5 mg/mL) in an anaerobic chamber filled with 85% nitrogen, 10% carbon dioxide, and 5% hydrogen (Martin et al., 2017). The growth medium may also be Reinforced Clostridial Medium (RCM) (Thermo Fisher, USA), which may also be supplemented with cysteine (0.5 mg/mL) or arginine (1 mg/mL). 
     At the end of the anaerobic culture, the culture supernatant and bacterial cells alone are saved for co-culture with PBMC&#39;s. Microbial culture supernatant is saved directly after centrifugation at −80° C. Cells are saved by washing with phosphate buffered saline (PBS) and then storing in PBS with 15% glycerol. Bacteria are quantified using phase contrast microscopy and stored at a final concentration of 10 5  or 10 6  cells per mL (Haller et al. (2000) Infection and Immunity 68; Rossi et al. (2015) Scientific Reports 6:18507) at −80° C. Bacteria may also be pasteurized prior to storage by treatment at 70° C. for 30 minutes (Plovier et al. (2017) Nature Medicine 23:107-113). 
     Prior to co-culture, supernatant is thawed on ice and 200 μL of supernatant is diluted in 1 mL of total volume of PBMC growth medium. Microbial growth medium is used as a negative control. This 1 mL is added to the 1 mL of PBMC in each well, resulting in a 10% final level of microbial culture supernatant in a 2 mL culture containing 1×10 6  PBMCs. Each combination of PBMCs and supernatant is performed in duplicate or triplicate. 
     Prior to co-culture, bacteria are thawed on ice and then washed at 4° C. with PBMC growth medium. 1 mL of the bacterial suspension is added to the 1 mL of PBMC culture in each well of the plate, resulting in a final 2 mL culture containing 1×10 6  PBMC&#39;s and 1×10 5  or 1×10 6  (potentially pasteurized) bacteria. 
     The co-culture of PBMC&#39;s and supernatant or purified bacteria is incubated for 2, 6, 16, 24, or 48 hours at 37° C. in 10% carbon dioxide. 
     After co-culture, the supernatant is harvested and treated with a protease inhibitor (Complete EDTA-Free protease inhibitor, Roche Applied Bioscience) to protect cytokines and stored directly at −80° C. for cytokine profiling. The pelleted cells are treated with RNAlater (Thermo Fisher, USA) and saved for RNA sequencing. 
     Cytokine analysis is performed on saved co-culture supernatant using ELISA or a Luminex system. Cytokines measured may include but are not limited to, IL-10, IL-2, and IFN-gamma. 
     RNA sequencing is performed on PBMC&#39;s saved in RNAlater post co-culture. Standard pseudo-alignment is performed using Kallisto (Bray et al. (2016) Nature Biotechnology 34:525-527) and differential expression is analyzed using DESeq2 (Love et al. (2014) Genome Biology 15:550) to identify differential expression between different microbes and different PBMC donors. 
     Statistical analyses are performed to identify microbes that exhibit desired immunomodulatory effects in vitro, which include but are not limited to inducing production of IFN-gamma and lowering expression of genes associated with T cell exhaustion (PD1, CTLA4, VISTA, TIM3, TIGIT, LAG3). 
     Example 12: Genetic Modification of Therapeutic Microbes 
     Microbes of interest, including microbes as provided herein, for example, as listed in Table 1, 4, 7 or 8, including bacteria from all the genuses listed herein, and including the combinations of microbes as provided herein, for example, the exemplary combinations 1 to 294 as described in Table 9, Example 10, and Table 42, Example 25, or as identified from the in vivo and ex vivo analyses described in Example 10 and Example 11, are interrogated or investigated to identify mechanisms of action, and the discovered mechanisms are leveraged using a genetic modification or modifications to amplify the microbe&#39;s therapeutic effect. 
     In alternative embodiments, this is accomplished in two stages. First, complementary bioinformatic and experimental approaches are used to identify the genes within a microbe of interest responsible for its therapeutic effect. Second, synthetic biology techniques are used to engineer over-expression of the identified genes within the original organism of discovery or inserted for overexpression in the genome of a chassis organism. Chassis organisms include any microbe as described herein, including genuses of bacteria as provided herein, and also include bacteria as listed in Tables 1, 3, 4, 5, 6, 7 and/or 8, including  Bacillus subtilis, Escherichia coli  Nissle, or any microbes listed in the combinations as provided herein in Table 9 and Table 42, Example 25, or the original organism of interest itself. 
     In alternative embodiments, microbes as provided herein are genetically modified to increase expression of existing therapeutically effective genes, or to install extra copies of these genes, or to install into a microbe lacking these functions any one of these genes. Methods for genetic engineering/augmenting a microbe of interest, for example, a gut microbe, to alter expression of existing therapeutically effective genes or to install extra copies of said genes or to install said genes in a microbe lacking these functions are numerous in the art. Techniques applied to gut microbes and related organisms for experimental gene disruption, gene replacement or gene expression modulation include CRISPR-Cas9 genome editing (Bruder et al (2016) Applied and Environmental Microbiology 82:6109-6119), bacterial conjugation (Cuiv et al (2015) Nature Scientific Reports 5:13282; Ronda et al. (2019) Nature Methods 16:167-170), gene replacement mutagenesis by homologous recombination (Cartman et al (2012) Applied Environmental Microbiology 78:4683-4690; Heap et al (2007) Journal of Microbiological Methods 70:452-464), random transposon mutagenesis (Cartman and Minton (2010) Applied Environmental Microbiology 76:1103-1109), and antisense-based gene expression attenuation (Forsyth et al (2002) Molecular Microbiology 43:1387-1400; Kedar et al (2007) Antimicrobial Agents and Chemotherapy 51:1708-1718. 
     Genes of interest inserted into microbes as provided herein, or whose expression is increased in microbes as provided herein, can be engineered to immediately follow and be under inducible control by various promotor elements that are functional in gut microbes. Highly inducible and controllable promoter elements are available for bacteria in the gram-negative genus  Bacteroides  (Lim et al (2017) Cell 169:547-558; Bencivenga-Barry et al (2019) Journal of Bacteriology doi: 10.1128/JB.00544-19). Some of these are responsive to various diet-derived polysaccharides, while those often most useful for use for inducible function determination in animal models such as mouse rely on induction by tetracycline derivatives like anhydrotetracycline at sub-bactericidal levels. Anhydrotetracycline can be employed as an inducer for engineered promoters in gut Clostridia (Dembek et al (2017) Frontiers of Microbiology 8:1793). Promoters that respond to bile acids are identified in gram-positive gut  Clostridium  species (Wells and Hyemon (2000) Applied Environmental Microbiology 66:1107-1113) and in  Eubacterium  species (Mallonee et al. (1990) Journal of Bacteriology 172:7011-7019. Also, inducible promoters that respond to sugars such as lactose (Banerjee et al (2014) Applied Environmental Microbiology 80-2410-2416) and arabinose (Zhang et al (2015) Biotechnology for Biofuels 8:36) are identified and useful in related Clostridial species. Genes inserted in exemplary recombinant bacterium can be induced under low-oxygen conditions from promoters driven by transcriptions factors such as FNR (fumarate and nitrate reductase) (Oxer et al (1991) Nucleic Acids Research, 19, 11: 2889-2892). Genes of interest inserted in microbes as provided herein can also be engineered to immediately follow and be under constitutive control by various promotor elements that are functional in gut microbes. Constitutive promoter libraries and promoter-RBS (ribosome binding site) pairs have been created for bacteria in the gram-negative genus  Bacteroides  (Mimee et al (2015) Cell Syst. 1, 62-71) and computational models have been developed from  Bacillus subtilis  promoter sequences data sets for promoter prediction in Gram-positive bacteria (Coelho et al (2018) Data Br. 19, 264-270). 
     Engineering of Metabolic Pathways in Therapeutic Microbes 
     In one embodiment, an organism used to practice embodiments as provided herein is genetically modified to overexpress a pathway for production of any short chain fatty acid (SCFA), including butyrate or butyric acid, propionate and acetate. Butyric acid is naturally produced in many gut microorganisms and is derived from two molecules of acetyl-CoA, a central metabolic intermediate that is ubiquitous in microorganisms. In one embodiment, the native pathway is overexpressed, for example, as discussed herein. In another embodiment, a heterologous pathway is constructed by introducing one or more genes from a different organism, including all genes derived from different organisms. Condensation of two acetyl-CoA molecules is catalyzed by a ketothiolase (EC:2.3.1.9), such as the atoB gene from  Escherichia coli , to produce one molecule of acetoacetyl-CoA (Sato et al. (2007) J. Biosci. Bioengineer. 103:38-44). Alternative candidates are obtained by Basic Local Alignment Search Tool (BLAST) search of this sequence (Altschul et al. (1997) Nuc. Acids. Res. 25:3389-3402), obtaining homologous genes either known or predicted to encode similar enzyme function. Exemplary gene candidates are obtained using the following GenBank accession numbers. 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 atoB 
                 
                   Escherichia coli 
                 
                 NP_416728.1 
               
               
                   
                 yqeF 
                 
                   Escherichia coli 
                 
                 NP_417321.2 
               
               
                   
                 phaA 
                 
                   Cupriavidus necator 
                 
                 YP_725941 
               
               
                   
                 bktB 
                 
                   Cupriavidus necator 
                 
                 AAC3 8322.1 
               
               
                   
                 thiA 
                 
                   Clostridium acetobutylicum 
                 
                 NP_349476.1 
               
               
                   
                 thiB 
                 
                   Clostridium acetobutylicum 
                 
                 NP_149242.1 
               
               
                   
                   
               
            
           
         
       
     
     The second step in the pathway involves reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA by a hydroxyacyl-CoA dehydrogenase (EC:1.1.1.35), such as that encoded by hbd in  Clostridium acetobutylicum  (Atsumi et al. (2008) Metab. Eng. 10(6):305-311). Similarly, to above, alternate candidates are identified in the literature or by BLAST. Exemplary candidates are as follows. 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 paaH 
                 
                   Escherichia coli 
                 
                 NP_415913.1 
               
               
                 hbd 
                 
                   Clostridium acetobutylicum 
                 
                 NP_349314.1 
               
               
                 hbd 
                 
                   Pseudomonas putida 
                 
                 KT2440 NC_002947.4 
               
               
                 RSP_3970 
                   Rhodobacter sphaeroides  2.4.1 
                 YP_345236.1 
               
               
                   
               
            
           
         
       
     
     The next step is the dehydration of 3-hydroxybutyryl-CoA to crotonyl-CoA by an enoyl-CoA hydratase, also known as crotonase (EC:42.1.55), such as that encoded by the crt gene of  Clostridium acetobutylicum  (Kim et al. (2014) Biochem. Biophys. 
     Res. Commun. 451:431-435) or the homologs listed below. 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 crt 
                 
                   Clostridium acetobutylicum 
                 
                 NC_003030.1 
               
               
                 echA18 
                   Mycobacterium bovis  AF2122/97 
                 NC_002945.4 
               
               
                 maoC 
                 
                   Escherichia coli 
                 
                 NP_415905.1 
               
               
                 crt 
                 
                   Bacillus thuringiensis 
                 
                 NC_005957.1 
               
               
                   
               
            
           
         
       
     
     Next, crotonyl-CoA is reduced to butyryl-CoA through the action of an enoyl-CoA reductase (EC:1.3.1.38 or EC:1.3.1.44), such as that encoded by the bcd gene of  Clostridium acetobutylicum  (Boynton et al. (1996) J. Bacteriol. 178:3015-3024). Activity of this enzyme can be enhanced by expressing bcd in conjunction with expression of the  C. acetobutylicum  etfAB genes, which encode an electron transfer flavoprotein. Several eukaryotic enzymes with this activity have also been identified, such as TER from  Euglena gracilis , that upon removal of the mitochondrial targeting leader sequence have demonstrated superior activity in  E. coli  (Hoffmeister et al. (2005) J. Biol. Chem. 280:4329-4338). Protein sequences for these and other exemplary sequences can be obtained using the following GenBank accession numbers. 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 bed 
                 
                   Clostridium acetobutylicum 
                 
                 NP_34.9317.1 
               
               
                 etfA 
                 
                   Clostridium acetobutylicum 
                 
                 NP_349315.1 
               
               
                 etfB 
                 
                   Clostridium acetobutylicum 
                 
                 NP_349316.1 
               
               
                 TER 
                 
                   Euglena gracilis 
                 
                 Q5EU90.1 
               
               
                 TDE0597 
                 
                   Treponema denticola 
                 
                 NP 97.1211.1 
               
               
                   
               
            
           
         
       
     
     The final step of this pathway is CoA removal from butyryl-CoA to generate butyric acid. Although numerous CoA hydrolases occur in most bacteria, for example, tesB from  E. coli  ((Naggert et al. (1991) J. Biol. Chem. 266:11044-11050), it is desirable to recover energy from hydrolysis of the thioester bond in the form of ATP. The sucCD complex of  E. coli  (EC:6.2.1.5) is one example of this, known to catalyze the conversion of succinyl-CoA and ADP to succinate and ATP (Buck et al. (1985) Biochem. 24:6245-6252). Another example is sucD, succinic semialdehyde dehydrogenase, from  Porphyromonas gingivalis  (Yim et al. (2011) Nat. Chem. Biol. 7:445-452). Another option, using phosphotransbutylase/butyrate kinase (EC:2.3.1.19, EC:2.7.2.7), is catalyzed by the gene products of buk1, buk2, and ptb from  C. acetobutylicum  (Walter et al. (1993) Gene 134:107-111) or homologs thereof. Finally, an acetyltransferase capable of transferring the CoA group from butyryl-CoA to acetate can be applied (EC:2.8.3.9), such as Cat3 from  C. kluyveri  (Sohling and Gottschalk (1996) J. Bacteriol. 178:871-880). Protein sequences for these and other exemplary sequences can be obtained using the following GenBank accession numbers. 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 ptb 
                 
                   Clostridium acetobutylicum 
                 
                 NP 349676 
               
               
                   
                 buk1 
                 
                   Clostridium acetobutylicum 
                 
                 NP 349675 
               
               
                   
                 buk2 
                 
                   Clostridium acetobutylicum 
                 
                 Q97II1 
               
               
                   
                 sucC 
                 
                   Escherichia coli 
                 
                 NP_415256.1 
               
               
                   
                 sueD 
                 
                   Escherichia coli 
                 
                 AAC73 823.1 
               
               
                   
                 cat3 
                 
                   Clostridium kluyveri 
                 
                 EDK35586.1 
               
               
                   
                 tesB 
                 
                   Escherichia coli 
                 
                 NP_414986 
               
               
                   
                   
               
            
           
         
       
     
     In another embodiment, a microbe used to practice embodiments as provided herein is genetically modified to metabolize bile acids, also referred to as bile salts to indicate the predominant form at neutral pH, that are produced in the liver and present in the gut at about 1 mM concentration. Two such types of bile acid conversion processes are catalyzed by bacteria. The first is deconjugation, which removes either taurine or glycine that is frequently found conjugated to bile acids (Ridlon et al. (2016) Gut Microbes 7:22-39; Masuda et al. (1981) Microbiol. Immunol. 25:1-11). This is catalyzed by bile salt hydrolase (BSH) enzymes (EC:3.5.1.24), which are widespread in many gut bacteria. Some BSHs have broad substrate specificity, while others are very specific for a particular bile salt. The substrate range of a BSH of interest is determined by assay of purified BSH or crude lysates from the native host, on a panel of glycine and taurine conjugated bile salts (Jones et al. (2008) Proc. Nat. Acad. Sci. USA 105:13580-13585). To enhance the activity and substrate range of bile salt deconjugation in the engineered microbe, native BSHs of interest and/or heterologous genes from other microbes are introduced. Exemplary genes are listed below. Still others are found by GenBank search or BLAST of these sequences to identify homologs. 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 bsh 
                 
                   Bifidobacterium longum 
                 
                 AF148138.1 
               
               
                   
                 bsh 
                 
                   Bifidobacterium animalis 
                 
                 AY530821.1 
               
               
                   
                 bsh 
                 
                   Enterococcus faecalis 
                 
                 GG688660.1 
               
               
                   
                 bsh3 
                 
                   Lactobacillus plantarum 
                 
                 ACL98170.1 
               
               
                   
                 cbh2 
                 
                   Bacteroides vulgatis 
                 
                 RIB33278.1 
               
               
                   
                 cbah 
                 
                   Clostridium butyricum 
                 
                 EEP54620.1 
               
               
                   
                   
               
            
           
         
       
     
     The other type of bile acid metabolism introduced into a microbe used to practice embodiments as provided herein is capable of converting primary to secondary bile acids, which entails removal of the 7-alpha-hydroxy or 7-beta hydroxy group from the primary bile acid; for example, the conversion of cholic acid to deoxycholic acid or chenodeoxycholic acid to lithocholic acid. The archetype pathway for this process is encoded by the bai gene cluster in  Clostridium scindens  (Coleman et al. (1987) J. Bacteriol. 169:1516-1521; Ridlon et al. (2006) J. Lipid. Res. 47:241-259) and has been well characterized. In addition, a functional  C. scindens  dihydroxylation was established in  Clostridium sporogenes  (Funabashi et al. (2019) BioRxiv). The first step is a bile acid-CoA ligase (baiB, EC:6.2.1.7) to activate the molecule for the subsequent reaction steps. Next, an alcohol dehydrogenase (baiA, EC:1.1.1.395) oxidizes the 3-hydroxyl to a keto group. An NADH:flavin oxidoreductase then introduces a double bond into the ring by either baiCD (EC:1.3.1.115) or baiH (EC:1.3.1.116), depending on the substrate. The coA is then removed or transferred to another primary bile acid by a CoA transferase (baiF, EC:2.8.3.25). The 7-alpha or 7-beta-hydroxy group is then removed by a dehydratase (baiE or baiI, respectively, EC:4.2.1.106) to form a second double bond in a conjugated position to the other one. Enzymes encoded by baiH and baiCD then serve to reduce the double bonds consecutively, and finally the alcohol dehydrogenase reduces the 3-keto back to a hydroxyl. High bile acid dihydroxylation activity has also been observed in  Eubacterium  sp. strain VPI 12708,  Eubacterium  sp. strain Y-1113,  Eubacterium  sp. strain I-10,  Eubacterium  sp. strain M-18,  Eubacterium  sp. strain TH-82,  Clostridium  sp. strain TO-931, and  Clostridium  sp. strain HD-17. Homologs for some of the bai genes have been identified in these organisms (Doemer et al. (1997) Appl. Environ. Microbiol. 63:1185-1188), and thus represent alternate gene candidates. Homologs of all essential genes for pathway function were also identified in  Clostridium hylemonae  DSM 15053 , Dorea  sp. D7, and a novel  Firmicutes  bacterium (Das et al. (2019) BMC Genomics 20:517). 
     To introduce the conversion pathway into the genetically modified host, the following  C. scindens  genes or suitable homologs are expressed: baiA, baiB, baiCD, baiE, baiF, and baiH. In some embodiments, the baiG gene, encoding a transporter, is also expressed. In other embodiments, the baiI gene predicted to encode a delta-5-ketoisomerase, is introduced in order to enable dihydroxylation of secondary bile acids requiring this step. 
     Tryptophan derivatives are produced by many microbes, including gut bacteria, and have been implicated in strengthening the epithelial cell barrier and modulating the expression of pro-inflammatory genes by T cells in the GI tract (Bercik et al. (2011) Gastroenterology 141:599-609). A gut microbe is engineered to overexpress one or more tryptophan derivatives by either overexpressing native genes or introducing heterologous genes described below. 
     In one embodiment, a microbe used to practice embodiments as provided herein is engineered to convert tryptophan to indole by introduction of a tryptophanase, such as that encoded by the tnaA gene of  E. coli  (Li and Young (2013) Microbiology 159:402-410). Other candidates are found by literature search or BLAST of the sequence to find homologs, as exemplified by the following: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 tnaA 
                 
                   Escherichia coli 
                 
                 NP_415256.1 
               
               
                 tnaA 
                 
                   Bacteroides thetaiotamicron 
                 
                 NP_810405.1 
               
               
                 tnaA 
                 
                   Vibrio tasmaniensis 
                 
                 LGP32VS_RS05915 
               
               
                 tnaA 
                 
                   Treponema denticola 
                 
                 TDE0251 
               
               
                   
               
            
           
         
       
     
     In another embodiment, a microbe used to practice embodiments as provided herein is engineered to convert tryptophan to indoleacetate. This pathway begins with a tryptophan aminotransferase (EC:2.6.1.27) such as that encoded by the Taml gene of  Ustilago maydis  (Zuther et al. (2008) Mol. Microbiol. 68:152-172), which uses a-ketoglutarate as the amino acceptor and produces indolepyruvate. Although a microbial sequence for this enzyme is not currently in GenBank, activity has been reported in  Clostridium sporogenes  (O&#39;Neil et al. (1968) Arch. Biochem. Biophys. 127:361-369). Alternatively, a deaminating tryptophan oxidase (EC:1.3.3.10) such as that encoded by the vioA gene of  Chromobacterium violaceum  (August et al. (2000) J. Mol. Microbiol. Biotechnol. 2:513-519) uses molecular oxygen to oxidize and deaminate tryptophan to produce indolepyruvate. Alternative candidates include those indicated as follows: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 vioA 
                 
                   Chromobacterium violaceum  
                 
                 CV_RS16140 
               
               
                 WP_133678757 
                 
                   Paludibacterium purpuratum  
                 
                 WP_133678757.1 
               
               
                 WP_034786442 
                 
                   Janthinobacterium lividum  
                 
                 WP_034786442.1 
               
               
                   
               
            
           
         
       
     
     The next gene to be introduced encodes an indolepyruvate decarboxylase (EC:4.1.1.74), which produces indole-3-acetaldehyde from indolepyruvate. An example is the ipdC gene from  Enterobacter cloacae  (Koga et al. (1991) Mol. Gen. Genet. 226:10-16). Other exemplary genes can be accessed by the GenBank accession numbers listed below: 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 ipdC 
                 
                   Enterobacter cloacae  
                 
                 WP_013098183.1 
               
               
                   
                 CFNIH1_ 
                 
                   Citrobacter freundii  
                 
                 CFNIH1_RS23020 
               
               
                   
                 RS23020 
                   
                   
               
               
                   
                 ipdC 
                 
                   Rhodopseudomonas palustris  
                 
                 TX73_RS15890 
               
               
                   
                   
                 CGA009 
                   
               
               
                   
                 ipdC 
                 
                   Azospirillum brasilense 
                 
                 AMK58_RS11560 
               
               
                   
                   
               
            
           
         
       
     
     Indole-3-acetaldehyde is then oxidized to indoleacetate by an aldehyde dehydrogenase (EC:1.2.1.3), such as that encoded by the aldA gene of  Pseudomonas syringae  (McClerklin et al. (2018) PLoS Pathog. 14:e1006811). Numerous aldehyde dehydrogenases exist, though the best candidates are those homologous to this aldA or others with known activity on indole-3-aldehyde or similar molecules. Exemplary gene candidates can be accessed by the GenBank accession numbers listed below: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 ald A 
                 
                   Pseudomonas syringae 
                 
                 PSPTO_0092 
               
               
                 CFNIH1_RS23020 
                 
                   Citrobacter freundii  
                 
                 CFNIH1_RS23020 
               
               
                 WP_005887684.1 
                 
                   Pseudomonas coronafaciens  
                 
                 WP_005887684.1 
               
               
                 SPOG_02634 
                 
                   Schizosaccharomyces cryophilus  
                 
                 OY26 SPOG_02634 
               
               
                   
               
            
           
         
       
     
     In another embodiment, a tryptophan decarboxylase (EC:4.1.1.28) is introduced into a microbe used to practice embodiments as provided herein to produce tryptamine. This activity is rare among bacteria, but two such enzymes have recently been identified: CLOSPO_02083 from  Clostridium sporogenes  and RUMGNA_01526 from  Ruminococcus gnavus  (Williams et al. (2014) Cell Host Microbe 16:495-503). 
     In another embodiment, the pathway to produce indolepropionate (IPA) is introduced into the genetically modified microbe. IPA has been implicated in intestinal barrier fortification by engaging the pregnane X receptor (Venkatesh et al. (2014) Immunity 41:296-310) and is known to be synthesized by a small number of gut bacteria (Elsden et al. (1976) Arch. Microbiol. 107:283-288). However, the pathway for its synthesis is uncharacterized. The genes encoding this pathway have recently been discovered in  Clostridium sporogenes , enabling a pathway to be proposed. Indolepyruvate, synthesized as described above, is reduced to indolelactate which is then dehydrated to produce indoleacrylate. Finally, indoleacrylate is reduced to IPA by an acyl-CoA dehydrogenase. These are encoded by the fldH, fldBC, and acdA genes in  C. sporogenes , respectively (Dodd et al. (2017) Nature 551:648-652). Homologs of these genes in other microbes are also candidates for expression, found by BLAST of the  C. sporogenes  genes. 
     In another embodiment, a microbe used to practice embodiments as provided herein is engineered to consume a sugar or polysaccharide, for example, a cellobiose, which is a reducing sugar consisting of two β-glucose molecules linked by a β(1→4) bond that is recalcitrant to catabolism by most gut microbes. Consumption of cellobiose first requires a specific enzyme II complex (EC:2.7.1.205) of the phosphotransferase system (PTS), such as the celABC operon in  E. coli  (Keyhani et al. (2000) J. Biol. Chem. 275:33091-33101). When expressed in a heterologous host, this component functions together with the native PTS machinery to import and phosphorylate cellobiose to generate cellobiose-6-phosphate. Alternate candidates for this step are listed below: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 celA 
                 
                   Enterococcus gilvus 
                 
                 WP_10781765.1 
               
               
                 celB 
                 
                   Enterococcus gilvus 
                 
                 WP_010780456.1 
               
               
                 celC 
                 
                   Enterococcus gilvus  
                 
                 WP_010780458.1 
               
               
                 celA 
                   Lactococcus lactis  subsp.  lactis   
                 NP_266573.1 
               
               
                 celB 
                   Lactococcus lactis  subsp.  lactis   
                 NP_266330.1 
               
               
                 ptcA 
                   Lactococcus lactis  subsp.  lactis   
                 NP_266570.1 
               
               
                 celB 
                 
                   Bacillus coagulans  
                 
                 BF29_RS14550 
               
               
                   
               
            
           
         
       
     
     A 6-phospho-beta-glucosidase (EC:3.2.1.86) is then required to convert the cellobiose-6P into one molecule of glucose and one molecule of glucose-6-P, both of which are readily used by the host. An example is the 6-phospho-beta-glucosidase from  Bacillus coagulans , which has successfully been expressed in  E. coli  (Zheng et al. (2018) Biotechnology for Biofuels 18:320). Alternate candidates are listed below: 
     
       
         
           
               
               
               
             
               
                   
               
             
            
               
                 celA 
                 
                   Enterococcus gilvus  
                 
                 WP 0781765.1 
               
               
                 celB 
                 
                   Enterococcus gilvus  
                 
                 WP_010780456.1 
               
               
                 celC 
                 
                   Enterococcus gilvus  
                 
                 WP_010780458.1 
               
               
                 celA 
                   Lactococcus lactis  subsp.  lactis   
                 NP_266573.1 
               
               
                 celB 
                   Lactococcus lactis  subsp.  lactis   
                 NP 266330.1 
               
               
                 ptcA 
                   Lactococcus lactis  subsp.  lactis   
                 NP_266570.1 
               
               
                 celB 
                 
                   Bacillus coagulans  
                 
                 BF29_RS14550 
               
               
                   
               
            
           
         
       
     
     In another embodiment, a microbe used to practice embodiments as provided herein is genetically modified by deleting or reducing expression of genes to eliminate or reduce production of metabolites, such as the polyamines putrescine, spermidine, and cadaverine. These molecules are essential for gastrointestinal mucosal cell growth and function, but excess of these compounds has been linked to gut dysbiosis and poor nutrient absorption (Forget et al. (1997) J. Pediatr. Gastroenterol. Nutr. 24:285-288). The primary routes for polyamine synthesis in bacteria are decarboxylation of the amino acid&#39;s arginine or ornithine. Ornithine decarboxylase (ODC, EC:4.1.1.17) converts ornithine to putrescine, while arginine decarboxylase (ADC, EC:4.1.1.19) converts arginine to agmatine, which is subsequently converted to putrescine by agmatinase (EC:3.5.3.11). Putrescine can then be converted to other derivatives such as spermidine. Therefore, a reduction in ODC and/or ADC expression will reduce polyamine production in the host microbe.  E. coli  contains two ODC isomers, encoded by the speC and speF genes, as well as two isomers of ADC encoded by speA and adiA. BLAST searches using these sequences, or other known bacterial ODC and ADC genes, applied to the genome of the organism of interest is used to identify genes encoding these functions in the organism to be genetically modified. One or both of these genes, or homologs thereof, are then deleted from the host genome using tools such as lambda-red mediated recombination (Datsenko and Wanner (2000) Proc. Nat. Acad. Sci. USA 97:6640-6645), CRISPR-Cas9 genome editing (Bruder et al (2016) Appl. Environ. Microbiol. 82:6109-6119), or any other method resulting in the removal of genes or portions of genes from the chromosome. In another embodiment, these methods are used to replace the native promoters of these genes with alternate promoters of different strengths, or to modify the ribosome binding site, resulting in reduced production of the ODC and ADC enzymes. In yet another embodiment, expression is reduced through a gene silencing mechanism such as antisense RNA-based attenuation (Nakashima et al. (2012) Methods Mol. Biol. 815:307-319) or CRISPR interference (Choudhary et al. (2015) Nat. Comm. 6:6267). 
     Bioinformatic Discovery of Putative Immunomodulatory Proteins and Genetic Modification of Exemplary Therapeutic Microbes 
     In alternative embodiments, genetically modified microorganisms as provided herein, including microorganisms as listed in Tables 1, 4 and 7, and a bacterium from a combination of microbes as provided herein, for example, as in Table 9 and/or Table 42, Example 25, are engineered to express immunomodulatory, for example, immunostimulatory, proteins, or to overexpress endogenous immunomodulatory proteins. In alternative embodiments, the immunomodulatory are secreted or are cell surface-expressed or membrane-expressed proteins. 
     Organisms of interest are bioinformatically interrogated for expression of putative immunomodulatory proteins. Based on immune correlation analysis and the differential relative abundance of organisms between cancer and control samples, certain organisms are identified as being missing from the cancer microbiome and potentially immunostimulatory and having anti-cancer properties. These identified organisms can be incorporated into formulations as provided herein, or into combinations of microbes as provided herein; or, the immunomodulatory proteins they express are identified and genetically engineered into organisms as provided herein, for example, as listed in Tables 1, 4, 7, 8 and 9. In alternative embodiments, an organism as provided herein (as used in a method as provided herein) is genetically modified to overexpress the discovered immunomodulatory protein or proteins. Organisms potentially immunostimulatory and having anti-cancer properties are highlighted in Example 10. 
     For example,  Dorea formicigenerans  is one such organism, with strong positive correlations in both cancer and control cohorts to CD3+ and CD3+CD56+ immune cells in peripheral blood. First, a database of proteins is downloaded and clustered by similarity. Predicted proteins are downloaded from the NCBI RefSeq genomic database for a representative set of microbial genome assemblies. All complete genome assemblies for bacteria and archaea are included. For the taxa of special interest, which include Verrucomicrobia, Clostridia, and Coriobacteria, all assemblies of any status are included. Predicted proteins are downloaded from RefSeq and clustered using mmseqs2 (Steinegger and Soding. (2017) Nature Biotechnology 35:1026-1028). The resulting clusters contain proteins with identical or highly similar sequences. For a specific organism of interest, the protein clustering analysis is used to identify genes that are mostly unique to the organism yet ubiquitous across the organism&#39;s pangenome. These genes are likely candidates to mediate the immunomodulatory functions that are specific to the organism of interest. A standard bioinformatic analysis is performed on genes unique to the organism of interest to identify protein domains within each gene as being signal, cytoplasmic, non-cytoplasmic, or transmembrane domains. Because immunomodulatory genes need to interact with immune cells, they are generally secreted proteins (Quevrain et al. (2016) Gut 65:415-425) or membrane proteins (Plovier et al. (2017) Nature Medicine 23:107-113). Secreted proteins are identified from the analysis using the signal domains, while membrane proteins are identified by the presence of transmembrane domains. Because proteins with several transmembrane domains tend to be transporters, the focus is on proteins with one or two transmembrane domains. Membrane proteins or secreted proteins from the analysis of genes unique to the organism are prioritized for overexpression in genetically modified microorganisms as provided herein. 
     In alternative embodiments, genetically modified microorganisms as provided herein are engineered to express exogenous membrane proteins or secreted proteins. Genes unique to the organism of interest that are also membrane proteins or secreted proteins are investigated in a bespoke manner using the publicly available BLAST or Pfam search engines. In one embodiment, the organism is genetically modified to express these or homologues of identified membrane proteins. From this analysis, one protein from  Dorea formicigenerans , NCBI Reference Sequence WP_118145075.1 is a particularly attractive candidate. The protein family for WP_118145075.1 contains 28 protein sequences, of which 26 are from  Dorea formicigenerans  genomes. There are 27 total  Dorea formicigenerans  assemblies in the database, so 26 out of 27 assemblies contains a version of protein WP_118145075.1. When analyzed on BLAST and Pfam, WP_118145075.1 is identified as a pilus-like protein. Pili and related proteins have a known role in interaction with human cells (Lizano et al. (2007) Journal of Bacteriology 189:1426-1434; Plovier et al. (2017) Nature Medicine 23:107-113; Ottman, N., et al. (2017) PLOS ONE 12(3):e0173004). Genes may also be identified as containing pilus-like structures or other known immunomodulatory structures using public available techniques such as PilFind (Imam et al. (2011) PLOS ONE 6(12):e28919). In alternative embodiments, these pilus-like structures or other known immunomodulatory structures are engineered into genetically modified microorganisms as provided herein. 
     Other pili-like proteins of interest and corresponding homologs used in genetically engineered organism as provided herein include the highly abundant outer membrane protein of  Akkermansia muciniphila , Amuc_1100 and members of the Amuc_1098 Amuc_102 gene cluster, have been shown to induce the production of specific cytokines (IL-8, IL-1β, IL-6, IL-10 and TNF-α) through activation of Toll-like receptors (TLR) 2 and TLR4 (Ottman et al (2017) PLoS One 12, e0173004). Similar outer membrane proteins are believed to be responsible for the induction of cytokine IL-10 by commensal gut microbes such as  Faecalibacterium prausnitzii  A2-165 and  Lactobacillus plantarum  WCFS1. 
     In another embodiment, a genetically engineered organism as provided herein is genetically modified to express homologues of bacterial flagellin to induce TLR5 signaling. TLR5 response to flagellin promotes both innate and adaptive immune functions for gut homeostasis (Leifer et al (2014) Immunol. Lett. 162, 3-9). Recently, flagellin been examined for anti-tumor and radioprotective properties and has shown potential in reducing tumor growth and radiation-associated tissue damage (Hajam et al (2017) Exp. Mol. Med. 49, e373-e373). Some flagellin-based anti-tumor vaccines have also successfully entered into human clinical trials. Flagellins (fliC) and homologues of interest include but are not limited to those from  Salmonella Typhimurium  (FliCi),  Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes , and  Serratia marcescens.    
     Identification of Immunomodulatory Proteins Via Pooled Screening 
     In alternative embodiments, microbes used in compositions as provided herein, or as used in methods as provided herein, have enhanced immunomodulatory effects, for example, immune-stimulatory effects, and these microbes can be generated or derived either by selection using assays, as described below, or by inserting or enhancing the microbe&#39;s immunomodulatory effects by genetic engineering, for example, by inserting a heterologous nucleic acid into the microbe. In alternative embodiments, microbes that can express or overexpress immunomodulatory proteins or peptides are used with (in addition to, are administered with) microbes used in compositions as provided herein, or microbes used to practice methods as provided herein. 
     Microbial populations are assayed directly for immunomodulatory effects on dendritic cells. Starting with a fecal sample of interest containing an endogenous microbial population or starting with a synthetic microbial population consisting of pooled microbial isolates of interest, the population can be tested against dendritic cells ex vivo. 
     Purified dendritic cells are generated as described in previous work (Svensson and Wick. (1999) European Journal of Immunology 29(1):180-188; Svensson et al. (1997) Journal of Immunology 158(9):4229-4236; Yrlid et al. (2001) Infection and Immunity 69(9):5726-5735). Heat-inactivated, incubated for 30 minutes at 70° C., or live bacteria are added at a 50:1 ratio and incubated for 4 hours at 37° C. in IMDM containing 5% FBS. Following incubation, cells are washed 3× in HBSS to remove excess antigen. A portion of the dendritic cells are saved in RNAlater for future RNA sequencing. When activated, dendritic cells express several co-stimulatory molecules that aid in activating T cells. These molecules (CD40, CD80, and CD86) are upregulated alongside the chemokine receptor CCR7 which homes the activated DC to the spleen or local lymph node (Wilson and O&#39;Neill. (2003) Blood 102(5):1661-1669; Ohl et al. (2004) Immunity 21(2):279-288). This set of genes can therefore be used to sort mature, activated DCs from immature DCs that do not stimulate T cells effectively. Cells are stained for expression of one or more of CD86, CD40 and CD80, and sorted via Fluorescence Activated Cell Sorting (FACS). 
     Purified cells are processed as described previously (Abelin et al. (2017) Immunity 46(2):315-326) for HLA-peptide identification. Briefly, purified cells are dissociated in protein lysis buffer containing protease inhibitors and DNAse, and then sonicated. Following sonication, soluble lysates are incubated with SEPHAROSE™ beads linked to W6/32 antibody which are washed with lysis buffer lacking protease inhibitor, and finally washed with DI water. Peptides are then eluted from the HLA complex on EMPORE C18 STAGETIPS™. Purified protein preparations are then subjected to nanoLC-ESI-MS/MS. 
     Following LC-MS/MS, individual peptides are identified and matched to the reference genomes of the mix of microbes used in the in vitro activation experiment. A list of candidate peptides is generated by combining peptide abundance data with bioinformatics analysis of protein conservation, localization data, and their likelihood to express and localize to the membrane (Marshall et al. (2016) Cell Reports 16(8):2169-2177; Saladi et al. (2018) Journal of Biological Chemistry 293(13):4913-4927). 
     Identification and Validation of Microbes that Activate Immune Cell Receptors 
     In alternative embodiments, microbes used in compositions as provided herein, or as used in methods as provided herein, can activate immune cell receptors (for example, such as T cell receptors), and these microbes can be generated or derived either by selection using assays, as described below, or by inserting or enhancing the microbe&#39;s immunomodulatory effects by genetic engineering, for example, by inserting a heterologous nucleic acid into the microbe. In alternative embodiments, microbes that can express or overexpress proteins or peptides that can activate immune cell receptors are used with (in addition to, are administered with) microbes used in compositions as provided herein, or microbes used to practice methods as provided herein. 
     In alternative embodiments, ex vivo analyses are used to identify microbes that activate immune cell receptors including but not limited to dendritic cell Toll-like receptors (TLR&#39;s). Briefly, microbes of interest are co-incubated with human dendritic cells as described in the previous section, except that the co-incubation occurs with a pasteurized and washed microbial isolate rather than a microbial population. Dendritic cells are washed post-incubation. As described in Example 11, dendritic cells are saved and analyzed using RNA sequencing to identify gene expression changes relative to control conditions. The control conditions include both no stimulation i.e. microbial media alone, as well as known agonists for different TLR&#39;s. A computational analysis is performed to ascribe the gene expression of dendritic cells in response to each microbe to some amount of activation of each TLR, thus predicting microbe-TLR interactions. 
     For each predicted microbe-TLR interaction, the pasteurized and washed microbe is co-incubated with TLR reporter cells (HEK-Blue, InvivoGen), and a plate-based colorimetric assay used to measure TLR activation over time. Validated microbes can be further screened as described previously for specific genes that mediate their mechanistic effects. 
     Amplification of Therapeutic Effect by Overexpression of Immunomodulatory Genes 
     In alternative embodiments, microbes used in compositions as provided herein, or as used in methods as provided herein, overexpress immunomodulatory genes (for example, immunostimulatory genes), and these microbes can be generated or derived either by selection using assays, as described below, or by inserting or enhancing the microbe&#39;s immunomodulatory effects by genetic engineering, for example, by inserting a heterologous nucleic acid into the microbe. 
     In alternative embodiments, microbes used in compositions as provided herein, or used to practice methods as provided herein, are selected to express, or overexpress, an anti-viral molecule (such as an anti-viral small molecule, peptide or polypeptide such as an anti-viral antibody; or an anti-viral drug as provided or as described herein), an immunostimulatory protein or peptide, which can be non-specific immunostimulatory proteins such as a cytokine, for example, a cytokine such as an interferon (for example, IFN-α2a, IFN-α2b) IL-2, IL-4, IL-6, IL-7, IL-12, IFNs, TNF-α, granulocyte colony-stimulating factor (G-CSF, also known as filgrastim, lenograstim or NEUPOGEN®) and granulocyte monocyte colony-stimulating factor (GM-CSF, also known as molgramostim, sargramostim, LEUKOMAX®, MIELOGEN® or LEUKINE®), or a specific immunostimulatory protein or peptide, for example, such as an immunogen that can generate a specific humeral or cellular immune response, for example, an immune response to a viral antigen. In alternative embodiments, microbes that can express or overexpress immunostimulatory proteins or peptides are used with (in addition to, are administered with) microbes used in compositions as provided herein or used to practice methods as provided herein. 
     In one embodiment, an organism used to practice embodiments as provided herein is genetically modified to overexpress proteins or peptides with antiviral properties or as immunogenic components of antiviral vaccines. Several peptides have been identified that have the potential to interfere with the course of infection by the SARS-CoV2 virus (Mahendran et al (2020) Frontiers in Pharmacology https://doi.org/10.3389/fphar.2020.578382). For instance, the 36-mer peptide EK1 binds to the HR1 domain of the SARS-CoV2 spike protein, thereby inhibiting viral fusion entry into target host cells (Xia et al (2019) Cell. and Molec. Immunol. 17:765 https://doi.org/10.1038/s41423-020-0374-2). In another example, the 17-mer peptide Mucroporin-M1 is a mutational variant of an active protein from the venom of the scorpion  Lychas mucronatus  that is optimized for insertion and disruption of viral lipid envelopes such as that of SARS-CoV1 (Li et al (2011) Peptides 32:1518 DOI: 10.1016/j.peptides.2011.05.015). In another example, a 30-mer peptide derived from mouse b-defensins binds to the S2 subunit of MERS-CoV viral particles and upon fusion-entry blocks further viral infection progression by preventing acidification of the endosome (Zhao et al (2016) Scientific Reports https://doi.org/10.1038/srep22008). In other examples, peptides or proteins can be produced by overexpression in bacterial scaffold expression hosts that can serve as immunogenic components of peptide-based antiviral vaccines (Di Natale et al (2020) Frontiers in Pharmacology https://doi.org/10.3389/fphar.2020.578382). For instance, the anti-COVID vaccine NVX-CoV2373 in development by the company Novavax is a protein subunit nanoparticle vaccine comprised of expressed SARS-CoV2 Spike Protein and Matrix-M1 protein (Keech et al (2020) New Eng. J. Med. 383:2320 DOI: 10.1056/NEJMoa2026920). In another example, bacterial expression chassis can serve to both express vaccine protein components as well as a delivery vehicle of such vaccine components to the gut mucosa (Thole et al (2000) Current Opinion in Molec. Therapeutics 2:94 PMID: 11249657), where it can elicit immune responses against gut-localized infection by SARS-CoV2 or other gastrointestinal viruses. 
     Genes identified from a bioinformatic or pooled experimental approach as having an immunomodulatory effect are validated using recombinant expression in an engineered chassis organism. In alternative embodiments, the engineered chassis organism is used as a strong modulator (for example, stimulator) of immune activity as a component of a live biotherapeutic as provided herein (for example, as a component of a combination of microbes as provided herein, for example, as a component of an exemplary combination as listed in Table 9 and/or Table 42, Example 25), or the engineered chassis organism can be used in addition to a live biotherapeutic as provided herein. 
     Nucleic acids encoding protein sequences capable of enhancing a microbe&#39;s immunomodulatory effects are synthesized and cloned or inserted into a microbe, for example, bacterium, used in a combination of microbes as provided herein (as in for example, Table 9 and/or Table 42, Example 25), including for example any bacterium as listed in Table 1, Table 4 or Table 7, for example, such as a  B. subtilis. B. subtilis  is a generally recognized as safe (GRAS) organism that has extensive tools available for the cloning and expression of synthetically encoded proteins (see for example, Popp et al. (2017) Scientific Reports 7(1):15058). Following cloning, colonies containing each different synthetic protein are grown until logarithmic phase. Each culture is pasteurized and washed as described previously. The cultures are validated for immunomodulatory activity relative to a negative control consisting of the unmodified chassis organism and positive control consisting of the unmodified original microbe of interest. 
     Each overexpressed gene can be validated for immunomodulatory activity using a TLR reporter assay as described previously, or a co-incubation with dendritic cells followed by mass spectrometry or RNA sequencing as described previously. Validated immunomodulatory engineered microbes can be incorporated into the candidate live biotherapeutic and advanced to in vivo screening in animal models. 
     Example 13: Whole Cell Mutagenesis and Selection Procedures for Therapeutic Microbes 
     In alternative embodiments, microbes as provided herein (including bacteria from all the genuses listed herein), and including the combinations of microbes as provided herein, for example, the exemplary combinations of microbes 1 to 294 as described in Table 9, Example 10, and/or Table 42, Example 25, are genetically modified to enhance antiviral capability, for example, increase the ability of the immune system to combat viral infections, stimulate activity of specific classes of immune cells, provide essential nutrients that may be depleted or blocked by the virus, produce compounds with antiviral activity, or other direct or indirect effect on cells of the innate or adaptive immune system. 
     Candidate live biotherapeutic strains are randomly mutagenized to generate a microbe with increased level of production of either a protein or metabolite of interest that may impact cancer treatment. When cells are mutagenized, changes occur in the DNA sequence that could result in changes of expression levels of certain genes. Often these mutations are lethal, but some strains survive and have altered phenotype, including some with increased expression of genes encoding proteins or metabolic pathways identified from patient data (Examples 9 and 10) or in vitro assays (Example 11). Mutagenesis is carried out by an established treatment such as ultraviolet light, N-ethyl-N-nitrosourea, or ethyl methanesulfonate, followed by culturing on non-selective media to obtain viable cells. Mutagen exposure is first tuned by varying the time or intensity of treatment to a small culture, then selecting the conditions which yield approximately 10-20% of the number of viable colonies compared to a non-treated control. These treatment conditions are then applied to a larger culture of cells, and mutagenized colonies obtained are screened for the phenotype of interest, such as increased production of a protein or metabolite of interest. Clones obtained from this screen are then further characterized by whole genome sequencing. 
     Example 14: Production of Live Biotherapeutics 
     In alternative embodiments, microbes as provided herein (including bacteria from all the genuses listed herein), and including the combinations of microbes as provided herein, for example, the exemplary combinations 1 to 294 as described in Table 9, Example 10, and/or Table 42, Example 25, comprise anaerobic bacteria, including anaerobic bacteria isolated from a fecal sample, cultured anaerobic bacteria, or a combination thereof. 
     Individual Culture of Anaerobic Microbes for Mouse Studies 
     Anaerobic microbes of interest are cultured in multiples of 1-liter volumes in anaerobic media bottles as follows. Microbes in cryostorage are plated and struck on appropriate anaerobic solid medium and then cultured at 37° C. to obtain isolated colonies. For each microbe, a single colony is inoculated into a Hungate tube containing 10 ml appropriate anaerobic growth medium and allowed to grow at 37° C. until turbid to create a starter culture. For each microbe of interest, multiple 0.9-liter volumes of appropriate liquid anaerobic medium in 1 L anaerobic bottles (as described in Example 1) are inoculated with 2 ml starter culture each using a needle and syringe. The number of 1-liter cultures for each microbe is dependent on the necessary final amount of live cell mass for formulation into live biotherapeutics for mouse studies. Inoculated bottles are placed upright on a platform shaker at 115 rpm at 37° C. for 48 hours or until growth turbidity is evident. Growth density is monitored by taking 1 ml samples during the cultures for optical density measurements at 600 nm. Optical densities of 1.0 to 4.0 can be obtained after 48 hours depending on the microbe cultured. Prior to large scale culture, cell densities are determined empirically for each microbe by dilution plating and colony counting to determine the colony forming units (CFU) per ml at an optical density of 1.0. 
     Large scale cultures are grown to attain a final live density of 1.0E8 to 1.0E9 CFU/ml, and then the culture bottles are brought into the anaerobic chamber for harvesting of live cell mass. Once in the chamber, the aluminum collars and butyl rubber bungs are removed, and the 1-liter contents of each culture bottle are poured into two 500 ml centrifuge bottles with rubber gasketed screw caps. After decanting growth medium, the caps of the centrifuge bottles are tightened for an airtight seal, brought out of the anaerobic chamber, then centrifuged for 20 minutes at 6000 g at 4° C. Centrifuged bottles are then brought into the anaerobic chamber, uncapped, and then the supernatants are poured off and discarded. The remaining cell pellets are then combined with 250 ml ice cold Vehicle Buffer (Phosphate Buffered Saline plus 1 g/L L-cysteine plus 15% glycerol, filter sterilized and made anoxic by bubbling with filtered nitrogen). The cell pellets are carefully resuspended in the Vehicle Buffer on ice; the resuspended volumes of two pellets are combined into one 500 ml bottle, recapped for an air-tight seal, removed from the anaerobic chamber, then centrifuged for 20 minutes at 6000 g at 4° C. After decanting supernatants in the anaerobic chamber, resulting cell pellets are then carefully resuspended once more with 250 ml ice cold Vehicle Buffer in the anaerobic chamber, removed from the anaerobic chamber, then centrifuged for 20 minutes at 6000 g at 4° C. After removal of supernatant in the anaerobic chamber, each pellet is resuspended in 100 ml ice cold Vehicle Buffer to establish a ten-fold concentration of the original culture cell density. 
     Within the anaerobic chamber, final resuspended cell pellet volumes for an anaerobic microbe of interest are combined and thoroughly mixed in a sterile bottle by gentle stirring on a stir plate on ice. The volume is then dispensed into 25 ml aliquots in 50 ml conical tubes using a serological pipette, then a stream of sterile filtered gaseous argon is introduced to each tube to displace the headspace and to serve as an oxygen barrier. Each tube is then tightly capped, and the seal is wrapped with several layers of parafilm. The tubes are then racked upright, removed from the anaerobic chamber, and then allowed to slowly freeze at −80° C. A smaller 5 ml aliquot is also made for each preparation and stored as described above. After 18 hours, the 5 ml aliquots for each microbial strain of interest are removed and allowed to thaw standing in ice water within the anaerobic chamber. The thawed volumes are gently mixed by inversion several times, then subjected to dilution plating on appropriate solid anaerobic medium to determine the live cell density in CFU/ml after freezer storage. 
     Live Biotherapeutic Assembly for Mouse Studies 
     Live biotherapeutic compositions of anaerobic microbes of interest, including the combinations of microbes as provided herein, for example, the exemplary combinations 1 to 294 as described in Table 9, Example 10, and/or Table 42, Example 25, are assembled in volumes that are pertinent for projected mouse studies. Enough aliquots for each microbe of interest are removed from storage at −80° C. and gently thawed in ice water in the anaerobic chamber. The thawed multiple aliquots are combined in a sterile bottle, gently remixed and then placed on ice. The amount of volume of each microbe to add to a mix is adjusted so that the determined live cell densities for each microbe are equivalent, and final total cell densities can be adjusted by further addition of ice-cold vehicle buffer. Once all requisite volumes for each microbe are added together in a larger sterile bottle, the volume is gently mixed by stirring on a stir plate on ice. 
     Live biotherapeutic volumes are then re-aliquoted in individual volumes that each comprise a projected daily dose of live microbes in anticipated mouse studies. Determined volumes are each dispensed in 15 ml conical tubes up to 10 ml per aliquot. The volume in each tube is overlaid with a stream of sterile filtered argon to displace oxygen, followed by capping. Live biotherapeutic aliquot tubes are racked upright and allowed to slowly freeze at −80° C. After 48 hours, one aliquot for each microbial mix preparation is thawed and dilution plated to validate the final total CFU/ml, optimally at greater than 1.0×10 9  CFU/ml. 
     Example 15—Efficacy of Anticancer Live Biotherapeutics with Checkpoint Inhibitors 
     The results described here were obtained from studies conducted with tumor mouse models evaluating the anticancer efficacy of generated live biotherapeutics as a monotherapy and in combination with checkpoint therapy. Microbes, gene functions, and metabolites elucidated as critical for anticancer treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbes beneficial for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. 
     Mice with and without tumors are given microbial cocktails by oral gavage, as described in the example above. The 16S RNA sequencing results are used to determine the distribution of organisms in each sample at both the phylum and genus level, and the distribution is compared across all fecal samples from mice without tumors to determine how these microbes colonize the gut. PCA is used to classify all samples of mice without tumors, showing that samples with the same microbial treatment type cluster together. In addition, the genera represented by each microbial treatment have increased representation in those samples compared to those of different treatment type. 
     Tumor size is measured in all animals receiving the different microbial treatments, with and without anti-CTLA4 therapy. On average, the animals receiving microbial mix 4 (equal amounts of  F. prausnitzii, C. coccoides, R. gnavus, C. scindens, E. lenta , and  G. urolithinfaciens ) in conjunction with ellagic acid and anti-CTLA4 have a reduction in tumor size compared to those with other microbes or not receiving any anti-CTLA-4 treatment, as illustrated in  FIG.  3   . Termination of dosing of both the microbial and anti-CTLA-4 treatments were performed at day 28 and mice were evaluated. Mice treated with microbial mix 4 and the anti-CTLA-4 therapy had minimal tumor growth in contrast to the other groups, as shown in  FIG.  29   . 
     FACS analysis of whole blood obtained from the animals at the end of the study indicated that CD4 and CD8 T-lymphocyte activity are increased by treatment with microbial mix 4 in conjunction with anti-CTLA-4 as shown in the “population table” of  FIG.  30   . Similarly, it has been shown in mice that the commensal microbiota critically regulates the generation of virus-specific CD4 and CD8 T cells and antibody responses following respiratory influenza virus infection (T. Ichinohe et al., Proc. Natl. Acad. Sci. U.S.A 108, 5354-9 (2011)). This further supports that live biotherapeutics described herein that are critical for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. 
       FIG.  31    graphically illustrates data showing the efficacy of anti-CTLA-4 treatment in mice with CT26 cancer tumor graft and supplemented with nutrients and/or microbial mixtures. Datapoints refer to tumor volume (mm 3 ) at each day measurements were taken, averaged over either 8 mice (no CTLA-4) or 8 mice (with CTLA-4) with standard error shown. 
     Tumor size is measured in all animals receiving the different microbial treatments, with and without anti-CTLA-4 therapy. On average, the animals receiving microbial mix 2 ( F. prausnitzii, C. coccoides, R. gnavus, C. scindens, A. muciniphila , and  E. hirae ) in conjunction with anti-CTLA-4 have a reduction in tumor size compared to those with other microbes or not receiving any anti-CTLA-4 treatment, as illustrated in  FIG.  31   . 
     Metabolomics 
     Commensal microbiota metabolites have been shown to be critical in suppressing influenza virus as well as the replication of herpes simplex virus (HSV)-2 (N. Li, et. al. Front. Immunol. 10 (2019), p. 1551). The results described here were obtained from studies conducted with tumor mouse models evaluating the anticancer efficacy of generated live biotherapeutics as a monotherapy and in combination with checkpoint therapy. Metabolites elucidated as critical for anticancer treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbial metabolites beneficial for rapid viral clearance. 
     Mouse fecal samples, either raw or resuspended in PBS, were kept frozen at −80 degrees C. until processing, then immediately placed in a lyophilizer and freeze-dried overnight. The resulting material was weighed, and lyophilized fecal samples were extracted and processed at a constant per-mass basis using an established procedure (Evans, A. et al. High resolution mass spectrometry improves data quantity and quality as compared to unit mass resolution mass spectrometry in high-throughput profiling metabolomics. J. Postgenomics Drug Biomark. Dev. 4, S24-S36 (2014)) by Metabolon, Inc. Recovery standards were added before the first step in the extraction process for quality-control purposes. Samples are prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards are added prior to the first step in the extraction process for QC purposes. Samples are extracted with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation to recover chemically diverse metabolites. The resulting extract is divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods using positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS using negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS using negative ion mode ESI, and one reserved for backup. Samples are placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts are stored overnight under nitrogen before preparation for analysis. 
     All analytical methods utilize a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract is dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot is analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract is gradient-eluted from a C18 column (Waters UPLC BEH C18-2.1×100 mm, 1.7 μm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). A second aliquot is also analyzed using acidic positive ion conditions but is chromatographically optimized for more hydrophobic compounds. In this method, the extract is gradient eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA, and is operated at an overall higher organic content. A third aliquot is analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts are gradient eluted from the column using methanol and water, however with 6.5 mM Ammonium Bicarbonate at pH 8. The fourth aliquot is analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1×150 mm, 1.7 μm) using a gradient consisting of water and acetonitrile with 10 mM Ammonium Formate, pH 10.8. The MS analysis alternates between MS and data-dependent MS n  scans using dynamic exclusion. The scan range varies slightly between methods, but covers approximately 70-1000 m/z. 
     Three types of controls were analyzed in concert with the experimental samples: a pooled sample generated from a small portion of each experimental sample of interest served as a technical replicate throughout the platform run; extracted water samples served as process blanks; and a cocktail of standards spiked into every analyzed sample allowed for instrument performance monitoring. Instrument variability was determined by calculation of the median relative s.d. (RSD) for the standards that were added to each sample before injection into the mass spectrometers (median RSDs were determined to be 3%). Overall process variability was determined by calculating the median RSD for all endogenous metabolites (i.e., non-instrument standards) present in 90% or more of the pooled technical-replicate samples (median RSD=8%, n=797 metabolites). 
     Compounds are identified by comparison to library entries of purified standards maintained by Metabolon, that contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data) on all molecules present in the library. Furthermore, biochemical identifications are based on three criteria: retention index within a narrow RI window of the proposed identification, accurate mass match to the library+/−10 ppm, and the MS/MS forward and reverse scores. MS/MS scores are based on a comparison of the ions present in the experimental spectrum to ions present in the library entry spectrum. While there may be similarities between these molecules based on one of these factors, the use of all three data points can be utilized to distinguish and differentiate biochemicals. Peaks are quantified as area-under-the-curve detector ion counts. 
     Metabolomics Performed on Fecal Samples 
     Metabolomics was performed on fecal samples taken from mice in the control group, treated with vehicle and no checkpoint inhibitor, the group treated with microbial mix 4 and ellagic acid only, the group treated with anti-CTLA-4 only, and the group treated with anti-CTLA-4, microbial mix 4, and ellagic acid. In the tables and figures that follow, these are referred to as the Control, Microbe, Drug, and Combo, respectively. Samples were processed from timepoint 1 (T1), prior to any treatment; timepoint 4 (T4), 10 days from start and 48 hours after the 3 rd  treatment dose; and timepoint 7 (T7), 20 days from start and 48 hours after the 6 th  treatment dose. 
     Principal components analysis (PCA) was applied on all samples to give a global view of the data. The Control group segregated by timepoint, indicating a gradual shift in the metabolome over time as the cancer progressed. A similar pattern was exhibited by the drug group, while the Microbe and Combo groups shifted in a different direction. There was little distinction among treatment groups at T1 and T4, while significant differences were observed at T7 ( FIG.  32   ). At T7, the microbe and combo groups had changes with p&lt;0.05 in 25% and 40% of all the metabolites detected, respectively, whereas the drug group only had such change in 9% of the metabolites. 
     Next, individual metabolic pathways and classes of metabolites were considered. The levels of amino acids (unmodified, gamma-glutamyl and acetylated) along with peptides (dipeptides and polypeptides) were lower in the Microbe and Combo groups relative to the Controls at T7 (Table 20). Declines in dipeptides and amino acids in the fecal samples highlight the possibility that proteolysis of both human and microbial-derived peptides, and microbial amino acid excretion, may have lessened following treatment with microbial mix 4. More evidence to support this notion came from the levels of gamma-glutamyl amino acids and N-acetylated amino acids, both of which were decreased in the fecal samples of Microbe and Combo groups. N-acetyl amino acids can be derived from proteins that have undergone post-translational acetylation reactions or from free amino acids reacting with acetyl groups. Gamma-glutamyl AAs are generated by gamma-glutamyl transpeptidase, which plays an important role in amino acid uptake. Decreased fecal levels of proteolysis markers may reflect diminished gut motility and increased transit time. 
     
       
         
           
               
             
               
                 TABLE 20 
               
             
            
               
                   
               
               
                 Amino acids, acylated amino acids, and gamma-glutamyl amino 
               
               
                 acids in mouse fecal samples at T7. Ratio of the mean peak areas for the  
               
               
                 specifie dmetabolites in each group relative to the control group. Up or down  
               
               
                 arrows indicate whether the increase or decrease in the treatment relative to  
               
               
                 the control is significant based on Welch’s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                 Compound 
                 Microbe T7 
                 Drug T7 
                 Combo T7 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Glycine 
                 0.59  
                 ↓ 
                 0.79 
                   
                 ↓ 
                 0.71 
               
               
                 Serine 
                 0.59  
                 ↓ 
                 0.81 
                   
                 ↓ 
                 0.60 
               
               
                 Threonine 
                 0.46  
                 ↓ 
                 0.84 
                   
                 ↓ 
                 0.57 
               
               
                 Alanine 
                 0.59  
                 ↓ 
                 0.97 
                   
                 ↓ 
                 0.65 
               
               
                 Aspartate 
                 0.49  
                 ↓ 
                 0.81 
                   
                   
                 0.62 
               
               
                 Asparagine 
                 0.30  
                 ↓ 
                 0.59  
                 ↓ 
                 ↓ 
                 0.42 
               
               
                 Glutamate 
                 0.51  
                 ↓ 
                 0.97 
                   
                 ↓ 
                 0.57 
               
               
                 glutamine 
                 0.91 
                   
                 0.71 
                   
                 ↓ 
                 0.62 
               
               
                 histidine 
                 0.77 
                   
                 0.84 
                   
                 ↓ 
                 0.62 
               
               
                 lysine 
                 0.50  
                 ↓ 
                 1.05 
                   
                 ↓ 
                 0.56 
               
               
                 Phenylalanine 
                 0.74 
                   
                 0.98 
                   
                 ↓ 
                 0.66 
               
               
                 tyrosine 
                 0.60  
                 ↓ 
                 0.97 
                   
                 ↓ 
                 0.57 
               
               
                 tryptophan 
                 0.79 
                   
                 0.91 
                   
                 ↓ 
                 0.67 
               
               
                 Leucine 
                 0.74 
                   
                 0.97 
                   
                 ↓ 
                 0.66 
               
               
                 isoleucine 
                 0.61  
                 ↓ 
                 0.92 
                   
                 ↓ 
                 0.65 
               
               
                 valine 
                 0.60 
                   
                 0.97 
                   
                 ↓ 
                 0.64 
               
               
                 Arginine 
                 0.95 
                   
                 1.39 
                   
                   
                 0.86 
               
               
                 proline 
                 1.14 
                   
                 1.12 
                   
                   
                 1.03 
               
               
                 N-acetylserine 
                 0.79 
                   
                 1.42 
                   
                   
                 0.53 
               
               
                 N-acetylthreonine 
                 0.59 
                   
                 1 
                   
                 ↓ 
                 0.42 
               
               
                 N-acetylalanine 
                 0.47  
                 ↓ 
                 1.05 
                   
                 ↓ 
                 0.52 
               
               
                 N-acetylaspartate 
                 0.27  
                 ↓ 
                 1.04 
                   
                 ↓ 
                 0.65 
               
               
                 N-acetylasparagine 
                 0.27  
                 ↓ 
                 0.93 
                   
                 ↓ 
                 0.36 
               
               
                 N-acetylglutamate 
                 0.36  
                 ↓ 
                 1.18 
                   
                 ↓ 
                 0.76 
               
               
                 N-acetylglutamine 
                 0.86 
                   
                 0.94 
                   
                 ↓ 
                 0.64 
               
               
                 N-acetylhistidine 
                 0.88 
                   
                 0.88 
                   
                   
                 0.67 
               
               
                 N2-acetyllysine 
                 0.37  
                 ↓ 
                 1.04 
                   
                 ↓ 
                 0.61 
               
               
                 N6-acetyllysine 
                 0.41  
                 ↓ 
                 1.05 
                   
                 ↓ 
                 0.56 
               
               
                 N-acetylphenylalanine 
                 0.71 
                   
                 0.95 
                   
                 ↓ 
                 0.53 
               
               
                 N-acetyltyrosine 
                 0.38  
                 ↓ 
                 0.96 
                   
                 ↓ 
                 0.36 
               
               
                 N-acetyltryptophan 
                 1.17 
                   
                 0.97 
                   
                   
                 1.01 
               
               
                 N-acetylleucine 
                 0.78 
                   
                 1.12 
                   
                   
                 0.58 
               
               
                 N-acetylisoleucine 
                 0.79 
                   
                 0.99 
                   
                 ↓ 
                 0.55 
               
               
                 N-acetylvaline 
                 0.99 
                   
                 1.3 
                   
                   
                 0.8 
               
               
                 N-acetylarginine 
                 0.59 
                   
                 1.2 
                   
                 ↓ 
                 0.51 
               
               
                 N-acetylcitrulline 
                 0.4  
                 ↓ 
                 1.23 
                   
                 ↓ 
                 0.35 
               
               
                 N-acetylproline 
                 0.85 
                   
                 0.97 
                   
                 ↓ 
                 0.66 
               
               
                 Gamma-glutamylglutamate 
                 0.48  
                 ↓ 
                 0.91 
                   
                 ↓ 
                 0.55 
               
               
                 Gamma-glutamylglutamine 
                 0.77 
                   
                 0.69 
                   
                 ↓ 
                 0.56 
               
               
                 Gamma-glutamylisoleucine 
                 1.07 
                   
                 0.79 
                   
                   
                 1.65 
               
               
                 Gamma-glutamylleucine 
                 0.57 
                   
                 0.83 
                   
                 ↓ 
                 0.50 
               
               
                 Gamma-glutamylalpha-lysine 
                 0.36  
                 ↓ 
                 0.69 
                   
                 ↓ 
                 0.36 
               
               
                 Gamma-glutamylepsilon-lysine 
                 0.48 
                   
                 0.72 
                   
                 ↓ 
                 0.24 
               
               
                 Gamma-glutamylmethionine 
                 0.33  
                 ↓ 
                 0.86 
                   
                 ↓ 
                 0.41 
               
               
                 Gamma-glutamylphenylalanine 
                 0.61 
                   
                 0.93 
                   
                 ↓ 
                 0.53 
               
               
                 Gamma-glutamylthreonine 
                 0.39  
                 ↓ 
                 0.82 
                   
                 ↓ 
                 0.58 
               
               
                 Gamma-glutamyltyrosine 
                 0.53 
                   
                 0.98 
                   
                 ↓ 
                 0.48 
               
               
                 Gamma-glutamylvaline 
                 0.30 
                   
                 0.89 
                   
                   
                 0.55 
               
               
                 Gamma-glutamylserine 
                 0.47  
                 ↓ 
                 0.74 
                   
                 ↓ 
                 0.42 
               
               
                 Gamma-glutamylcitrulline 
                 0.25 
                 ↓ 
                 0.83 
                   
                   
                 0.51 
               
               
                   
               
            
           
         
       
     
     Cysteine is an important amino acid for redox balance because it contains a highly reactive thiol group which imparts the ability to participate in numerous reactions. Cysteine can be synthesized from methionine and serves as a precursor to antioxidants such as glutathione and taurine. Cysteine levels, as were upstream and downstream metabolites, were lower in the Microbe and Combo groups relative to Control (Table 21). This was consistent with the overall pattern of amino acid detection. Changes in cysteine metabolites may be signals of changes in redox status, as they are precursors for glutathione synthesis. 
     
       
         
           
               
             
               
                 TABLE 21 
               
             
            
               
                   
               
               
                 Methionine and derivatives in mouse fecal samples at time T7.  
               
               
                 Ratio of the mean peak areas for the specified metabolites in each  
               
               
                 group relative to the control group. Up or down arrows indicate whether  
               
               
                 the increase or decrease in the treatment relative to the control is  
               
               
                 significant based on Welch’s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                 Compound 
                 Microbe T7 
                 Drug T7 
                 Combo T7 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Methionine 
                 0.43  
                 ↓ 
                 0.95 
                 0.5 
                 ↓ 
               
               
                 N-acetylmethionine 
                 0.56  
                 ↓ 
                 0.99 
                 0.58  
                 ↓ 
               
               
                 N-formylmethionine 
                 0.64 
                   
                 1.09 
                 0.57  
                 ↓ 
               
               
                 Methionine sulfoxide 
                 0.52  
                 ↓ 
                 0.93 
                 0.6  
                 ↓ 
               
               
                 N-acetylmethionine sulfoxide 
                 0.76 
                   
                 0.88 
                 0.64  
                 ↓ 
               
               
                 cysteine 
                 0.59  
                 ↓ 
                 1 
                 0.72  
                 ↓ 
               
               
                 N-acetylcysteine 
                 0.44  
                 ↓ 
                 1.16 
                 0.49  
                 ↓ 
               
               
                 Cysteine sulfate 
                 0.87 
                   
                 0.72 
                 1.33 
                   
               
               
                 cystine 
                 0.39  
                 ↓ 
                 0.68 
                 0.32  
                 ↓ 
               
               
                 taurine 
                 1.19 
                   
                 1.75 
                 1.85 
                   
               
               
                 3-sulfo-L-alanine 
                 0.3  
                 ↓ 
                 1.04 
                 0.54  
                 ↓ 
               
               
                   
               
            
           
         
       
     
     Carboxyethyl amino acids were elevated only following Microbe monotherapy. Interestingly, this increase was not sustained during the combination treatment (Table 22). The Drug potentially had an opposing effect on the production of these analytes. Indeed, although never reaching significance, these levels tended to be lower in the Drug T7 group relative to Control. 
     
       
         
           
               
             
               
                 TABLE 22 
               
             
            
               
                   
               
               
                 Carboxyethyl amino acids in mouse fecal samples at time T7. Ratio 
               
               
                 of the mean peak areas for the specified metabolites in each group  
               
               
                 relative to the control group. Up or down arrows indicate whether  
               
               
                 the increase or decrease in the treatment relative to the control is  
               
               
                 significant based on Welch’s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                 Compound 
                 Microbe T7 
                 Drug T7 
                 Combo T7 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 1-carboxy ethylisoleucine 
                 1.56 
                 0.64 
                 0.89 
               
               
                 1-carboxy ethylleucine 
                 2.43  
                 0.67 
                 0.82 
               
               
                 1-carboxy ethylphenylalanine 
                 2.77  
                 0.69 
                 0.92 
               
               
                 1-carboxy ethyltyrosine 
                 2.52  
                 0.8 
                 1 
               
               
                 1-carboxy ethylvaline 
                 3.26  
                 0.84 
                 1.19 
               
               
                   
               
            
           
         
       
     
     Pterins make up a group of small metabolites that serve as cofactors for various cell processes. Pterins are excreted by human urine and elevated levels have been detected when the cellular immune system is activated by diseases such as cancer (Koslinski, P., et al., Metabolic profiling of pteridines for determination of potential biomarkers in cancer diseases. Electrophoresis, 2011. 32(15): p. 2044-54). In humans, 5,6,7,8-tetrahydrobiopterin (BH4) is the most important unconjugated pterin and a cofactor for the hydroxylation of aromatic amino acids (phenylalanine, tyrosine, and tryptophan), the biosynthesis of the neurotransmitters serotonin and dopamine and the vasodilator nitric oxide (NO) (Thony, B., G. Auerbach, and N. Blau, Tetrahydrobiopterin biosynthesis, regeneration and functions. Biochem J, 2000. 347 Pt 1: p. 1-16), and for the biosynthesis of thymidine. Pterins may be host or bacterial-derived. BH4 is absorbed in the small intestine but in the colon, it is decomposed by enteric bacteria (Sawabe, K., et al., Tetrahydrobiopterin in intestinal lumen: its absorption and secretion in the small intestine and the elimination in the large intestine. J Inherit Metab Dis, 2009. 32(1): p. 79-85). Pterin and biopterin are BH4 degradation products. BH4 was not detected in these samples, but the degradation products increased over time in the Drug and Control group; however, levels were stationary in the Combo group and decreased after an initial rise in the Microbe group (see  FIG.  33   ). 
     The polyamines, putrescine, spermidine and spermine, are organic polycations present in all eukaryotes and are essential for cell proliferation. Polyamines have been proposed to regulate cellular activities at transcriptional, translational and post-translational levels. The main sources for polyamines in mammals are cellular synthesis, food intake and microbial synthesis in the gut. The rate limiting enzyme in polyamine biosynthesis is ODC (ornithine decarboxylase) that converts ornithine to putrescine. Spermidine is then synthesized from putrescine by spermidine synthase, and spermine from spermidine. Over the course of the study, spermidine, diacetylspermadine and N1, N12-diacetylspermine increased in the feces receiving Control, Drug or Combo treatments. Conversely, these levels remained low in the Microbe group (Table 23). Since no differences in putrescine were observed, altered spermidine synthase activity could explain these findings. Polyamines stimulate mucosal growth and impacts intestinal enzyme activity (Wang, J. Y., et al., Stimulation of proximal small intestinal mucosal growth by luminal polyamines. Am J Physiol, 1991. 261(3 Pt 1): p. G504-11). Potential bacterial sources of polyamines include species of  Bacteroides, Fusobacterium , and  Clostridium  (Matsumoto, M. and Y. Benno., Microbiol Immunol, 2007. 51(1): p. 25-35). 
     
       
         
           
               
             
               
                 TABLE 23 
               
             
            
               
                   
               
               
                 Polyamines in mouse fecal samples at time T7. Ratio of the mean  
               
               
                 peak areas for the specified metabolites in each group relative to  
               
               
                 the control group. Up o rdown arrows indicate whether the 
               
               
                 increase or decrease in the treatment relative to the control is  
               
               
                 significant based on Welch’s two-sample t-test with p &lt; 0.05. 
               
            
           
           
               
               
               
               
            
               
                 Compound 
                 Microbe T7 
                 Drug T7 
                 Combo T7 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 spermidine 
                 0.23  
                 ↓ 
                 1.46 
                 0.75 
                   
               
               
                 diacetyl spermidine 
                 0.27  
                 ↓ 
                 0.91 
                 0.79  
                 ↓ 
               
               
                 N1,N12-diacetyl spermine 
                 0.25  
                 ↓ 
                 1.18 
                 0.87 
               
               
                   
               
            
           
         
       
     
     Nucleotides are the building blocks for DNA and RNA biosynthesis, and they are composed of a nitrogenous base, a five-carbon sugar, and at least one phosphate group. Nucleotides carry energy, participate in cell signaling, and are incorporated into important cofactors. Nucleotides can be synthesized de novo or recycled through salvage pathways. In energy-preserving salvage reactions, nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of nucleotide biosynthesis (inter-conversion). Thus, nucleotide levels may reflect epithelial cell turnover. Nucleotides tended to decline in response to the Microbe treatment. 5′-AMP, 5′-GMP and 5′-CMIP were notable exceptions although the biological meaning of these changes remains unknown (Table 24). These nucleic monophosphates may serve as signaling molecules or reflect the degradation of nucleotides. 
     
       
         
           
               
             
               
                 TABLE 24 
               
             
            
               
                   
               
               
                 Nucleotide synthesis, degradation, and salvage intermediates in 
               
               
                 mouse fecal samples at time T7. Ratio of the mean peak  
               
               
                 areas for the specified metabolites in each group 
               
               
                 relative to the control group. Up or down arrows indicate 
               
               
                 whether the increase or decrease in the treatment relative  
               
               
                 to the control is significant 
               
               
                 based on Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Microbe  
                 Drug  
                 Combo 
               
               
                 Compound 
                 T7 
                 T7 
                 T7 
               
               
                   
               
               
                 Inosine 
                 0.51 
                 1.59 
                 0.88 
               
               
                 Hypoxanthine 
                 0.44 
                 1.17 
                 0.54 ↓ 
               
               
                 Xanthine 
                 0.23 ↓ 
                 1.29 
                 0.61 
               
               
                 Xanthosine 
                 0.65 
                 1.31 
                 0.40 
               
               
                 2′-deoxyinosine 
                 0.48 
                 1.16 
                 0.68 
               
               
                 Urate 
                 0.33 ↓ 
                 1.15 
                 0.91 
               
               
                 Allantoin 
                 1.1 
                 1.07 
                 0.61 
               
               
                 1-methylhypoxanthine 
                 0.66 
                 0.96 
                 0.75 
               
               
                 AMP 
                 3.41 ↑ 
                 0.99 
                 4.50 ↑ 
               
               
                 3′-AMP 
                 0.02 ↓ 
                 0.11 
                 0.20 ↓ 
               
               
                 Adenosine-2′,3′-cyclic 
                 0 ↓ 
                 0.01 ↓ 
                 0.04 ↓ 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 Adenosine 
                 0.07 ↓ 
                 0.65 
                 0.96 
               
               
                 Adenine 
                 0.23 ↓ 
                 0.51 ↓ 
                 0.92 
               
               
                 l-methyladenine 
                 0.27 ↓ 
                 1.24 
                 0.37 ↓ 
               
               
                 N1-methyladenosine 
                 1.24 
                 1.05 
                 0.08 
               
               
                 2′-deoxyadenosine 5′- 
                 1.62 
                 1.09 
                 3.61 ↑ 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 2′-deoxyadenosine 
                 0.28 ↓ 
                 0.76 ↓ 
                 0.84 
               
               
                 3′-GMP 
                 0.15 
                 0.98 
                 0.56 
               
               
                 Guanosine-2′,3′-cyclic 
                 0.13 ↓ 
                 0.68 
                 0.43 ↓ 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 Guanosine 
                 0.41 
                 1.73 
                 0.96 
               
               
                 Guanine 
                 0.62 
                 0.83 
                 0.67 
               
               
                 7-methylguanine 
                 0.53 ↓ 
                 1.18 
                 0.53 
               
               
                 8-hydroxyguanine 
                 0.53 
                 1.12 
                 0.94 
               
               
                 dGMP 
                 1.22 
                 1 
                 1.9 
               
               
                 2′-deoxyguanosine 
                 0.64 
                 0.92 
                 0.88 
               
               
                 N-carbamoylaspartate 
                 0.14 ↓ 
                 0.89 
                 0.25 ↓ 
               
               
                 orotate 
                 0.14 ↓ 
                 0.97 
                 0.29 ↓ 
               
               
                 UMP 
                 1.25 
                 0.84 
                 1.66 ↑ 
               
               
                 3′-UMP 
                 0.29 
                 0.98 
                 0.89 
               
               
                 Uridine-2′,3′-cyclic 
                 0.13 ↓ 
                 0.59 
                 0.45 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 Uridine 
                 0.82 
                 1.12 
                 1 
               
               
                 Uracil 
                 0.24 ↓ 
                 1.26 
                 0.55 
               
               
                 Pseudouridine 
                 0.14 ↓ 
                 1.16 
                 0.29 ↓ 
               
               
                 5,6-dihydrouridine 
                 0.24 ↓ 
                 1.3 
                 0.49 
               
               
                 2′-O-methyluridine 
                 0.11 ↓ 
                 1.41 
                 0.46 
               
               
                 5-methyluridine 
                 0.29 
                 2.28 
                 0.50 
               
               
                 2′-deoxyuridine 
                 0.44 
                 1.29 
                 0.71 
               
               
                 3-ureidopropionate 
                 0.09 ↓ 
                 1.37 
                 0.37 
               
               
                 Beta-alanine 
                 0.21 ↓ 
                 1.16 
                 0.28 ↓ 
               
               
                 5′-CMP 
                 2.84 ↑ 
                 1 
                 3.32 ↑ 
               
               
                 3′-CMP 
                 0.44 ↓ 
                 1.14 
                 0.83 
               
               
                 Cytidine 2′,3′-cyclic 
                 0.07 ↓ 
                 0.4 
                 0.29 ↓ 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 Cytidine 
                 0.81 
                 0.87 
                 1.15 
               
               
                 Cytosine 
                 0.56 
                 0.43 
                 1.39 
               
               
                 5-methylcytidine 
                 0.45 
                 0.93 
                 0.47 ↓ 
               
               
                 5-methylcytosine 
                 0.72 
                 1.15 
                 0.99 
               
               
                 2′-deoxycytidine 5′- 
                 1.74 
                 0.87 
                 2.51 ↑ 
               
               
                 monophosphate 
                   
                   
                   
               
               
                 2′-deoxycytidine 
                 1.2 
                 0.86 
                 1.47 
               
               
                 2′-O-methylcytidine 
                 0.66 
                 1.17 
                 0.92 
               
               
                 5-methyl-2′-deoxycytidine 
                 1.06 
                 0.89 
                 1.11 
               
               
                 Thymidine 5′-monophosphate 
                 1.69 
                 0.81 
                 2.26 ↑ 
               
               
                 Thymidine 
                 0.66 
                 1.21 
                 0.8 
               
               
                 thymine 
                 0.17 ↓ 
                 1.56 
                 0.54 
               
               
                 3-aminoisobutyrate 
                 0.8 
                 1.31 
                 0.86 
               
               
                   
               
            
           
         
       
     
     Most dietary triacylglycerol (TAG) digestion is completed in the lumen of the small intestine. The products of TAG digestion, primarily 2-monoacylglycerols (MAG), fatty acids (FA), cholesterol, and lysophospholipids combine with bile salts, forming micelles. The lipid contents of micelles then diffuse into the enterocytes in the distal duodenum and the jejunum, whereas the bile salts are absorbed in the ileum. Within the enterocytes, TAG, cholesterol ester, and phospholipids are reformed from MAG, FA, cholesterol, and lysophospholipids. These reformed lipids are then incorporated into the lipoprotein chylomicrons, from which tissues like skeletal muscle, adipose tissue, and liver can release and take up free FA. Phospholipids were consistently elevated only in the Microbe monotherapy group (Table 25). Microbe treatment may have impacted membrane stability and potentially reflect cellular turnover. This would be consistent with changes in nucleotide levels. Interestingly, these elevations were not observed in the Combo treatment groups, suggesting that the Drug treatment may have negated this influence of Microbe exposure. In addition to dietary sources, these phospholipids could be the result of the shedding of intestinal epithelial cells. 
     
       
         
           
               
             
               
                 TABLE 25 
               
             
            
               
                   
               
               
                 Phospholipids and related species in mouse fecal samples at time 
               
               
                 T7. Ratio of the mean peak areas for the specified metabolites in each group  
               
               
                 relative to the control group. Up or down arrows indicate whether the  
               
               
                 increase or decrease in the treatment relative to the control is significant  
               
               
                 based on Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Microbe 
                 Drug  
                 Combo 
               
               
                 Compound 
                 T7 
                 T7 
                 T7 
               
               
                   
               
               
                 1,2-dipalmitoyl-GPC 
                 1.13 
                 0.72 
                 0.74 ↓ 
               
               
                 1-palmitoyl-2-oleoyl-GPC 
                 1.43 
                 0.82 
                 0.82 
               
               
                 1-palmitoly-2-linoleoyl-GPC 
                 1.71 ↑ 
                 0.84 
                 0.77 
               
               
                 1-stearoyl-2-arachidonoyl-GPC 
                 0.78 
                 0.88 
                 0.94 
               
               
                 1-oleoyl-2-linoleoyl-GPC 
                 1.95 ↑ 
                 0.82 
                 0.66 
               
               
                 1,2-dilinoleoyl-GPC 
                 2.21 ↑ 
                 0.80 
                 0.62 
               
               
                 1-linoleoyl-2-linolenoyl-GPC 
                 1.98 ↑ 
                 0.74 
                 0.61 
               
               
                 1-palmitoyl-2-linoleoyl-GPE 
                 1.61 
                 1.03 
                 1.06 
               
               
                 1-stearoyl-2-arachidonoyl-GPE 
                 1.27 
                 0/.81 
                 1.07 
               
               
                 1-oleoyl-2-linoleoyl-GPE 
                 1.61 
                 0.79 
                 0.77 
               
               
                 1,2-dilinoleoyl-GPE 
                 2.11 ↑ 
                 0.77 
                 0.6 
               
               
                 1-palmitoyl-2-oleoyl-GPI 
                 3.20 ↑ 
                 0.94 
                 1.19 
               
               
                 1-palmitoyl-2-linoleoyl-GPI 
                 3.03 ↑ 
                 0.81 
                 1.01 
               
               
                 1-oleoyl-GPA 
                 0.9 
                 0.85 
                 0.67 
               
               
                 1-linoleoyl-GPA 
                 1.54 ↑ 
                 0.83 
                 1.3 
               
               
                 1-palmitoyl-GPC 
                 2.71 ↑ 
                 0.88 
                 1.44 
               
               
                 2-palmitoyl-GPC 
                 3.89 ↑ 
                 1.01 
                 2.17 ↑ 
               
               
                 1-stearoyl-GPC 
                 1.26 
                 0.85 
                 1.27 
               
               
                 1-oleoyl-GPC 
                 2.93 ↑ 
                 1.01 
                 1.66 
               
               
                 1-linoleoyl-GPA 
                 3.78 ↑ 
                 0.87 
                 1.54 
               
               
                 1-lignoceroyl-GPC 
                 1.07 
                 0.95 
                 1 
               
               
                 1-palmitoyl-GPE 
                 1.92 ↑ 
                 1.22 
                 1.28 
               
               
                 1-stearoyl-GPE 
                 0.75 
                 0.86 
                 1.32 
               
               
                 2-stearoyl-GPE 
                 0.63 
                 0.72 
                 1.58 
               
               
                 1-oleoyl-GPE 
                 1.78 ↑ 
                 1.16 
                 1.24 
               
               
                 1-linoleoyl-GPE 
                 3.22 ↑ 
                 0.89 
                 1.28 
               
               
                 1-palmitoyl-GPS 
                 3.41 ↑ 
                 1.83 ↑ 
                 2.48 ↑ 
               
               
                 1-linoleoyl-GPG 
                 1.11 
                 1.18 
                 1.27 
               
               
                 1-palmitoyl-GPI 
                 3.13 ↑ 
                 0.67 
                 1.33 
               
               
                 1-stearoyl-GPI 
                 1.38 
                 0.93 
                 1.87 
               
               
                 1-oleoyl-GPI 
                 2.90 ↑ 
                 0.84 
                 2.92 
               
               
                 1-linoleoyl-GPI 
                 3.28 ↑ 
                 0.93 
                 2.68 
               
               
                   
               
            
           
         
       
     
     Nicotinamide adenine dinucleotide (NAD + ) is a coenzyme that plays an essential role in energy metabolism and redox status. NAD +  can be synthesized from the amino acid tryptophan through intermediates including kynurenine and quinolinate or salvaged from nicotinic acid and nicotinamide. Prokaryotic and eukaryotic NAD synthetic pathways are similar. Metabolites involved in NAD metabolism were lower in the Combo group at T7, and to a lesser extent the Microbe group (Table 26). Declines in NAD +  metabolites in the feces may reflect retention within the colon or decreased production. Increasing NAD +  levels in aged mice decreases colon degradation and increases motility (Zhu, X., et al., Nicotinamide adenine dinucleotide replenishment rescues colon degeneration in aged mice. Signal Transduct Target Ther, 2017. 2: p. 17017). 
     
       
         
           
               
             
               
                 TABLE 26 
               
             
            
               
                   
               
               
                 Nicotinamide and related metabolites in mouse  
               
               
                 fecal samples at time T7. Ratio of the 
               
               
                 mean peak areas for the specified  
               
               
                 metabolites in each group relative to the 
               
               
                 control group. Up or down arrows indicate whether  
               
               
                 the increase or decrease in the treatment  
               
               
                 relative to the control is significant based on  
               
               
                 Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 Microbe  
                 Drug  
                 Combo  
               
               
                 Compound 
                 T7 
                 T7 
                 T7 
               
               
                   
               
               
                 N1-methyl-4-pyridone-3- 
                 0.65 
                 0.89 
                 0.45 
               
               
                 carboxamide 
                   
                   
                   
               
               
                 N′-methylnicotinate 
                 0.51 
                 1.04 
                 0.53 ↓ 
               
               
                 1-methylnicotinamide 
                 1.01 
                 1.03 
                 0.87 
               
               
                 Nicotinamide 
                 1.33 
                 0.94 
                 1 
               
               
                 Nicotinate ribonucleoside 
                 0.71 
                 0.47 
                 0.44 ↓ 
               
               
                 Nicotinate 
                 0.37 ↓ 
                 1.25 
                 0.52 ↓ 
               
               
                 quinolinate 
                 0.68 
                 1.05 
                 0.65 ↓ 
               
               
                   
               
            
           
         
       
     
     Metabolomics data was used to determine metabolic signatures that could differentiate response to checkpoint inhibitor treatment. Of the mice receiving anti-CTLA4, responders to the treatment (R) were defined as those mice with tumor size less than 400 mm 3  at the end of the study (21 days from first treatment). Those with tumor size greater than 400 mm 3  were considered non-responders (NR). Of the 16 mice given anti-CTLA4 in the metabolomics study (Microbe and Combo groups), there were 12 responders and 4 non-responders. 
     High level views of the responder data demonstrate relatively low numbers of metabolites were significantly different between R and NR during the study (9% at T1, 6% at T4 and 4% at T7). However, there were clear differences in specific metabolites, though each only at a specific timepoint. Guanosine 3′-monophosphate (3′-GMP) and guanosine-2′,3′-cyclic monophosphate was present in R but not detected in any NR at T1. At T4, multiple primary and secondary bile acids were elevated in the feces of R compared to NR (Table 27). Bile acids are necessary for the efficient absorption of dietary lipids. They are synthesized and conjugated in the liver and secreted into the intestine via the bile duct. Most of the bile acid pool is reabsorbed into enterohepatic circulation; however, a small percentage is excreted in the feces. Interestingly, the differences observed here seemed to be unique to taurine-conjugated bile acids. Taurine levels were not different between these groups at any timepoint; however, cysteine, a precursor to taurine was lower in R versus NR at T1. Secondary bile acids are generated by the gut microbiota, and thus differences in these metabolites may reflect differences in microbial population or metabolism. At T7, diacylglycerols (DAGs) and monoacylglycerols (MAGs) were lower in R versus NR at T7 (Table 28). The bulk of DAGs and MAGs in the colon are derived from dietary sources. Assuming the dietary intake was identical between mice included in the study, changes in these metabolites likely reflect differences in digestion and absorption of these metabolites between R and NR. 
     
       
         
           
               
             
               
                 TABLE 27 
               
             
            
               
                   
               
               
                 Primary and secondary bile acids in mouse fecal samples at each 
               
               
                 timepoint. Ratio of the mean peak areas for the specified metabolites  
               
               
                 in responders (R) relative to non-responders (NR). Up or down arrows  
               
               
                 indicate the increase or decrease in the treatment relative to the control is  
               
               
                 significant based on Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 R/NR  
                 R/NR 
                 R/NR 
               
               
                 Compound 
                 T1 
                 T4 
                 T7 
               
               
                   
               
               
                 Taurocholate 
                 0.9 
                  4.81 ↑ 
                 0.85 
               
               
                 Tauro-beta-muricholate 
                 0.56 
                  5.34 ↑ 
                 1.5 
               
               
                 Taurodeoxycholate 
                 0.49 
                 15.26 ↑ 
                 1.31 
               
               
                 Taurolithocholate 
                 0.87 
                  5.95 ↑ 
                 1.41 
               
               
                 Taurohyodeoxycholic acid 
                 0.54 
                  7.20 ↑ 
                 1.13 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 28 
               
             
            
               
                   
               
               
                 Monoacylglycerols and diacylglycerols in  
               
               
                 mouse fecal samples at each timepoint. Ratio of 
               
               
                 the mean peak areas for the specified metabolites in 
               
               
                 responders (R) relative to non-responders (NR).  
               
               
                 Up or down arrows indicate the 
               
               
                 increase or decrease in the treatment relative  
               
               
                 to the control is significant based on 
               
               
                 Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 R/NR  
                 R/NR 
                 R/NR 
               
               
                 Compound 
                 T1 
                 T4 
                 T7 
               
               
                   
               
               
                 1-myristoylglycerol 
                 0.91 
                 0.71 
                 0.73 
               
               
                 1-palmitoylglycerol 
                 0.96 
                 1.11 
                 0.61 ↓ 
               
               
                 1-oleoylglycerol 
                 0.88 
                 1.46 
                 0.47 ↓ 
               
               
                 1-linoleoylglycerol 
                 0.94 
                 2.03 
                 0.41 ↓ 
               
               
                 1-linolenoylglycerol 
                 1.04 
                 2.24 
                 0.44 ↓ 
               
               
                 2-palmitoylglycerol 
                 0.91 
                 1.05 
                 0.63 ↓ 
               
               
                 2-oleoylglycerol 
                 0.99 
                 1.2 
                 0.47 ↓ 
               
               
                 2-linoleoylglycerol 
                 0.98 
                 1.47 
                 0.41 ↓ 
               
               
                 1-heptadecenoylglycerol 
                 0.93 
                 1.69 
                 0.52 ↓ 
               
               
                 Palmitoyl-linoleoyl-glycerol 
                 0.89 
                 1.36 
                 0.63 ↓ 
               
               
                 Oleoyl-oleoyl-glycerol 
                 0.82 
                 1.09 
                 0.63 ↓ 
               
               
                 Oleoyl-linoleoyl-glycerol 
                 0.84 
                 1.33 
                 0.66 ↓ 
               
               
                 Linoleoyl-lineoyl-glycerol 
                 0.84 
                 1.54 
                 0.63 ↓ 
               
               
                 Linoleoyl-linolenoyl-glycerol 
                 0.91 
                 1.61 
                 0.60 ↓ 
               
               
                   
               
            
           
         
       
     
     Metabolomics Performed on Fecal Samples 
     In a separate experiment, metabolomics was performed on fecal samples taken from mice treated with anti-CTLA-4 only and the group treated with anti-CTLA-4 in combination with microbial mix 2. In the tables and figures that follow, these are referred to as the Drug (D) and Drug+Microbe (D+M) groups. Samples were processed from timepoint 2 (T2), 48 hours after the first treatment dose; timepoint 4 (T4), 10 days from start and 48 hours after the 3 rd  treatment dose; and timepoint 6 (T6), 17 days from start and 48 hours after the 5 th  treatment dose. All mice in the study were classified as responders or non-responders to CTLA-4 treatment. responders to the treatment (R) were defined as those mice with tumor size less than 400 mm 3  at the end of the study (21 days from first treatment). Those with tumor size greater than 400 mm 3  were considered non-responders (NR). Of the 16 mice given anti-CTLA4 in the study, there were 8 responders and 8 non-responders. 
     As in the above example, instrument variability was determined by calculation of the median relative s.d. (RSD) for the standards that were added to each sample before injection into the mass spectrometers (median RSDs were determined to be 3%). Overall process variability was determined by calculating the median RSD for all endogenous metabolites (i.e., noninstrument standards) present in 90% or more of the pooled technical-replicate samples (median RSD=10%, n=802 metabolites). 
     Several metabolites were differentially present in the R and NR groups, as summarized in Table 29. Proline is consistently elevated in NR samples but only significantly at the mid-time-point. Correlation analysis shows that, although proline is the sentinel signal, the top correlating metabolites to its abundance across the samples are primarily other amino acids. Hence, amino acids generally increase in NR samples at the mid-point. The increase observed in the NR samples in the feces reflects a difference in the potential availability for the tumor for anabolic processes such as protein synthesis. Also elevated in responder samples were particular sugars, mannose and myo-inositol, and trace amines. Mannose (an epimer of glucose) and myo-inositol are both monosaccharides that can be made from glucose and they are abundant in the diet. Mannose is most prominently known for its role in posttranslational modification of proteins through N-linked glycosylation while inositol is most known for its role as a second messenger in the form of inositol phosphates. However, the increase in abundance in the feces of NR animals most plausibly indicates differences in either the use or potential use of these sugars as carbon sources by microbes within the lumen of the intestine. Trace amines such as tyramine, tryptamine and phenethylamine are best known for having neuroactive activity. They are present in the diet and can be produced by the microbiota. All three were detected in this study but only phenethylamine was identified as significant for differences between R and NR groups. These amines act through trace amine-associated receptors (TAARs). TAAR1 may regulate immune responses through leukocyte differentiation and activation. So, the elevation in phenylethylamine in NR samples could reflect the potential to modulate the immune response. 
     Steroids were more abundant in the responder group, particularly at the last timepoint. Steroids include progestogens, androgens, estrogens, glucocorticoids, and mineralocorticoids, and they have vital roles in coordinating changes in metabolism, inflammation, and immune function. Since the steroids detected in this data all change in a similar manner and are from 3 of these 5 classes of steroids, a general change in steroid metabolism—perhaps at the earliest steps (cholesterol conversion to pregnenolone) is most likely. 
     
       
         
           
               
             
               
                 TABLE 29 
               
             
            
               
                   
               
               
                 Select metabolites with different abundance in  
               
               
                 responders and non-responders to the anti-CTLA-4 
               
               
                 treatment. Ratio of the mean peak areas for the 
               
               
                 specified metabolites in responders (R) relative  
               
               
                 to non-responders (NR) are shown. 
               
               
                 Up or down arrows indicate the increase or  
               
               
                 decrease in the treatment relative to the 
               
               
                 control is significant based on Welch′s  
               
               
                 two-sample t-test with p&lt;0.05. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 R/NR  
                 R/NR 
                 R/NR 
               
               
                   
                 Compound 
                 T2 
                 T4 
                 T6 
               
               
                   
                   
               
               
                   
                 Phenethylamine 
                 0.79 
                 0.49 ↓ 
                 0.77 
               
               
                   
                 Proline 
                 1.08 
                 0.58 ↓ 
                 0.66 
               
               
                   
                 Mannose 
                 1.02 
                 0.82 
                 0.47 ↓ 
               
               
                   
                 Myo-inositol 
                 1.1 
                 0.62 ↓ 
                 0.64 
               
               
                   
                 5alpha-pregnan-3beta,20alpha-diol 
                 0.94 
                 0.77 
                 2.88 ↓ 
               
               
                   
                 disulfate 
                   
                   
                   
               
               
                   
                 5alpha-pregnan-diol disulfate 
                 0.72 
                 0.88 
                 2.67 ↓ 
               
               
                   
                 pregnanolone/allopregnanolone 
                 1.28 
                 1.37 
                 3.93 ↓ 
               
               
                   
                 sulfate 
                   
                   
                   
               
               
                   
                 5 alpha-androstan-3beta, 17beta-diol 
                 0.85 
                 0.87 
                 2.27 ↓ 
               
               
                   
                 disulfate 
               
               
                   
                   
               
            
           
         
       
     
     Several metabolites were differentially abundant in the R and NR groups, but only when comparing just those mice treated with D+M. These are listed in Table 30 and include several fatty acids and ceramides as well as serotonin. Serotonin is a key neurotransmitter in the brain-gut axis and significant amounts of peripheral serotonin is synthesized from tryptophan in the gastrointestinal tract by enterochromaffin cells. Various studies have shown that the production of serotonin in the gut is highly influenced by the presence of microbes and their metabolic products. Serotonin trends higher for the non-responder group. The metabolite that serotonin is derived from -tryptophan—does not correlate with the pattern of serotonin change, indicating that the serotonin change is not simply due to changes in tryptophan levels. Tryptophan can also be metabolized into the anti-inflammatory metabolite kynurenine which naturally then has an immunosuppressive role. However, the steady state pools in these fecal samples for kynurenine are unchanged between the R/NR groups. 
     Certain bile acids also changed between microbe R and NR groups; in particular, minor secondary bile acids that are the products of bacterial metabolism of primary bile acids. Bile acids such as lithocholate (LCA) are reduced with responders and slightly elevated with non-responders. Thus, since these bile acids are by-products of microbial activity, their changes represent the clearest indication of differential microbe activity between the R and NR groups. How this precisely impacts response is not clear but LCA is known to be biologically potent. For example, it is the most powerful known endogenous agonist for a GPCR that regulates vast aspects of metabolism—TGR5. And, bile acids such as LCA also act on receptors involved in the innate immune response G protein-coupled bile acid receptor 1 (GPBAR1 or Takeda G-protein receptor 5) and the Farnesoid-X-Receptor (FXR). GPBAR1 and FXR are reported to modulate the liver and intestinal innate immune system and therefore contribute to tolerance. 
     
       
         
           
               
             
               
                 TABLE 30 
               
             
            
               
                   
               
               
                 Select metabolites with different abundance in responders  
               
               
                 and non-responders to anti-CTLA-4 and microbial  
               
               
                 mix 2 combination treatment. Ratio of the 
               
               
                 mean peak areas for the specified metabolites in  
               
               
                 responders (R) relative to non-responders (NR) are shown, 
               
               
                 just for the D + M group. Up or down arrows indicate the 
               
               
                 increase or decrease in the treatment relative to the  
               
               
                 control is significant based on 
               
               
                 Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 R/NR  
                 R/NR 
                 R/NR 
               
               
                   
                 Compound 
                 T2 
                 T4 
                 T6 
               
               
                   
                   
               
               
                   
                 Serotonin 
                 0.88 
                 0.8 
                 0.6 ↓ 
               
               
                   
                 Stearate (18:0) 
                 1.09 
                 1.41 ↑ 
                 1.03 
               
               
                   
                 Arachidate (20:0) 
                 1.05 
                 1.44 ↑ 
                 1.04 
               
               
                   
                 Behenate (22:0) 
                 0.93 
                 1.53 ↑ 
                 1.1 
               
               
                   
                 Nervonate (24:1n9) 
                 1.01 
                 1.75 ↑ 
                 1.18 
               
               
                   
                 1-palmitoyl-2-arachidonoyl-GPC 
                 0.68 
                 2.73 ↑ 
                 1.22 
               
               
                   
                 (16:0/20:4n6) 
                   
                   
                   
               
               
                   
                 1-stearoyl-GPS (18:0) 
                 0.73 
                 2.77 ↑ 
                 1.09 
               
               
                   
                 1-stearoyl-GPG (18:0) 
                 2.56 ↑ 
                 2.23 ↑ 
                 1.46 
               
               
                   
                 1-stearoyl-GPI (16:0) 
                 0.66 
                 1.8 ↑ 
                 1.11 
               
               
                   
                 1-palmitoyl-galactosylglycerol (16:0) 
                 1.33 
                 3.18 ↑ 
                 1.04 
               
               
                   
                 Sphingadienine 
                 1.25 
                 0.65 
                 0.65 
               
               
                   
                 Ceramide (d18:1/14:0, d16:1/16:0) 
                 1.13 
                 1.25 
                 0.84 
               
               
                   
                 Glycosyl-N-palmitoyl-sphingosine 
                 0.64 
                 0.51 
                 0.4 
               
               
                   
                 (d18:1/16:0) 
                   
                   
                   
               
               
                   
                 Eicosanoylsphingosine (d20:1) 
                 1.25 
                 0.94 
                 0.7 
               
               
                   
                 Pregnenediol disulfate 
                 1.11 
                 1.39 
                 1.15 
               
               
                   
                 5alpha-pregnan-3beta, 20alpha-diol 
                 1.52 
                 2.03 ↑ 
                 2.69 ↑ 
               
               
                   
                 disulfate 
                   
                   
                   
               
               
                   
                 5alpha-pregnan-diol disulfate 
                 1.01 
                 1.71 
                 2.64 ↑ 
               
               
                   
                 Pregnanolone/allopregnanolone 
                 2.54 
                 4.19 
                 3.3 ↑ 
               
               
                   
                 sulfate 
                   
                   
                   
               
               
                   
                 5alpha-androstan-3beta, 17beta-diol 
                 1.41 
                 1.22 
                 2.03 ↑ 
               
               
                   
                 disulfate 
                   
                   
                   
               
               
                   
                 6-oxolithocholate 
                 0.97 
                 0.41 
                 0.51 
               
               
                   
                 Isohyodeoxycholate 
                 1.39 
                 0.61 
                 0.48 
               
               
                   
                 nicotinamide 
                 1.28 
                 2.38 ↑ 
                 1.81 
               
               
                   
                   
               
            
           
         
       
     
     The strongest signal in the data is from microbe treatment (G8 D+M) independent of R/NR. Despite not correlating with response, the changes induced solely by the microbe could provide insights into how the microbe treatment works. Compounds with increased concentration as a result of microbe treatment include those derived from aromatic catabolism, histamine side products, acylglycines, creatine, and NAD+ catabolites. Table 31 indicates the ratio of these metabolites in the D+M treatment group relative to the D group. 
     Many metabolites that typically arise from microbial catabolism of aromatic amino acids (for example, p-cresol sulfate, p-cresol glucuronide, and 4-hydroxyphenylacetate) and benzoate metabolites (for example, benzoate, hippurate, catechol sulfate, etc.) are increased by microbe treatment. Benzoate metabolites are simple carboxylic acids produced from the microbial degradation of dietary aromatic compounds in the intestine, such as polyphenols, purines and aromatic organic acids. There is precedent for several aromatic amino acid metabolites having biological activity. For example, tryptophan metabolites such as kynurenate, indole, indoxyl sulphate, and indolepropionate, are ligands for the aryl hydrocarbon receptor (AhR). The AhR mediates tumor-promoting effects of dioxin and AhR signaling is also important for the immune response at barrier sites. These examples illustrate the potential for these types of metabolites to have important biological functions, particularly given that many are at fairly high levels in the blood. 
     While histamine itself is not elevated, many side-products and metabolites of it such as 1-methylhistamine and 1-ribosyl-imidazoleacetate are. This may be important since histamine is involved in inflammatory responses and gut physiology. Histamine may also have specific microbe-induced influences in specific tumors. For example, it was shown that administration of histidine decarboxylase (HDC) from  Lactobacillus reuteri  resulted in luminal histamine production of Hdc−/− mice and an associated decrease in the number and size of colon tumors. If the microbe treatment has the potential to alter histamine, it may have similar effects as those described in colon tumors. 
     Several acylglycines are recognized in biology to have important biological properties. Consequently, they are sometimes described as having “endocannabinoid-like” properties. N-arachidonoyl glycine (NAGly) is probably the best studied acylglycine and has been described to influence things such as inflammation, analgesia and, vasorelaxation. In these data, two acylglycines (3,4-methylene heptanoylglycine and picolinoylglycine) increased in the microbe treated group. However, these acylglycines are probably distantly related to versions like NAGly and there are many missing values, likely contributing to the large fold changes. 3,4-methylene heptanoylglycine is glycine conjugated to a short (C7) unsaturated acyl chain, in contrast to long fatty acyl chains that comprise most canonical acylglycines such as the C20-bearing NAGly. Picolinoylglycine is a pyridine-like ring structure conjugated to glycine. Hence, these molecules are highly unique; given the biosynthetic capacity of the microbiome, these unconventional acylglycines may be synthesized by microbes for some biological function. For example, a recent study revealed that one commensal bacteria effector gene family (Cbeg12) encoded enzymes for the production of the acylglycine N-acyl-3-hydroxypalmitoyl-glycine (commendamide). 
     Creatine is a key metabolite for cellular energy homeostasis in highly dynamic tissues such as brain, skeletal muscle and the gut. Creatine facilitates channeling of high energy phosphates (via phosphocreatine) to maintain ATP generation. In addition to creatine, several of its metabolites are also elevated by microbe treatment. Relevant to the effects in the gut, creatine supplementation is reported to maintain intestinal homeostasis and protect against colitis through rapidly replenishing ATP within colonic epithelial. Notably, gut microbiota produces specific enzymes that can mediate creatine and creatinine breakdown. 
     Catabolites of NAD+ and/or nicotinamide (NAM) are increased with microbe treatment. NAD+ has numerous critical cellular functions—a coenzyme for energy metabolism and redox status, holistic regulation of metabolism as a substrate for sirtuins, and in DNA repair through Poly (ADP-ribose) polymerases (PARPs). In this study, the methylated metabolites of NAM increased: N1-methyl-2-pyridone-5-carboxamide (2py) and N1-methyl-4-pyridone-3-carboxamide (4py) are increased by microbe treatment, suggesting an upregulation of NAD+/NAM catabolism. 2py and 4py are produced through methylation of NAM by Nicotinamide N-methyltransferase (NNMT) followed by aldehyde oxidase (Aox) oxidation. These reactions have generally been regarded as clearance pathways as 2py and 4py are excreted in the urine. However, recent studies suggest that the products of this pathway may possess biological activity. For example, pharmacological doses of N1-methylnicotinamide (MNAM) is reported to inhibit cyclooxygenase 2 (COX2) and endothelial nitric oxide synthase (eNOS). This may have relevance in an immunotherapy context as inhibition may help combat COX-2 immune evasion. 
     
       
         
           
               
             
               
                 TABLE 31 
               
             
            
               
                   
               
               
                 Select metabolites with different abundance in mice  
               
               
                 treated with microbial mix 2. Ratio of the mean peak 
               
               
                 areas for the specified metabolites in the D + M group 
               
               
                 compared to the D group is shown. Up or down  
               
               
                 arrows indicate the increase or decrease in the 
               
               
                 treatment relative to the control is significant based  
               
               
                 on Welch′s two-sample t-test with p &lt;0.05. 
               
            
           
           
               
               
               
               
            
               
                   
                 D + M/D 
                 D + M/D  
                 D + M/D  
               
               
                 Compound 
                 T2 
                 T4 
                 T6 
               
               
                   
               
               
                 Phenol sulfate 
                 1 
                 55.66 ↑ 
                 22.17 
               
               
                 N-formylphenylalanine 
                 1.25 
                  0.64 ↓ 
                  0.61 ↓ 
               
               
                 4-hydroxyphenylacetate sulfate 
                 0.96 
                 46.99 ↑ 
                  8.24 ↑ 
               
               
                 Kynurenate 
                 0.57 
                  3.03 
                  1.86 
               
               
                 N-formylanthranilic acid 
                 1.1 
                  5.59 ↑ 
                  1.74 
               
               
                 Xanthurenate 
                 1.04 
                  5.43 
                  3.04 
               
               
                 Serotonin 
                 1.07 
                  0.81 
                  0.92 
               
               
                 5-hydroxyindoleacetate 
                 0.74 
                  1.65 
                  2.02 
               
               
                 Tryptamine 
                 1.78 ↑ 
                  1.21 
                  1.06 
               
               
                 Indole-3-carboxylate 
                 0.93 
                  0.51 ↓ 
                  0.7 
               
               
                 Indoleacetylglycine 
                 1 
                 71.31 ↑ 
                  5.71 ↑ 
               
               
                 3-indoxyl sulfate 
                 1 
                 44.11 
                 47.76 
               
               
                 Hippurate 
                 1.31 
                 96.34 ↑ 
                 11.88 
               
               
                 Benzoate 
                 1.47 
                  2.76 
                  2.32 ↑ 
               
               
                 4-hydroxybenzoate 
                 0.93 
                  1.83 ↑ 
                  0.97 
               
               
                 Catechol sulfate 
                 1 
                  4.01 
                  4.29 ↑ 
               
               
                 Imidazole lactate 
                 0.7 
                  2.42 
                  1.41 
               
               
                 Histamine 
                 1.25 
                  1.09 
                  0.82 
               
               
                 1-methylhistamine 
                 0.61 
                  8.99 ↑ 
                  3.94 
               
               
                 1-methyl-4-imidazoleacetate 
                 1.06 
                  8.52 
                  3.13 
               
               
                 1-methyl-5-imidazoleacetate 
                 1.07 
                  0.6 
                  0.92 
               
               
                 1-ribosyl-imidazoleacetate 
                 1 
                 27.27 ↑ 
                  5.14 
               
               
                 3,4-methylene heptanoylglycine 
                 1 
                 16.15 ↑ 
                  4.83 
               
               
                 picolinoylglycine 
                 1 
                 24.6 ↑ 
                  5.78 
               
               
                 Guanidinoacetate 
                 0.5 
                 37.6 ↑ 
                  9.04 
               
               
                 Creatine 
                 0.47 
                 16.4 ↑ 
                  2.92 
               
               
                 Creatinine 
                 0.41 
                 15.91 ↑ 
                  4.88 
               
               
                 4-guanidinobutanoate 
                 1.66 
                  4.95 ↑ 
                  3.71 
               
               
                 Nicotinate 
                 1.93 
                  0.91 
                  0.69 
               
               
                 Nicotinate ribonucleoside 
                 1.28 
                  1.37 
                  0.5 
               
               
                 Nicotinic acid mononucleotide 
                 1.39 
                  1.22 
                  0.59 
               
               
                 Nicotinamide 
                 1.43 
                  0.78 
                  1.16 
               
               
                 Nicotinamide ribonucleotide 
                 0.76 
                  0.82 
                  0.89 
               
               
                 Nicotinamide riboside 
                 2.06 
                  1.2 
                  1.03 
               
               
                 1-methylnicotinamide 
                 1.05 
                  2.48 
                 12.05 
               
               
                 Trigonelline (N′-methylnicotinate) 
                 0.8 
                 10.26 ↑ 
                  2.28 
               
               
                 N1-methyl-2-pyridone-5- 
                 0.64 
                  4.65 ↑ 
                  3.11 
               
               
                 carboxamide 
                   
                   
                   
               
               
                 N1-methyl-4-pyridone-3- 
                 0.8 
                  9.25 ↑ 
                  3.67 
               
               
                 carboxamide 
               
               
                   
               
            
           
         
       
     
     Example 16—Efficacy of Anticancer Live Biotherapeutics as Monotherapies 
     The results described here were obtained from studies conducted with tumor mouse models evaluating the anticancer efficacy of generated live biotherapeutics as a monotherapy. Microbes, gene functions, and metabolites elucidated as critical for anticancer treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbes beneficial for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. 
     Animals and Tumor Model 
     BALB/c mice were obtained from Shanghai Lingchang Biotechnology Co., Ltd (Shanghai, China). 6-8-week-old female mice are used. For tumor growth experiments, mice are injected subcutaneously with 2.5×10 5  CT-26 colon cancer tumor cells (Griswold and Corbett (1975) Cancer 36:2441-2444). Tumor size was measured twice a week until endpoint, and tumor volume determined as length×width×0.5. 
     Tumor Cell Preparation 
     Cryo vials containing CT-26 tumor cells are thawed and cultured according to manufacturer&#39;s protocol (ATCC CRL-2638). On the day of injection cells are washed in serum free media, counted, and resuspended in cold serum free media at a concentration of 250,000 viable cells/100 μl. 
     Flow Cytometry 
     A whole-blood flow cytometry-based assay is utilized to assess T cell activation in response to microbial treatment. Whole blood via cardiac puncture is collected into an EDTA tube at the end of the experiment. 100 μL of whole mouse blood is transferred to a 15 mL conical tube. 1 mL of RBC Lysis Buffer is added to the tube and allowed to incubate at room temperature for 10 minutes. Lysis is quenched by adding 10 mL of cold DPBS. Samples are centrifuged at 1500 rpm for 5 minutes at 4° C. The pellet is aspirated and resuspend in another 10 mL of cold DPBS. Samples are recentrifuged at 1500 rpm for 5 minutes at 4° C. Samples are resuspended in 500 μL of FACS buffer and transferred to a 96-well plate. Samples are stained with Fixable Viability ef780™ (eBioscience), CD45-PEcy7 (BioLegend), CD3-BV605™ (BioLegend), CD8-AF700™ (BioLegend), and CD4-AF488™ (BioLegend). Stained samples are run on a BD LSRFortessa™ flow cytometer and analyses are performed with FlowJo™ (Tree Star). 
     Tumor Challenge and Treatment 
     Tumor size is routinely monitored by means of a caliper. Stool is collected on day 0 and 48 hours after each subsequent administration of treatment until the end of the study. 
     To test whether manipulation of the microbial community is effective as a monotherapy, microbial mix 4 was evaluated in the presence or absence of ellagic acid and/or ellagitannin is administered. In some groups, ellagic acid is administered separately via oral gavage (0.2 mL of a 5.5 mg/mL suspension) prior to administration of the microbe cocktails. Each mouse treated by monotherapy is given 200 l of the suspension by oral gavage three times a week for the duration of the study starting from day 1. Tumor growth and tumor-specific T cell responses are compared among the different treatment groups. 
     GI Tract Removal and Analysis 
     After mice are euthanized at the termination of the study, the intact digestive tract of each mouse from stomach to rectum are removed and kept in a 5 ml Eppendorf tube on ice prior to dissection. Forceps are sterilized by soaking in 100% ethanol and then used to remove the intestine length and stretch it on a work surface covered with cellophane. With the use of ethanol-sterilized dissection scissors, 3 cm lengths of the jejunum nearest to the stomach and the ilium nearest to the cecum/large intestine are excised and then each placed with forceps in a 1.5 ml Eppendorf tube and placed on ice. A 2 cm segment of the cecum/ascending colon is then excised, as are 2 cm segments of the transcending colon and the descending colon, and all are placed in 1.5 ml Eppendorf tubes on ice. Dissection instruments are sterilized by dipping in 100% ethanol between each intestine fragment removal. To each tube containing dissected intestinal segments is added 0.5 ml ice cold PBS buffer. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice and then stored at −80° C. for later analysis. 
     Tumor size is measured in all animals receiving the different microbial treatments. On average, the animals receiving Microbial mix 4 (equal amounts of  F. prausnitzii, C. coccoides, R. gnavus, C. scindens, E. lenta , and  G. urolithinfaciens ) alone or in conjunction with ellagic acid have a reduction in tumor size compared to those receiving vehicle as illustrated in  FIG.  34   . 
     Flow cytometry is used to perform immunophenotyping of mice subjected to cancer receiving the different microbial treatments. Measurements are conducted on both peripheral blood and on the tumor itself, with stains for various cell surface markers. The results show that CD3+ cells, which includes both helper and killer T cells, are upregulated in mice that respond better to therapy. Furthermore, the results also show that mice receiving the therapy had both higher CD3+ proportions as well as much lower final tumor volumes. CD8+T-lymphocytes are also upregulated in the presence of the microbial treatments. These results provide evidence that the microbial mix therapeutic impacts tumor volume via a mechanism of stimulating the CD3+ cells of the immune system as well as cytotoxic CD8+ T cells. Similarly, it has been shown in mice that the commensal microbiota critically regulates the generation of virus-specific CD4 and CD8 T cells and antibody responses following respiratory influenza virus infection (T. Ichinohe et al., Proc. Natl. Acad. Sci. U.S.A 108, 5354-9 (2011)). This further supports that live biotherapeutics described herein that are critical for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. Flow cytometry results are graphically presented in  FIG.  35   . 
     Example 17—Therapeutic Effect of Live Biotherapeutics on Efficacy of Cancer Immunotherapy with Antibiotic Pretreatment 
     The results described here were obtained from studies conducted with tumor mouse models evaluating the anticancer efficacy of generated live biotherapeutics on cancer immunotherapy with antibiotic pretreatment. It has been demonstrated that antibiotic-treated (ABX) mice exhibit impaired innate and adaptive antiviral immune responses and substantially delayed viral clearance after exposure to systemic lymphocytic choriomeningitis virus (LCMV) or mucosal influenza virus (M. C. Abt et al., Immunity. 37, 158-170 (2012)). Microbes, gene functions, and metabolites elucidated as critical for anticancer treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. As such, it is reasonable to expect that microbes beneficial for immuno-oncology treatment will also be beneficial or even essential for rapid viral clearance. 
     Anaerobe Basal Broth Supplemented with Rumen Fluid (ABB+RF) 
     34.5 grams of anaerobic basal broth dry powder (Fisher Scientific/Oxoid) is combined with 600 ml distilled water and is brought to a gentle boil while stirring on a heated stirplate until the solution clarifies. 150 ml of rumen fluid (Bar Diamond Inc., Parma Id.) that has been centrifuge-clarified is then added, along with 1 ml 2.5 mg/ml resazurin (ACROS Organics™) solution followed by distilled water to one-liter final volume. The medium is kept at 55° C. in a water bath while it is dispensed in 50 ml volumes into 100 ml serum bottles. Nitrogen is bubbled through a metal canula into each bottle for 15 minutes to displace oxygen from the medium, then the bottles are quickly sealed by insertion of a butyl-rubber bung that is secured by a crimped collar. The medium bottles are then sterilized by autoclaving and then stored in the dark until use. L-cysteine is added to 1 mM final concentration to each ABB+RF bottle one hour prior to use to fully reduce the medium prior to inoculation with microorganisms. 
     Preparation of Centrifuge-Clarified Rumen Fluid 
     Rumen fluid is the liquid obtained from the rumen of fistulated cows and is obtained in one-liter volumes from Bar Diamond Inc., Parma Id. The rumen fluid is aliquoted in 50 ml volumes into 50 ml conical tubes and centrifuged at 4000 g for 30 minutes at 4° C. to pellet large fibrous material. After centrifugation the supernatant is decanted into fresh 50 ml conical tubes that are then subjected to centrifugation at 34,000 g for 90 minutes at 4° C. The supernatant from this centrifugation is then decanted into fresh 50 ml conical tubes and stored at −20° C. until use. 
     Microorganisms in Mouse Study 
     The following obligate anaerobic microbes are obtained from the American Type Culture Collection (ATCC):  Faecalibacterium prausnitzii  (ATCC-27768),  Clostridium coccoides  (ATCC-29236),  Ruminococcus gnavus  (ATCC-29149),  Clostridium scindens  (ATCC-35704),  Akkermansia muciniphila  (BAA-835),  Enterococcus hirae  (ATCC-9790),  Bacteroides thetaiotamicron  (ATCC-29148),  Bacteroides  caccae (ATCC-43185),  Bifidobacterium breve  (ATCC-15700),  Bifidobacterium longum  (ATCC BAA-999) and  Gemmiger formicilis  (ATCC-27749).  Eggerthella lenta  (DSM-2243),  Gordonibacter urolithinfaciens  (DSM-27213),  Gordonibacter  species CEBAS 4A4 ; Alistipes indistinctus  (DSM-22520),  Dorea formicigenerans  (DSM-3992),  Senegalimassilia anaerobia  (DSM-25959),  Collinsella aerofaciens  (DSM-3979),  Adlercreutzia equolifaciens  (DSM-19450),  Ellagibacter isourolithinifaciens  (DSM-104140),  Slackia isoflavoniconvertens  (DSM-22006),  Slackia equolifaciens  (DSM-2485) and  Paraeggerthella hongkongensis  (DSM-16106) are obtained from the Leibnitz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). 
     The following organisms were obtained from stool of healthy donors as described in Example 16 : Dorea longicatena  and  Blautia  sp. SG-772. Whole genome sequencing of these organisms indicated they are more than 95% identical to the published strains. 
     Culture of Individual Microbes for Mouse Study 
     0.5 ml starter cultures of  C. coccoides, R. gnavus, C. scindens, A. muciniphila, E. hirae, B. thetaiotamicron, B. caccae, B. breve, B. longum, G. formicilis, E. lenta, G. urolithinfaciens, A. indistinctus, D. formicigenerans, S. anaerobia, C. aerofaciens, A. equolifaciens, E. isourolithinifaciens, S. isoflavoniconvertens, S. equolifaciens and P. hongkongensis, E. hallii, D. longicatena , and  Blautia  sp. SG-772 are each inoculated into four 50 ml anaerobic bottles of fully reduced ABB+RF anaerobic medium and cultured at 37° C.  F. prausnitzii  is inoculated into fifteen 7 ml tubes of YCFAC (Anaerobe Systems) and cultured at 37° C. Cultures are harvested after 48 hours when they achieve 0.1 to 1.0×10 9  cells/ml as measured by optical absorbance at 600 nm by spectrophotometer (1 OD 600 =1.0×10 9  cells/ml). Bacterial starter cultures may be modified to achieve 1.0×10 10  cells/ml, 1.0×10 11  cells/ml or 1.0×10 12  cell/ml. 
     To harvest cultures, they are first brought into the anaerobic chamber where they are opened and decanted into 50 ml conical tubes that are tightly capped and sealed by wrapping the caps in parafilm. These are brought out of the anaerobic chamber and then centrifuged at 4000 g for 15 minutes at 4° C. The centrifuged tubes are brought back into the anaerobic chamber where the supernatant is decanted and discarded. The cell pellets are each combined with anoxic Phosphate Buffered Saline with 2.5 mM L-Cysteine and 15% glycerol (PBS-C-G) followed by tight capping and parafilm seal. The capped and sealed tubes are brought out of the anaerobic chamber and are centrifuged at 4000 g for 15 minutes. The culture tubes are again brought into the anaerobic chamber where the supernatant is decanted and discarded. Pelleted cells are resuspended in volumes of PBS-C-G to attain effective cell densities of each microbial strain at 1×10 9  cells/ml, 1.0×10 10  cells/ml, 1.0×10 11  cells/ml or 1.0×10 12  cell/ml. 
     Animals and Tumor Model 
     BALB/c mice are obtained from Jackson laboratory, Taconic farms or Shanghai Lingchang Biotechnology Co., Ltd (Shanghai, China). 6-8-week-old female mice are used. For tumor growth experiments, mice are injected subcutaneously with 2.5×10 5  CT-26 colon cancer tumor cells (Griswold and Corbett (1975) Cancer 36:2441-2444). Tumor size is measured twice a week until endpoint, and tumor volume determined as length×width×0.5. 
     Tumor Cell Preparation 
     Cryo vials containing CT-26 tumor cells are thawed and cultured according to manufacturer&#39;s protocol (ATCC CRL-2638). On the day of injection cells are washed in serum free media, counted, and resuspended in cold serum free media at a concentration of 250,000 viable cells/100 μl. Cells will be prepared for injections by withdrawing 100 μL cell suspension into a 1 ml syringe. The cell suspension and filled syringes will be kept on ice. 
     Tumor Implantation 
     Animals will be prepared for injection using standard approved anesthesia, the mice will be shaved prior to injection. Once mouse at a time will be immobilized and the site of injection will be disinfected with an alcohol swab. 100 μl of the cell suspension will be subcutaneously injected into the rear flank of the mouse. During implantation, a new syringe and needle will be used for every mouse inoculated to minimize tumor ulceration. The cells will be drawn up into a 1 mL syringe (no needle attached) to 150 μL with the 50 μL nearest to the plunger being air and 100 μL of cell suspension. Once the cells are drawn up the needle will be attached (without priming the needle). For implant, lift up or tent the skin using forceps to ensure a subcutaneous injection. Inject the cells, twist the syringe/needle and then pull the needle out. Mice will be marked by ear tagging. 
     Antibiotics Protocols 
     Mice are treated daily with 200 μL of water or antibiotics via oral gavage 1-2 weeks before tumor implantation and continued for a duration of 2-3 weeks. Mouse fecal samples were collected twice a week for 5 collections in total (timepoints 1-5). Animals are given a mix of ampicillin (1 mg/mL)(Alfa Aesar J6380706), gentamicin (1 mg/mL)(Acros Organics AC455310050), metronidazole (1 mg/mL)(Acros Organics AC210440050), neomycin (1 mg/mL)(Alfa Aesar AAJ6149922), and vancomycin (0.5 mg/mL)(Alfa Aesar J6279006) via oral gavage. Antibiotic activity is analyzed by macroscopic changes observed at the level of caecum (dilatation) and by cultivating the fecal pellets resuspended in BHI+15% glycerol on blood agar and anaerobic blood agar plates for 48h at 37° C. with 5% CO2 for aerobic conditions or in anaerobic conditions respectively. 16S RNA and Whole Genome Sequencing are applied to determine the distribution of organisms in fecal samples collected from the water and antibiotic treated groups at both the phylum and genus level, and the distribution is compared across all collected fecal samples. PCA is used to classify all samples of mice without antibiotic treatment, showing that samples with the same microbial treatment type cluster together. Mice are treated with antibiotics or water for two weeks and fecal samples are collected at three different time points. 
     Isolation of Lamina Propria Cells from Small Intestine 
     Whole duodenum and ileum are harvested, Peyer&#39;s patches are removed, as well as all fat residues and fecal content. Small fragments are obtained by cutting them first longitudinally along the length and then transversally into pieces of 1-2 cm length. After removing the intra-epithelial lymphocytes (IELs), the gut pieces are further cut and incubated with 0.25 mg/ml collagenase VIII and 10 U/ml DNaseI for 40 min at 37° C. under shaking to isolate lamina propria cells (LPCs). After digestion, intestinal pieces are mashed on a cell strainer. For FACS analysis, cell suspensions are subjected to a percoll gradient for 20 min at 2100 RPM, while for RNA extraction, cells are directly lysed in RNALater buffer (Thermo Fisher Scientific) and frozen at −80° C. 
     Analyses of Dendritic Cell Subsets in Treated Mice 
     Cell suspensions from mouse spleen and lymph nodes are prepared by digestion with collagenase and DNase for 60 min and subsequently strained through a 70 mm mesh. Colonic and small intestinal lymphocytes are isolated as previously described (Viaud, S. et al. Science (80-.). 342, 971-976 (2013). In brief, cecum, colon and small intestine are digested in PBS containing 5 mM EDTA and 2 mM DTT shaking at 37° C. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice in RNALater (Thermo Fisher Scientific) and then stored at −80° C. for later analysis. 
     After initial digestion colonic and small intestinal tissue pieces are digested in collagenase/DNase containing RPMI medium for 30 min. Tissue pieces are further strained through a 70 mm mesh. For flow cytometry analyses, cell suspensions are stained with antibodies against the following surface markers: CD11c (N418), CD11b (M1/70), Ly6c (HK1.4), MHC class II (M5/114.15.2), CD24 (M1/69), CD64 (X54-5/7.1), CD317 (ebio927), CD45 (30-F11), F4/80 (C1:A3-1), CD8a (53-6.7). DAPIis used for dead cell exclusion. Antibodies are purchased from eBiosciences, BD Biosciences or BioLegend respectively. Cell populations are gated as follows: small intestine (migratory fraction): CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+CD103+(CD45+CD11c+MHC-II+CD103+CD11b+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+), large intestine: CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+). 
     Flow cytometry analyses were performed on small intestine, cecum and colon tissue collected from mice pretreated with water and antibiotics and treatments including vehicle, anti-PD-1 and vehicle, anti-PD-1 in combination with microbial mix 4 and ellagic acid and anti-PD-1 in combination with microbial mix 2. Spearman correlation was computed between final tumor volume and each flow gate for all treatments in each GI location. Correlations passing a false discovery rate threshold of 0.25 are reported in Table 32. Spearman correlations between each flow gate, final tumor volume and their magnitude by GI location is reported in  FIG.  36   . The strongest correlations between final tumor volume and the flow results occur in the colon. Final tumor volume for all treatment groups was plotted against the IA/IE (MIC Class II) immune population in the colon, which revealed a statistically significant negative correlation as reported in  FIG.  37   . 
     
       
         
           
               
               
               
               
             
               
                 TABLE 32 
               
               
                   
               
               
                 Category 
                 P 
                 rho 
                 location 
               
               
                   
               
             
            
               
                 Colon: CD11b-IA-IE+ 
                 0.001495129 
                 −0.537953832 
                 Colon 
               
               
                 Colon: IA-IE+ 
                 0.002046607 
                 −0.524752511 
                 Colon 
               
               
                 Colon: Monocytes 
                 0.011114461 
                 −0.442977661 
                 Colon 
               
               
                 Colon: cDC 
                 0.013117759 
                  0.433810077 
                 Colon 
               
               
                   
               
            
           
         
       
     
     Fecal Microbiota Transplantation (FMT) 
     Fecal Microbiota Transplantation (FMT) of a favorable gut microbiome into antibiotic treated mice is a method for standardizing microbiome composition. FMT is performed in some experiments with fecal material derived from healthy and cancer patients, as well as mouse stools. Colonization is performed by oral gavage with 200 μl of suspension obtained by homogenizing the fecal samples in PBS. Efficient colonization is first checked before tumor inoculation. Mouse fecal samples are collected 1-2 times during this period. So that the efficacy of the FMT can be evaluated. Following FMT, a rest period of 5-7 days occurs prior to checkpoint inhibitor and/or microbe dosing. Blood and fecal pellets are collected at different time points during the experiment. 
     Flow Cytometry of Peripheral Blood 
     A whole-blood flow cytometry-based assay is utilized to assess T cell activation in response to anti-CTLA-4, anti-PD-1 and microbial treatment. Whole blood via cardiac puncture is collected into an EDTA tube at the end of the experiment. 100 μL of whole mouse blood is transferred to a 15 mL conical tube. 1 mL of RBC Lysis Buffer is added to the tube and allowed to incubate at room temperature for 10 minutes. Lysis is quenched by adding 10 mL of cold DPBS. Samples are centrifuged at 1500 rpm for 5 minutes at 4° C. The pellet is aspirated and resuspend in another 10 mL of cold DPBS. Samples are recentrifuged at 1500 rpm for 5 minutes at 4° C. Samples are resuspended in 500 μL of FACS buffer and transferred to a 96-well plate. Samples are stained with Fixable Viability ef780 (eBioscience), CD45-PEcy7 (BioLegend), CD3-BV605 (BioLegend), CD8-AF700 (BioLegend), and CD4-AF488 (BioLegend). Stained samples are run on a BD LSRFortessa™ flow cytometer and analyses are performed with FlowJo™ (Tree Star). 
     Flow cytometry analysis was performed on mice and CD3+ percentage is displayed against tumor volume at day 28 post-inoculation as shown in  FIG.  38   . There is a strong inverse relationship between CD3+ percentage and tumor volume where CD3+ cells are increased by treatment with microbial mixes 2 and 4. 
     Tumor Challenge and Treatment 
     After pre-treatment is complete, animals will be randomized when average tumor volume reaches 40-60 mm 3  (Study Day 0). Dosing of Microbes, Vehicle, anti-CTLA-4, anti-PD1 and Ellagic Acid will begin the following day (Study Day 1) below and continue for 3 weeks. Animals are given at least 48 hrs of no treatment between antibiotic pre-treatment and regular study treatment to allow for antibiotics to go through system. Mice are divided into immunotherapy treatment and non-treatment groups. The treatment group is injected intraperitoneally once the tumor reached a size of 40 to 60 mm 3  (day 0) with 100 μg anti-PD1 mAb (BioXCell), or with 100 μg anti-PD-L1 mAb, or with 100 μg anti-CTLA-4 mAb (BioXCell) in 100 μl PBS twice a week for three weeks starting from day 1. Tumor size is routinely monitored by means of a caliper. Stool is collected on day 0 and 8 hours after each subsequent administration of treatment until the end of the study. 
     Tumor size was measured in all animals receiving the different microbial treatments, with and without anti-CTLA-4, anti-PD1 or anti-PD-L1 therapy. On average, the animals receiving microbial mix 2 (equal amounts of  F. prausnitzii, C. coccoides, R. gnavus, C. scindens, A. muciniphila , and  E. hirae ) in conjunction with anti-PD1 have a reduction in tumor size compared to those with other microbes or not receiving any anti-PD1 treatment, as illustrated in  FIG.  39   . Mice treated with microbial mix 2 and the anti-PD1 therapy had reduced tumor growth in contrast to the anti-PD1 monotherapy as shown in  FIG.  40   . Tumor volumes were measured 28 days post inoculation and displayed by both pre-treatment and treatment groups as shown in  FIG.  41   . On average, the animals receiving microbial mix 2 (equal amounts of  F. prausnitzii, C. coccoides, R. gnavus, C. scindens, A. muciniphila , and  E. hirae ) in conjunction with anti-CTLA-4 in both pre-treatment groups, have a reduction in tumor size compared to those with other microbes or the anti-CTLA-4 monotherapy. Tumor volumes were measured at multiple time points post-inoculation. Mean and standard error of the mean are displayed for each treatment group within water and antibiotic pre-treatment groups are shown in  FIG.  42   . 
     Mice were pre-treated with antibiotics, fecal microbiota transplantation (FMT) was performed, and tumors were inoculated. Randomization and treatment began at a tumor volume of 50 mm 3 . Tumor size was measured in all animals receiving microbial treatments, antibiotic pre-treatment, followed by FMT transfer from cancer patients with and without anti-CTLA-4, anti-PD1 or anti-PD-L1 therapy. Four FMTs (1-4) were selected for administration to the mice based on donor cancer patient response to therapy. FMTs 1 and 3 are derived from non-responding cancer patients and FMTs 2 and 4 are from cancer patients that respond to immunotherapy. On average, the mice receiving FMTs 1 and 3 from non-responding cancer patients had larger overall tumors than those receiving FMTs 2 and 4 from responding cancer patients, as illustrated in  FIG.  47   . On average, the animals receiving microbial mix 2 (equal amounts of  F. prausnitzii, C. coccoides, R. gnavus, C. scindens, A. muciniphila , and  E. hirae ) in conjunction with anti-CTLA-4 and FMTs 1 and 3 have a reduction in tumor size compared to those only receiving FMTs 1 and 3 in combination with anti-CTLA-4 as illustrated in  FIG.  43   . Tumor volume mean and standard error of the mean are displayed for each treatment group, as illustrated in  FIG.  44   . Tumor volume mean curves and individual tumor sizes plotted as dots are displayed for each treatment group, as illustrated in  FIG.  45   . 
     Antibiotic induced depletion of mouse microbiota has been shown to significantly reduce the diversity of the microbiota, gut motility and increase the weight and size of the gastrointestinal tract (Ge et al. J Transl Med (2017) 15:13). Images of the gastrointestinal tract (GI) for mice in both water and antibiotic pre-treatment groups are shown in  FIG.  46 A-D . The GI tract for antibiotic pre-treatment groups with vehicle or anti-CTLA-4 treatments was enlarged compared to the equivalent water pre-treatment groups. Treatment groups with microbial mix 2 in combination with anti-CTLA-4 and microbial mix 4+ ellagic acid in combination with anti-CTLA-4 had similar sized GI tracts for both pre-treatment groups. The normal size of the GI tract suggests that microbial mixes 2 and 4 have anti-inflammatory properties that may contribute to the observed anti-cancer efficacy. 
     Example 18—Efficacy of Live Biotherapeutics as an Antiviral Monotherapy 
     Microorganisms in Mouse Study 
     The sets of microbes to be administered are chosen from either Table 9 (1-294), described in Example 10, and/or Table 42, Example 25, or from engineered microbes described in Examples 12 and 13. Each microbe is isolated from healthy donors, as described in Example 3, or the genetically modified derivatives described in Examples 12 and 13. The live biotherapeutic is cultured and assembled as described in Example 14. 
     After assembly, PBS-C-G is added to each live biotherapeutic to reduce the total cell density of each live biotherapeutic to the desired dosage level, which can be between 1×10 8 /0.2 ml and 1×10 12 /0.2 ml. Live biotherapeutics are aliquoted into eight 5.0 ml volumes into 15 ml conical tubes and stored at −20° C. until required. 
     Mice and Viruses 
     Several strains of mice including BALB/c, C57BL/6, 129S and transgenic mice (K18-hACE2, A70-hACE2) are obtained from Shanghai Lingchang Biotechnology Co., Ltd (Shanghai, China) or Jackson Laboratory. 6-8-week-old female mice are used. Strains of SARS-CoV, SARS-CoV-2, LCMV, recombinant influenza expressing the LCMV GP33 epitope (PR8-GP33), RSV and A/PR8 (H1N1) viruses are obtained and propagated and titered on Vero E6 cells. Viral titers from 10 5  to 10 7  PFU/ml are used. Mice are lightly anesthetized with halothane and infected intranasally with the dosage of virus. Infected mice are examined and weighed daily. To obtain specimens for virus titers, animals are sacrificed, and organs are aseptically removed into sterile phosphate-buffered saline. 
     Antibiotic Pre-Treatment 
     In some studies, mice are treated daily with 200 μL of antibiotic solution via oral gavage for a duration of 1-4 weeks. The antibiotic solution consists of ampicillin (1 mg/mL)(Alfa Aesar J6380706), gentamicin (1 mg/mL)(Acros Organics AC455310050), metronidazole (1 mg/mL)(Acros Organics AC210440050), neomycin (1 mg/mL)(Alfa Aesar AAJ6149922), and vancomycin (0.5 mg/mL) (Alfa Aesar J6279006) via oral gavage. Animals are given at least 48 hours rest period between antibiotic pre-treatment and the treatment phase to allow for antibiotics to go through the system. 
     Fecal Microbiota Transplantation (FMT) 
     Fecal Microbiota Transplantation (FMT) of a human gut microbiome into antibiotic treated mice is a method for standardizing microbiome composition. FMT is performed in some experiments with fecal material derived from healthy donors, donors infected with viruses and responders to checkpoint inhibitor therapy (R) or non-responders to checkpoint inhibitor therapy (NR). Not only does this standardize the mice microbiomes, but also conditions them to favor response or non-response, respectively. Following antibiotic pre-treatment, colonization is performed by oral gavage with 200 μl of suspension obtained by homogenizing the fecal samples in PBS. Mouse fecal samples are collected 1-2 times during this period, so that the efficacy of the FMT can be evaluated. Following FMT, a rest period of 5-7 days is allowed to pass prior to treatment initiation. 
     Histology and Immunohistochemistry 
     Organs are harvested from infected and uninfected mice and fixed in zinc formalin. For histology, sections are stained with hematoxylin and eosin. To detect viral antigen, sections are probed with a monoclonal antibody (MAb) to the SARS-CoV and SARS-CoV-2 N protein (Zymed, San Francisco, Calif.), or any viral antigen or a control immunoglobulin G2a Mab (E-Bioscience, San Diego, Calif.) followed by a biotinylated goat anti-mouse secondary antibody (1:200; Jackson Immunoresearch, West Grove, Pa.). Samples are developed by sequential incubation with a streptavidin-horseradish peroxidase conjugate (Jackson Immunoresearch) and diaminobenzidine (Sigma-Aldrich). 
     Peripheral Blood Extraction and Processing 
     Whole blood is taken via cardiac puncture at the end of the experiment, or via tail bleed during the experiment, and collected into an EDTA tube. Plasma is isolated from an aliquot of the whole blood by centrifugation at 1500×g for 10 minutes, taking the supernatant. A second centrifugation is performed to remove any residual blood cells. 
     Peripheral blood mononuclear cells (PBMCs) are isolated from blood using a standard kit and stored in liquid nitrogen at 1×10 6  cells/mL until use. Prior to storage, PBMC&#39;s may be processed using flow sorting or antibody spin separation kit to select for a certain purified lymphocyte subpopulation, such as T cells. 
     GI Tract Removal and Analysis 
     After mice are euthanized at the termination of the study, the intact digestive tract of each mouse from stomach to rectum are removed and kept in a 5 ml Eppendorf tube on ice prior to dissection. Forceps are sterilized by soaking in 100% ethanol and then used to remove the intestine length and stretch it on a work surface covered with cellophane. With the use of ethanol-sterilized dissection scissors, 3 cm lengths of the jejunum nearest to the stomach and the ilium nearest to the cecum/large intestine are excised and then each placed with forceps in a 1.5 ml Eppendorf tube and placed on ice. A 2 cm segment of the cecum/ascending colon is then excised, as are 2 cm segments of the transcending colon and the descending colon, and all are placed in 1.5 ml Eppendorf tubes on ice. Dissection instruments are sterilized by dipping in 100% ethanol between each intestine fragment removal. To each tube containing dissected intestinal segments is added 0.5 ml ice cold PBS buffer. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice and then stored at −80° C. for later analysis. 
     Analyses of Dendritic Cell Subsets in Treated Mice 
     Cell suspensions from mouse spleen and lymph nodes are prepared by digestion with collagenase and DNase for 60 min and subsequently strained through a 70 mm mesh. Colonic and small intestinal lymphocytes are isolated as previously described (Viaud, S. et al. Science 80(342): 971-976 (2013). In brief, cecum, colon and small intestine are digested in PBS containing 5 mM EDTA and 2 mM DTT shaking at 37° C. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice in RNALater (Thermo Fisher Scientific) and then stored at −80° C. for later analysis. 
     After initial digestion colonic and small intestinal tissue pieces are digested in collagenase/Dnase containing RPMI medium for 30 min. Tissue pieces are further strained through a 70 mm mesh. For flow cytometry analyses, cell suspensions are stained with antibodies against the following surface markers: CD11c (N418), CD11b (M1/70), Ly6c (HK1.4), MHC class II (M5/114.15.2), CD24 (M1/69), CD64 (X54-5/7.1), CD317 (ebio927), CD45 (30-F11), F4/80 (C1:A3-1), CD8a (53-6.7). DAPIis used for dead cell exclusion. Antibodies are purchased from eBiosciences, BD Biosciences or BioLegend respectively. Cell populations are gated as follows: small intestine (migratory fraction): CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+CD103+(CD45+CD11c+MHC-II+CD103+CD11b+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+), large intestine: CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+). 
     Whole Genome Sequencing 
     Fecal gDNA is extracted for whole genome sequencing (WGS). Experimental methods for DNA extraction and library preparation are performed using protocols modeled after the Human Microbiome Project (Lloyd-Price et al. (2017) Nature 550(7674):61-66) and validated with samples from healthy volunteers. Sequencing is performed by an outside service provider, using a HISEQ-X® (Illumina) with 2×150 bp paired-end reads, providing approximately 4 million reads per sample. Analysis software such as Centrifuge (Kim, D., et al., Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res, 2016. 26(12): p. 1721-1729) are used to align sequence reads to reference genomes and obtain species and strain-level identification. 
     Metabolomics 
     Metabolites are extracted from fecal material or blood plasma, using methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation to recover chemically diverse metabolites. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods using positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS using negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS using negative ion mode ESI, and one reserved for backup. Samples are placed briefly on a TurboVap® (Zymark) to remove the organic solvent, followed by injection on one of the instruments mentioned above. Compounds are identified by comparison to library entries of purified standards, that contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data) on all molecules present in the library. Furthermore, biochemical identifications are based on three criteria: retention index within a narrow RI window of the proposed identification, accurate mass match to the library+/−10 ppm, and the MS/MS forward and reverse scores. MS/MS scores are based on a comparison of the ions present in the experimental spectrum to ions present in the library entry spectrum. While there may be similarities between these molecules based on one of these factors, the use of all three data points can be utilized to distinguish and differentiate biochemicals. Peaks are quantified as area-under-the-curve detector ion counts. 
     Immunophenotyping Assays 
     Immune profiling of whole blood is utilized to assess T cell activation in response to microbial treatment. In some experiments, immune phenotyping is also performed on tissue obtained from the GI tract. 
     For flow cytometry analysis, 1 mL of RBC Lysis Buffer is added to 0.1 mL of whole blood or homogenized tissue and allowed to incubate at room temperature for 10 minutes. Lysis is quenched by adding 10 mL of cold DPBS. Samples are centrifuged at 1500 rpm for 5 minutes at 4° C. The pellet is aspirated and resuspend in another 10 mL of cold DPBS. Samples are recentrifuged at 1500 rpm for 5 minutes at 4° C. Samples are resuspended in 500 μL of FACS buffer and transferred to a 96-well plate. Samples are stained with Fixable Viability ef780™ (eBioscience), CD45-PEcy7 (BioLegend), CD3-BV605™ (BioLegend), CD8-AF700™ (BioLegend), and CD4-AF488™ (BioLegend). Stained samples are run on a BD LSRFortessa™ flow cytometer and analyses are performed with FlowJo™ (Tree Star). 
     Alternatively, CyTOF® is applied to characterize the immune profile of the PBMCs. This work is conducted by the Bioanalytical and Single-Cell Facility at the University of Texas, San Antonio, and entails a comprehensive panel of 29 different immune markers, allowing for deep interrogation of cellular phenotype and function (https://www.fluidigm.com/products/helios). To complement these results, RNA sequencing is applied to the entire population of the PBMCs, sorted populations, and also to single cells. Single cell RNAseq is applied using the method developed by 10×Genomics (https://www.10xgenomics.com/solutions/single-cell/). Finally, cytokine levels are determined using the Human Cytokine 30-Plex Luminex assay (https://www.thermofisher.com/order/catalog/product/LHC6003M). 
     Example 19—Therapeutic Effect of Microbes on Efficacy of Antiviral Therapy 
     In this study, live biotherapeutics as provided herein, including combinations of microbes as provided herein, are administered in combination with antiviral therapies (a small molecule, a vaccine, an antibody, a cell therapy, a natural killer (NK) cell therapy, angiotensin II receptor blockers, a defensin-mimetic, a nanobody, a peptide, an immune modulator, an immunotherapy, an anti-necrosis, a nucleoside, a quinoline compound, a protease inhibitor, a sphingosine kinase-2 (SK2) inhibitor, an interleukin receptor antagonist and nanoviricide) to demonstrate the ability of these microbes to enhance antiviral immunity. 
     Microorganisms in Mouse Study 
     The sets (or combinations) of microbes to be administered are chosen from the list of exemplary bacterial combinations as set forth in Table 9, listing combinations 1 to 294, as described in Example 10, or from the exemplary engineered microbes described in Examples 12 and 13, or from Table 42, Example 25. Each microbe is isolated from healthy donors, as described in Example 3, or the genetically modified derivatives described in Examples 12 and 13. The live biotherapeutic is cultured and assembled as described in Example 14. 
     After assembly, PBS-C-G is added to each microbial mix to reduce the total cell density of each microbial mix to the desired dosage level, which can be between 1×10 8/ 0.2 ml and 1×10 12 /0.2 ml. Live biotherapeutics are aliquoted into eight 5.0 ml volumes into 15 ml conical tubes and stored at −20° C. until required. 
     Mice and Viruses 
     Several strains of mice including BALB/c, C57BL/6, 129S and transgenic mice (K18-hACE2, A70-hACE2) are obtained from Shanghai Lingchang Biotechnology Co., Ltd (Shanghai, China) or Jackson Laboratory. 6-8-week-old female mice are used. Strains of SARS-CoV, SARS-CoV-2, LCMV, recombinant influenza expressing the LCMV GP33 epitope (PR8-GP33) and A/PR8 (H1N1) viruses are obtained and propagated and titered on Vero E6 cells. Viral titers from 10 5  to 10 7  PFU/ml are used. Mice are lightly anesthetized with halothane and infected intranasally with the dosage of virus. Infected mice are examined and weighed daily. To obtain specimens for virus titers, animals are sacrificed, and organs are aseptically removed into sterile phosphate-buffered saline. 
     Antibiotic Pre-Treatment 
     In some studies, mice are treated daily with 200 μL of antibiotic solution via oral gavage for a duration of 1-2 weeks. The antibiotic solution consists of ampicillin (1 mg/mL)(Alfa Aesar J6380706), gentamicin (1 mg/mL)(Acros Organics AC455310050), metronidazole (1 mg/mL)(Acros Organics AC210440050), neomycin (1 mg/mL)(Alfa Aesar AAJ6149922), and vancomycin (0.5 mg/mL) (Alfa Aesar J6279006) via oral gavage. Animals are given at least 48 hrs rest period between antibiotic pre-treatment and the treatment phase to allow for antibiotics to go through system. 
     Fecal Microbiota Transplantation (FMT) 
     In alternative embodiments, methods as provided herein comprise use of Fecal Microbiota Transplantation (FMT), or elements used to practice FMT, as described for example, in U.S. Pat. Nos. 10,493,111; 10,463,702; 10,383,519; 10,369,175; 10,328,107. 
     FMT of a human gut microbiome into antibiotic treated mice is a method for standardizing microbiome composition. FMT is performed in some experiments with fecal material derived from responders to checkpoint inhibitor therapy (R) or non-responders to checkpoint inhibitor therapy (NR). Not only does this standardize the mice microbiomes, but also conditions them to favor response or non-response, respectively. Following antibiotic pre-treatment, colonization is performed by oral gavage with 200 μl of suspension obtained by homogenizing the fecal samples in PBS. Mouse fecal samples are collected 1-2 times during this period, so that the efficacy of the FMT can be evaluated. Following FMT, a rest period of 5-7 days can pass prior to treatment initiation. 
     Histology and Immunohistochemistry 
     Organs are harvested from infected and uninfected mice and fixed in zinc formalin. For histology, sections are stained with hematoxylin and eosin. To detect viral antigen, sections are probed with a monoclonal antibody (MAb) to the SARS-CoV and SARS-CoV-2 N protein (Zymed, San Francisco, Calif.), or any viral antigen or a control immunoglobulin G2a Mab (E-Bioscience, San Diego, Calif.) followed by a biotinylated goat anti-mouse secondary antibody (1:200; Jackson Immunoresearch, West Grove, Pa.). Samples are developed by sequential incubation with a streptavidin-horseradish peroxidase conjugate (Jackson Immunoresearch) and diaminobenzidine (Sigma-Aldrich). 
     Peripheral Blood Extraction and Processing 
     Whole blood is taken via cardiac puncture at the end of the experiment, or via tail bleed during the experiment, and collected into an EDTA tube. Plasma is isolated from an aliquot of the whole blood by centrifugation at 1500×g for 10 minutes, taking the supernatant. A second centrifugation is performed to remove any residual blood cells. 
     Peripheral blood mononuclear cells (PBMCs) are isolated from blood using a standard kit and stored in liquid nitrogen at 1×10 6  cells/mL until use. Prior to storage, PBMC&#39;s may be processed using flow sorting or antibody spin separation kit to select for a certain purified lymphocyte subpopulation, such as T cells. 
     GI Tract Removal and Analysis 
     After mice are euthanized at the termination of the study, the intact digestive tract of each mouse from stomach to rectum are removed and kept in a 5 ml Eppendorf tube on ice prior to dissection. Forceps are sterilized by soaking in 100% ethanol and then used to remove the intestine length and stretch it on a work surface covered with cellophane. With the use of ethanol-sterilized dissection scissors, 3 cm lengths of the jejunum nearest to the stomach and the ilium nearest to the cecum/large intestine are excised and then each placed with forceps in a 1.5 ml Eppendorf tube and placed on ice. A 2 cm segment of the cecum/ascending colon is then excised, as are 2 cm segments of the transcending colon and the descending colon, and all are placed in 1.5 ml Eppendorf tubes on ice. Dissection instruments are sterilized by dipping in 100% ethanol between each intestine fragment removal. To each tube containing dissected intestinal segments is added 0.5 ml ice cold PBS buffer. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice and then stored at −80° C. for later analysis. 
     Analyses of Dendritic Cell Subsets in Treated Mice 
     Cell suspensions from mouse spleen and lymph nodes are prepared by digestion with collagenase and DNase for 60 min and subsequently strained through a 70 mm mesh. Colonic and small intestinal lymphocytes are isolated as previously described (Viaud, S. et al. Science (80-.). 342, 971-976 (2013). In brief, cecum, colon and small intestine are digested in PBS containing 5 mM EDTA and 2 mM DTT shaking at 37° C. A plastic pestle is used to press and massage the intestinal segment in each tube to expel ruminal matter, which is then removed by pipette and placed in a fresh Eppendorf tube. Tubes containing expelled ruminal matter from each intestinal segment are immediately placed on dry ice and then stored for later analyses at −80° C. Remaining intestinal tissues are then rinsed twice by adding and then removing 0.5 ml ice cold PBS. Rinsed intestinal fragment tissues are then frozen on dry ice in RNALater (Thermo Fisher Scientific) and then stored at −80° C. for later analysis. 
     After initial digestion colonic and small intestinal tissue pieces are digested in collagenase/DNase containing RPMI medium for 30 min. Tissue pieces are further strained through a 70 mm mesh. For flow cytometry analyses, cell suspensions are stained with antibodies against the following surface markers: CD11c (N418), CD11b (M1/70), Ly6c (HK1.4), MHC class II (M5/114.15.2), CD24 (M1/69), CD64 (X54-5/7.1), CD317 (ebio927), CD45 (30-F11), F4/80 (C1:A3-1), CD8a (53-6.7). DAPIis used for dead cell exclusion. Antibodies are purchased from eBiosciences, BD Biosciences or BioLegend respectively. Cell populations are gated as follows: small intestine (migratory fraction): CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+CD103+(CD45+CD11c+MHC-II+CD103+CD11b+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+), large intestine: CD103+DC (CD45+CD11c+MHC-II+CD103+CD24+), CD11b+(CD45+CD11c+MHC-II+CD11b+CD24+), inflammatory DC (CD45+CD11c+MHC-II+CD11b+CD64+Ly6c+). 
     Analysis of Fecal and Blood Samples 
     Whole genome sequencing, metabolomics, and immunophenotyping are performed on samples collected, as described in Example 15. 
     Example 20: Method of Treating a Subject with a Live Exemplary Biotherapeutic 
     This example describes administration of a live exemplary biotherapeutic as provided herein, including a combination of bacteria as provided herein, for example, as set forth in Table 9, Example 10, and/or Table 42, Example 25, to an individual in need thereof. 
     A patient is suffering from a viral infection, such as that caused by SARS-CoV-2 or other coronaviruses, or any influenza virus. The patient is administered live biotherapeutic compositions, i.e., a formulation or a pharmaceutical composition comprising a combination of microbes (for example, bacteria) as provided herein, (Table 9, and as described in Example 10, and/or Table 42, Example 25) either in monotherapy or in combination with a reverse transcriptase inhibitor, protease inhibitor, integrase inhibitor, fusion inhibitor, chemokine receptor antagonist, cell therapy, immunotherapy, or any other antiviral treatment, or a vaccine, and the patient can be administered the live biotherapeutic for the duration of treatment or for only one or several segments of treatment. 
     In alternative embodiments, each or one of the microbes used in the bacterial combination is (at least initially) isolated from a healthy donor or donors, as described in Example 3, or is a genetically modified derivative as described in Examples 12 and 13, or is a cultured derivative either. 
     In alternative embodiments, the patient is administered a live biotherapeutic at a dose of between about 10 5  to 10 15  bacteria, or at a dose of about 10 10 , 10 11  or 10 12  bacteria total or per dose, which can be in a lyophilized form, for example, or formulated in an enteric coated capsule. In alternative embodiments, the patient takes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 or more live biotherapeutic capsules (for example, by mouth or suppository) once, twice or three times or more per day, and the patient can resume a normal diet after about 1, 2, 4, 8, 12, or 24 or more hours. 
     In another embodiment, the patient may take the live biotherapeutic capsule(s) by mouth before, during, and/or immediately after a meal. 
     In another embodiment, the patient is given a course of antibiotics before treatment, for example, between one to seven days, or between about one to two weeks prior to the first dose of the live biotherapeutic (for example, as capsule(s)). 
     In another embodiment, dosing of the live biotherapeutic, for example, as capsule(s), is started one to seven days prior to administration of a first dose of antiviral treatment. 
     In another embodiment, dosing of the live biotherapeutic capsule(s) is continued 1 month, 6 months, 1 year, or more, or between about one week and 2 years, following termination of antiviral treatment or full recovery from disease. 
     In alternative embodiments, severity of the disease and patient response to the therapy can be scored based on time to viral clearance, time to symptom-free recovery, number of days with high fever, or severity of symptoms. 
     Example 21: Method of Treating a Subject with an Exemplary Live Biotherapeutic Based on Stool Biomarkers 
     This example describes administration of a live exemplary biotherapeutic as provided herein, including a combination of bacteria as provided herein, for example, as set forth in Table 9, Example 10, and/or Table 42, Example 25, to an individual in need thereof. 
     A patient is suffering from a viral infection, such as that caused by SARS-CoV-2 or other coronaviruses, or any influenza virus. The patient&#39;s stool is collected and analyzed using the methods described in Example 9. In one embodiment, whole genome sequencing is performed and the presence of microbes that are characteristic of patients with less severe symptoms and faster recovery is evaluated. The complete organism abundance profile is also plotted on the PCA axes shown in  FIG.  3   . Based on the abundance profiles of test subjects, a classifier is developed to predict if any given microbiome composition represents someone who recovers well from the viral infection or someone who has poor recovery. This may be based on the amount of one or more particular organisms present, position in the PCA plot, or other criteria that combines aspects of the whole genome sequence data. This classifier is applied to the patient&#39;s microbiome composition to determine if the patient is at risk for severe symptoms. 
     In another embodiment, metabolomics is performed on the stool or plasma; a classifier is developed based concentrations of one or more metabolites in all patient data collected to date, and the patient prognosis is predicted based on this classification. 
     If the patient is classified as at risk, a live biotherapeutic will be administered to change the microbiome to be more like that of someone who recovers quickly. The patient is administered one of the present live biotherapeutics (Table 9, and as described in Example 10, and/or Table 42, Example 25) in combination with a reverse transcriptase inhibitor, protease inhibitor, integrase inhibitor, fusion inhibitor, chemokine receptor antagonist, or any other antiviral treatment, and the patient can be administered the live biotherapeutic for the duration of treatment. Each microbe is isolated from healthy donors, as described in Example 3, or the genetically modified derivatives described in Examples 12 and 13. 
     In alternative embodiments, the patient is administered a live biotherapeutic at a dose of between about 10 5  to 10 15  bacteria, or at a dose of about 10 10 , 10 11  or 10 12  bacteria total or per dose, which can be in a lyophilized form, for example, formulated in an enteric coated capsule. The patient takes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 or more live biotherapeutic capsules by mouth once, twice or three times per day, and resumes a normal diet after 2, 4, 8, 12, or 24 hours. 
     In another embodiment, the patient takes the capsule by mouth before, during, or immediately after a meal. 
     In another embodiment, the patient is given a course of antibiotics before treatment, for example, between one to seven days, or between about one to two weeks prior to the first dose of microbial cocktail. 
     In another embodiment, dosing of the live biotherapeutic capsule(s) is continued 1 month, 6 months, 1 year, or more, or between about one week and 2 years, following termination of antiviral treatment or full recovery from disease. 
     In alternative embodiments, severity of the disease and patient response to the therapy can be scored based on time to viral clearance, time to symptom-free recovery, number of days with high fever, or severity of symptoms. 
     Example 22: Diagnosis of Disease and Method of Treating a Subject with an Exemplary Microbial Therapeutic 
     This example describes administration of a live exemplary biotherapeutic as provided herein, including a combination of bacteria as provided herein, for example, as set forth in Table 9, Example 10, and/or Table 42, Example 25, to an individual in need thereof. 
     Stool biomarkers based on microbes present in patients that recover quickly from viral infections, that are also lacking in patients that have severe symptoms or recover from the infection slowly, can be used to predict the composition of live biotherapeutics for antiviral applications. Conversely, the absence of these microbes in stool samples, as well as the presence of others found to associate with patients with poor recovery, as detected in NGS analysis of stool samples taken from individuals during routine biomedical tests and procedures, can form a diagnostic pattern of biomarkers that can predict the likelihood that said individuals are at risk for severe symptoms or poor recovery upon viral infection. This diagnostic may be based on the amount of one or more organisms present, position in the PCA plot, or other criteria that combines aspects of the whole genome sequence data. Reliability of such diagnostic is determined by the area under the ROC curve, as exemplified in  FIG.  8   . The diagnostic method can also detect gut microbial population patterns that can predict poor prognosis upon viral infection, thereby redirecting a patient to further diagnoses, appropriate life-style changes, or prophylactic treatments such as the administration of a live biotherapeutic or live biotherapeutics to restore healthy gut microbe populations. 
     In another embodiment, stool analysis is used as a diagnosis for viral infection. For example, specific DNA viruses of concern are detected by PCR or real time PCR (RT-PCR) using primers specific to the virus of concern. An analogous procedure is used for RNA viruses, with reverse transcription followed by RT-PCR. Alternatively, viruses can be detected non-specifically by whole genome sequencing. Total genomic DNA is extracted from the stool using the MagAttract PowerMicrobiome DNA/RNA EP kit (Qiagen), and from blood using the QIAamp DNA Blood Mini Kit (Qiagen). Genomic DNA is then prepared for Whole Genome Sequencing analysis using the sparQ DNA Frag &amp; Library Prep kit (Quantabio). RNA is extracted from the stool or blood sample by binding to an RNeasy™ column (Qiagen) followed by washing and elution using the reagents provided in the RNeasy™ kit (Qiagen). Sequencing libraries are prepared from RNA by fragmentation, ribodepletion, cDNA synthesis, PCR amplification, and barcoding as described in the TRUSEQ® mRNA sample preparation kit (Illumina). Sequencing analysis is conducted on the Illumina platform using paired-end 150 bp reads. Reads not mapping to human or bacterial DNA are then aligned to a viral sequence database, for example the NCBI viral genomes database (https://www.ncbi.nlm.nih.gov/genome/viruses/). If a pathogenic virus is detected, remedial action can begin immediately. 
     Example 23: Prophylactic Application of a Live Exemplary Biotherapeutic to Reduce Risk of Viral Infection or Improve Prognosis Upon Infection in Healthy Individuals 
     This example describes administration of a live exemplary biotherapeutic as provided herein, including a combination of bacteria as provided herein, for example, as set forth in Table 9, Example 10, and/or Table 42, Example 25, to an individual as a prophylactic in healthy individuals or individuals determined to be at risk of severe reaction to viral infection, such as those individuals that are immunocompromised, have a heart condition, or are over 70 years of age. 
     An individual is administered one of the present live biotherapeutics (Table 9, as described in Example 10, or genetically modified variants described in Examples 12 and 13, and/or as described in Table 42, Example 25), thereby conditioning the microbiome to best enable the individual&#39;s immune system to eliminate a virus rapidly upon infection. Specifically, the individual is administered a live biotherapeutic at a dose of between about 10 5  to 10 15  bacteria, or at a dose of about 10 10 , 10 11  or 10 12  bacteria total or per dose, which can be in a lyophilized form, for example, formulated in an enteric coated capsule. The individual takes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 or more live biotherapeutic capsules by mouth once, twice or three times per day, and resumes a normal diet after 2, 4, 8, 12, or 24 hours. In another embodiment, the individual may take the capsule by mouth before, during, or immediately after a meal. 
     Example 24: Patient Data Collection from Clinical Trials and Machine Learning and Data Analysis on the Same 
     The results described here were obtained from a study involving cancer patients undergoing immunotherapy treatment and healthy controls. Microbes, gene functions, and metabolites elucidated as being absent in patients not responding well to treatment are relevant for the treatment of viral infections because in both cases a healthy immune response is required to combat the disease. Therefore, it is reasonable to expect that microbes beneficial for immuno-oncology treatment will also be beneficial or even essential for treating or ameliorating a viral infection, or for rapid viral clearance. 
     Eligible patients were selected based on current health condition, cancer status (current or in remission), and treatment program. Prior patient medical history was also collected and analyzed when available. This includes but is not limited to prior cancer history, diabetes, autoimmune disease, neurodegenerative disease, heart disease, metabolic syndrome, digestive disease, psychological disorders, HIV, and allergies. In addition, lifestyle and dietary habits were collected, including diet regimen, exercise routine, alcohol, nicotine, and caffeine intake, medical as well as recreational drug use, recent courses of antibiotics, vitamins, and probiotics. In some cases, information and data collected from wearable devices that monitor but is not limited to heart rate, calories burned, steps walked, blood pressure, biochemical release, time spent exercising and seizures. This data was assembled and used as input to the machine learning algorithms with the goal of determining correlations between patient history, wearable devices and treatment efficacy. In addition, relationships between this data and the results of sample analysis described below were elucidated. 
     In another embodiment, eligible patients testing positive for infection with COVID-19 (SARS-CoV2) or other coronavirus, or influenza virus, were selected as well as age-matched healthy controls. Information is also collected on the severity of disease, symptoms, time of recovery, and response to any treatment, if applicable. Prior patient medical history is also collected and analyzed, including but not limited to cancer, diabetes, autoimmune disease, neurodegenerative disease, heart disease, metabolic syndrome, digestive disease, psychological disorders, coronaviruses, influenza virus, HIV, and allergies. In addition, lifestyle and dietary habits are collected, including diet regimen, exercise routine, alcohol, nicotine, and caffeine intake, medical as well as recreational drug use, recent courses of antibiotics, vitamins, and probiotics. This data is assembled and used as input to the machine learning algorithms with the goal of determining correlations between patient history, course of illness, and results of stool and blood sample analysis 
     For current cancer patients, tumor size and cancer progression were tracked over time and classified based on radiographic assessment using the Response Criteria in Solid Tumors version 1.1 (Schwartz et al. Eur. J. Cancer 2016, 62:132-137) criteria. This is based on longitudinal measurements of lesions in cancer tissue, given a strict set of guidelines for lesion selection and measurement techniques. Responders to checkpoint inhibitor treatment are defined as patients that were cured or had stable disease lasting at least 6 months, while non-responders are defined as those whose cancer progressed or was stable for less than 6 months. Classification of responders and non-responders implies robust and insufficient immune response, respectively, and thus serves as a proxy for COVID-19, influenza, or other viral disease patients that will effectively clear the virus or have severe symptoms, respectively. 
     Each patient provided stool samples using the procedures as outlined in Example 2 and buccal swabs of the oral biome. In some cases, Urine, Blood and plasma samples were also taken by healthcare personnel within 1-2 days of the stool samples. Stool, urine and buccal samples were kept on ice or at 4° C. until processed. Whole blood was collected into an EDTA tube. Plasma was isolated from the blood by centrifugation at 1000×g for 10 minutes, followed by centrifugation at 2000×g for 10 minutes. At least three timepoints were taken for each patient, roughly every 6 to 8 weeks. 
     Whole Genome Sequencing of Patient Fecal Samples 
     Whole genome sequencing was performed as previously described in Example 9 on a total of 450 fecal samples. Of the 450 samples, 322 samples were from cancer patients, 96 were from control subjects, and 32 were from subjects in remission. The results were classified, and abundance was estimated for each sample using centrifuge, using the publicly available GTDB database (Parks et al. (2019) bioRxiv 771964, Méric et al. (2019) bioRxiv 712166). 
     The results were analyzed for differential relative abundance of organisms between cancer and control cohorts, as well as correlations between relative abundance of organisms and immune markers, as measured by flow cytometry. Additionally, machine learning was performed to train a model capable of discriminating between a subject with cancer and a control subject. 
     Metagenomic sequences are also scanned to identify novel CRISPR sequences using a scoring algorithm such as that described in (Moreno-Mateos et al. (2015) Nat. Met. 12:982-988), and for predicted natural product gene clusters using the antiSMASH routine (Medema et al. (2011) Nuc. Acids Res. 39:W339-W346). 
     Table 33, illustrated as  FIG.  47   . Whole genome sequencing was performed on fecal samples from subjects with and without cancer and the reads were classified using the GTDB database and abundance of each species was estimated computationally (Centrifuge). For classified hits with a mean relative abundance of at least 0.005%, The fold change difference and statistical significance (inverse p value, Mann Whitney U test) was calculated for abundances between cancer and control sample cohorts. 
     Cytokine Analysis of Blood Plasma 
     Plasma was obtained from 1 mL blood by centrifugation at 2000×g for 10 minutes. The plasma fraction was removed from the top and transferred to a clean tube. To remove any residual cells that may have carried over, the plasma was centrifuged again at 2000×g for 10 minutes, and the top layer was transferred to another tube, taking care to not take any red blood that may have settled to the bottom of the tube. Cytokine analysis was performed on 25 selected plasma samples by Eve Technologies (https://www.evetechnologies.com/) using the 48-plex Luminex assay. 
     Mann-Whitney test was applied to each cytokine to identify those with significant differential abundance between samples corresponding to checkpoint inhibitor complete responders (CR, N=6) and non-responders (NR, N=8). The remaining 11 samples were from patients identified as partial responders (PR) or stable disease (SD); due to the unclear phenotype, these were not included in the statistical analysis. Compounds with significant concentration differences between CR and NR samples (p&lt;0.05) are listed in Table 34. 
                     TABLE 34                  Average fluorescence values for CR and NR samples        exhibiting significant differential abundance.                                             CR    NR   CR/NR                Compound   Average   Average   ratio   P-value                                                     Eotaxin   20.91   36.11   0.58   0.0046           IFNgamma   0.51   4.41   0.12   0.0132           IL.2   0.55   1.77   0.31   0.0141           IL.27   1065.91   2326.60   0.46   0.0337           MIP.1a   30.02   44.87   0.67   0.0132                        
CyTOF Analysis of PBMCs Isolated from Whole Blood
 
     Peripheral blood mononuclear cells (PBMCs) were isolated from approximately 8 mL blood using SEPMATE™ tubes following the manufacturer&#39;s instructions. Following isolation, cells were resuspended in 1 mL PBS+2% FBS. 10 uL of the cell suspension was mixed with 10 uL if Trypan Blue Stain 0.4% and applied to a cell counter plate to determine viable cell concentration. The cell suspension was then diluted in 90% PBS+10% DMSO to achieve a cell density of 1×10{circumflex over ( )}7 cells/mL. Cells were then frozen at a controlled rate of 1° C./min to a final temperature of −150° C. in liquid nitrogen. 
     Mass cytometry (CyTOF) was performed on 25 selected PBMC samples by the University of Texas Health Center at San Antonio (UTHCSA). A 30 marker antibody panel focused on human immune-oncology relevant markers (Fluidigm) was used to quantify different cell populations. The markers and associated metal labels are given in Table 35. Markers were gated using the strategy shown in  FIG.  48    to determine the immune cell types and subtypes. Cell populations were reported either as a percentage of all viable cells and/or of the parent cell type. 
     
       
         
           
               
             
               
                 TABLE 35 
               
             
            
               
                   
               
               
                 List of antibodies and metal labels used for CyTOF analysis 
               
            
           
           
               
               
               
            
               
                   
                 Immune Marker 
                 Metal 
               
               
                   
                   
               
               
                   
                 CCR4 
                 158Gd 
               
               
                   
                 CCR5 
                 144Nd 
               
               
                   
                 CCR7 
                 159Tb 
               
               
                   
                 CD11a 
                 142Nd 
               
               
                   
                 CD127 
                 176Yb 
               
               
                   
                 CD134 [OX40] 
                 150Nd 
               
               
                   
                 CD137 [4-1BB] 
                 173Yb 
               
               
                   
                 CD152 [CTLA-4] 
                 161Dy 
               
               
                   
                 CD16 
                 148Nd 
               
               
                   
                 CD161 
                 164Dy 
               
               
                   
                 CD2 
                 151Eu 
               
               
                   
                 CD223 [LAG3] 
                 175Lu 
               
               
                   
                 CD25 
                 149Sm 
               
               
                   
                 CD27 
                 167Er 
               
               
                   
                 CD278 [ICOS] 
                 168Er 
               
               
                   
                 CD279 [PD-1] 
                 155Gd 
               
               
                   
                 CD28 
                 160Gd 
               
               
                   
                 CD3 
                 170Er 
               
               
                   
                 CD366 [Tim-3] 
                 153Eu 
               
               
                   
                 CD4 
                 145Nd 
               
               
                   
                 CD44 
                 166Er 
               
               
                   
                 CD45 
                 154Sm 
               
               
                   
                 CD45RA 
                 169Tm 
               
               
                   
                 CD45RO 
                 165Ho 
               
               
                   
                 CD49d 
                 141Pr 
               
               
                   
                 CD5 
                 143Nd 
               
               
                   
                 CD57 
                 172Yb 
               
               
                   
                 CD69 
                 162Dy 
               
               
                   
                 CD7 
                 147Sm 
               
               
                   
                 CD8a 
                 146Nd 
               
               
                   
                 CD9 
                 171Yb 
               
               
                   
                 CD95 [Fas] 
                 152Sm 
               
               
                   
                 CXCR3 
                 156Gd 
               
               
                   
                 HLA-DR 
                 174Yb 
               
               
                   
                   
               
            
           
         
       
     
     Mann-Whitney test was applied to each population type or subtype to identify those with significant differential abundance between samples corresponding to checkpoint inhibitor complete responders (CR, N=6) and non-responders (NR, N=8). The remaining 11 samples were from patients identified as partial responders (PR) or stable disease (SD); due to the unclear phenotype, these were not included in the statistical analysis. Cell populations with significant abundance differences between CR and NR samples (p&lt;0.05) are listed in Table 36. 
     
       
         
           
               
             
               
                 TABLE 36 
               
             
            
               
                   
               
               
                 Cell population abundance values, as a percentage either of total  
               
               
                 live cells or of the parent cell type, as indicated, for CR  
               
               
                 and NR samples exhibiting significant 
               
               
                 differential abundance. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 CR 
                 NR 
                 CR/ 
                 P- 
               
               
                 Cell Population 
                 Average 
                 Average 
                 NR 
                 value 
               
               
                   
               
               
                 % of CD3−CD44+CD11a+  
                 13.09 
                 31.67 
                 0.41 
                 0.0132 
               
               
                 in Siglet alive 
                   
                   
                   
                   
               
               
                 % of B cells in Siglet alive 
                  9.92 
                  4.92 
                 2.02 
                 0.0046 
               
               
                 % of CD3−HLADR+CD45RA_ 
                 10.44 
                 23.57 
                 0.44 
                 0.0095 
               
               
                 low in Siglet alive 
                   
                   
                   
                   
               
               
                 % of Monocytes in Siglet alive 
                 10.12 
                 22.29 
                 0.45 
                 0.0183 
               
               
                 % of CD3+CD4−CD8+CD45RO_ 
                 13.40 
                  8.28 
                 1.62 
                 0.0337 
               
               
                 lo CD45RA+ in alive 
                   
                   
                   
                   
               
               
                 % in B cells in CD45+CD3− 
                 43.37 
                 26.18 
                 1.66 
                 0.0132 
               
               
                   
               
            
           
         
       
     
     Example 25: Data Driven and Machine Learning Approaches for Therapeutic Design 
     Whole genome sequencing and flow cytometry analysis were performed on human fecal and blood samples, respectively, as described in Example 24. A machine learning model was fit to discriminate cancer and control samples, using all fecal data collected to date. The model developed using the GTDB database was validated using Stratified Group K-Fold Cross Validation (Tables 37 to 38). In addition, linear discriminant analysis (LDA) effect size method (LEfSe) was used to classify microbes identified using the GTDB database enriched in cancer or control (Table 39). 
     
       
         
           
               
             
               
                 TABLE 37 
               
             
            
               
                   
               
               
                 A logistic regression classifier was trained to classify  
               
               
                 samples as corresponding to cancer or control on  
               
               
                 samples with a mean relative abundance of at 
               
               
                 least 0.005% using the GTDB database. An  
               
               
                 ROC curve was generated on 322 cancer 
               
               
                 samples and 92 control samples using  
               
               
                 Stratified Group K-Fold Cross Validation 
               
               
                 (AUC = 0.79). Following validation, the model  
               
               
                 was trained on all the samples and 
               
               
                 feature importance values are reported. 
               
            
           
           
               
               
               
            
               
                   
                 Feature Importance  
                   
               
               
                   
                 (Logistic Regression) 
                 Organism Name 
               
               
                   
                   
               
               
                   
                  0.514417994 
                   Collinsella  sp900548935 
               
               
                   
                  0.486287437 
                   Clostridium  sp900539375 
               
               
                   
                  0.381613445 
                 UBA1191 sp900545775 
               
               
                   
                  0.310730798 
                 
                   Raoultibacter 
                   massiliensis 
                 
               
               
                   
                  0.289945387 
                 
                   Christensenella 
                   minuta 
                 
               
               
                   
                  0.283774901 
                 CAG-145 sp900540145 
               
               
                   
                  0.27456207 
                 
                   Bacteroides 
                   stercoris 
                 
               
               
                   
                  0.26468198 
                   Erysipelatoclostridium  sp900544435 
               
               
                   
                  0.263480075 
                 
                   Phocaeicola 
                   salanitronis 
                 
               
               
                   
                  0.250041885 
                   Marvinbryantia  sp900066075 
               
               
                   
                  0.249755758 
                   Odoribacter  sp900544025 
               
               
                   
                  0.216103903 
                 UBA738 sp003522945 
               
               
                   
                  0.207027879 
                 An200 sp900550095 
               
               
                   
                  0.195934646 
                 
                   Mediterraneibacter 
                   faecis 
                 
               
               
                   
                  0.185692545 
                 CAG-170 sp000436735 
               
               
                   
                  0.179847461 
                 
                   Megasphaera 
                   elsdenii 
                 
               
               
                   
                  0.162281593 
                 
                   Methanosphaera 
                   stadtmanae 
                 
               
               
                   
                  0.159663737 
                 UMGS1611 sp900553435 
               
               
                   
                  0.157611925 
                 CAG-177 sp003538135 
               
               
                   
                  0.157485555 
                 UBA6398 sp003150315 
               
               
                   
                  0.155329072 
                 CAG-492 sp000434015 
               
               
                   
                  0.153100473 
                   Dorea  sp000433215 
               
               
                   
                  0.151760426 
                   Evtepia  sp004556345 
               
               
                   
                  0.14588862 
                 UMGS1071 sp900542375 
               
               
                   
                  0.145040782 
                   Collinsella  sp900554585 
               
               
                   
                  0.136236542 
                   Clostridium  Q. sp003024715 
               
               
                   
                  0.131388743 
                 CAG-460 sp900544625 
               
               
                   
                  0.130605804 
                   Blautia  Asp900551715 
               
               
                   
                  0.12874627 
                   Niameybacter  sp900549765 
               
               
                   
                  0.127187848 
                 CAG-45 sp002299665 
               
               
                   
                  0.098447454 
                   Mailhella  sp900541395 
               
               
                   
                  0.092072207 
                 SFFHOlsp900548125 
               
               
                   
                  0.080714744 
                 
                   Dorea 
                   longicatena 
                 
               
               
                   
                  0.079070946 
                   Sutterella   wadsworthensis _A 
               
               
                   
                  0.076582096 
                   Negativibacillus  sp000435195 
               
               
                   
                  0.073355953 
                 UMGS1590 sp900552455 
               
               
                   
                  0.061020643 
                   Coprococcus _A sp900548825 
               
               
                   
                  0.059560254 
                   Blautia _A sp900066335 
               
               
                   
                  0.058625801 
                   Eubacterium _ sp900557275 
               
               
                   
                  0.048160806 
                 Firm-11 sp900540045 
               
               
                   
                  0.0465729 
                   Dorea   longicatena _B 
               
               
                   
                  0.045683691 
                 UMGS1491 sp900554775 
               
               
                   
                  0.044846674 
                 UMGS1241 sp900549955 
               
               
                   
                  0.044173983 
                 CAG-1427 sp000436075 
               
               
                   
                  0.040847644 
                   Alistipes  sp900541585 
               
               
                   
                  0.040245741 
                 
                   Gemmiger 
                   variabilis 
                 
               
               
                   
                  0.039602886 
                 CAG-495 sp000432275 
               
               
                   
                  0.036058062 
                 
                   Bariatricus 
                   comes 
                 
               
               
                   
                  0.035781984 
                 
                   Oxalobacter 
                   formigenes 
                 
               
               
                   
                  0.03030392 
                 
                   Frisingicoccus 
                   caecimuris 
                 
               
               
                   
                  0.025478979 
                 CAG-314 sp000437915 
               
               
                   
                  0.023104086 
                 QALW01 sp003150515 
               
               
                   
                  0.021151433 
                   Collinsella  sp900554325 
               
               
                   
                  0.020407288 
                 CAG-485 sp900541835 
               
               
                   
                  0.020130762 
                 CAG-452 sp000434035 
               
               
                   
                  0.017010213 
                   Agathobacter  sp900546625 
               
               
                   
                  0.016426446 
                 UBA5394sp003150565 
               
               
                   
                  0.005947673 
                   Blautia _A  obeum _B 
               
               
                   
                  0.004390397 
                 
                   Coprobacillus 
                   cateniformis 
                 
               
               
                   
                  0.002233086 
                   Akkermansia  sp004167605 
               
               
                   
                  0.00152013 
                   Anaerostipes   hadrus _A 
               
               
                   
                 −0.001234426 
                   Limosilactobacillus   fermentum _A 
               
               
                   
                 −0.003827343 
                 CAG-115sp003531585 
               
               
                   
                 −0.008153089 
                   Fusobacterium _B sp900541465 
               
               
                   
                 −0.014246241 
                   Prevotella  sp900552515 
               
               
                   
                 −0.016286555 
                   Collinsella  sp900551665 
               
               
                   
                 −0.021479219 
                 
                   Anaerotignum 
                   lactatifermentans 
                 
               
               
                   
                 −0.023122468 
                 UMGS1781 sp900553695 
               
               
                   
                 −0.024041329 
                 
                   Odoribacter 
                   laneus 
                 
               
               
                   
                 −0.034455465 
                 UBA11471sp000434215 
               
               
                   
                 −0.037849311 
                   Prevotellamassilia  sp000437675 
               
               
                   
                 −0.039128417 
                   Angelakisella  sp900547385 
               
               
                   
                 −0.039646845 
                   Agathobaculum  sp900291975 
               
               
                   
                 −0.041056608 
                   Eubacterium _R sp000434995 
               
               
                   
                 −0.04266878 
                   Eubacterium _F sp900539115 
               
               
                   
                 −0.044059805 
                   Alistipes  sp000434235 
               
               
                   
                 −0.050522202 
                 UMGS1590 sp900553245 
               
               
                   
                 −0.051836169 
                 UMGS1688 sp900554085 
               
               
                   
                 −0.057847833 
                 
                   Butyricimonas 
                   faecalis 
                 
               
               
                   
                 −0.066253286 
                   Akkermansia   muciniphila _A 
               
               
                   
                 −0.067189759 
                 
                   Coprobacter 
                   fastidiosus 
                 
               
               
                   
                 −0.067646141 
                 CAG-83 sp900550585 
               
               
                   
                 −0.083533993 
                   Prevotella  sp900554045 
               
               
                   
                 −0.085318406 
                 
                   Intestinimonas 
                   butyriciproducens 
                 
               
               
                   
                 −0.093860595 
                   Eubacterium _F sp000434115 
               
               
                   
                 −0.103834319 
                   Eubacterium _R sp900540305 
               
               
                   
                 −0.106144597 
                 
                   Desulfovibrio 
                   fairfieldensis 
                 
               
               
                   
                 −0.113985815 
                   Lachnospira  sp900316325 
               
               
                   
                 −0.117390396 
                   Porphyromonas  sp000768875 
               
               
                   
                 −0.122672447 
                 
                   Acidaminococcus 
                   intestini 
                 
               
               
                   
                 −0.126358887 
                 CAG-303 sp000437755 
               
               
                   
                 −0.127237507 
                 
                   Bacteroides 
                   caccae 
                 
               
               
                   
                 −0.136509832 
                   Prevotella  sp900548745 
               
               
                   
                 −0.136915786 
                   Dorea  sp000433535 
               
               
                   
                 −0.137055372 
                 
                   Ligilactobacillus 
                   salivarius 
                 
               
               
                   
                 −0.151411951 
                   Blautia _A sp900551465 
               
               
                   
                 −0.174551647 
                 CAG-83 sp000431575 
               
               
                   
                 −0.182703866 
                 
                   Streptococcus 
                   vestibularis 
                 
               
               
                   
                 −0.188088114 
                 CAG-302 sp900543825 
               
               
                   
                 −0.191528797 
                 
                   Butyricimonas 
                   virosa 
                 
               
               
                   
                 −0.207519696 
                   Dialister  sp900343095 
               
               
                   
                 −0.208796646 
                   Streptococcus  sp000314795 
               
               
                   
                 −0.21979495 
                 QANA01 sp900554725 
               
               
                   
                 −0.220254926 
                   Enterococcus _B  faecium   
               
               
                   
                 −0.249373565 
                 COE1 sp001916965 
               
               
                   
                 −0.249871731 
                   Mailhella  sp003150275 
               
               
                   
                 −0.251086664 
                 
                   Lachnospira 
                   eligens 
                 
               
               
                   
                 −0.299023203 
                   Catenibacterium  sp000437715 
               
               
                   
                 −0.303053041 
                 GCA-900066755 sp900066755 
               
               
                   
                 −0.30357643 
                 CAG-1031sp000431215 
               
               
                   
                 −0.306860922 
                 UBA1691sp900544375 
               
               
                   
                 −0.318039896 
                 CAG-495 sp001917125 
               
               
                   
                 −0.32832744 
                 AM07-15 sp003477405 
               
               
                   
                 −0.387480395 
                   Ruthenibacterium  sp003149955 
               
               
                   
                 −0.441806113 
                 
                   Parabacteroides 
                   johnsonii 
                 
               
               
                   
                 −0.513157387 
                 
                   Bariatricus 
                   massiliensis 
                 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 38 
               
             
            
               
                   
               
               
                 A logistic regression classifier was trained to  
               
               
                 classify samples as corresponding to cancer  
               
               
                 (non-responder) or control on samples with a mean  
               
               
                 relative abundance of at least 0.005% using the  
               
               
                 GTDB database. An ROC curve was generated  
               
               
                 on 43 non-responder samples and 92 control  
               
               
                 samples using Stratified Group K-Fold Cross  
               
               
                 Validation (AUC = 0.71). Following validation,  
               
               
                 the model was trained on all the samples 
               
               
                 and feature importance values are reported. 
               
            
           
           
               
               
               
            
               
                   
                 Feature Importance  
                   
               
               
                   
                 (Logistic Regression) 
                 Organism Name 
               
               
                   
                   
               
               
                   
                  0.568597444 
                 CAG-170 sp000436735 
               
               
                   
                  0.543705645 
                 
                   Coprobacillus 
                   cateniformis 
                 
               
               
                   
                  0.509426281 
                   Mailhella  sp900541395 
               
               
                   
                  0.482820632 
                   Blautia _A sp003474435 
               
               
                   
                  0.471483202 
                 UMGS1611 sp900553435 
               
               
                   
                  0.244782119 
                 UMGS911sp900557415 
               
               
                   
                  0.184527891 
                 CAG-354 sp900553015 
               
               
                   
                  0.174892874 
                   Blautia _A  massiliensis   
               
               
                   
                  0.158545809 
                   Agathobacter  sp900317585 
               
               
                   
                  0.140717769 
                   Negativibacillus  sp000435195 
               
               
                   
                  0.127151205 
                   Prevotella  sp002251385 
               
               
                   
                  0.122995374 
                   Coprococcus _A sp900548825 
               
               
                   
                  0.118746116 
                   Alistipes _A  indistinctus   
               
               
                   
                  0.118323236 
                 UMGS1071 sp900542375 
               
               
                   
                  0.115663494 
                   Erysipelatoclostridium  sp900544435 
               
               
                   
                  0.10338765 
                   Collinsella  sp900547285 
               
               
                   
                  0.102410987 
                   Prevotella  sp900556825 
               
               
                   
                  0.094993875 
                 UMGS172 sp900539855 
               
               
                   
                  0.06348916 
                   Phocaeicola  sp900551445 
               
               
                   
                  0.061539232 
                 
                   Agathobacter 
                   rectalis 
                 
               
               
                   
                  0.056113717 
                 
                   Anaerobutyricum 
                   hallii 
                 
               
               
                   
                  0.053598211 
                   Blautia _A sp900066335 
               
               
                   
                  0.053249701 
                   Anaerostipes   hadrus _A 
               
               
                   
                  0.045497159 
                   Clostridium  sp001916075 
               
               
                   
                  0.037406556 
                   Holdemanella  sp003458715 
               
               
                   
                  0.021590668 
                 
                   Christensenella 
                   minuta 
                 
               
               
                   
                  0.002218293 
                   Collinsella  sp900541725 
               
               
                   
                  4.2957E−05 
                 
                   Phascolarctobacterium 
                   faecium 
                 
               
               
                   
                 −0.004703489 
                 
                   Bacteroides 
                   togonis 
                 
               
               
                   
                 −0.008809374 
                 
                   Paraprevotella 
                   clara 
                 
               
               
                   
                 −0.03119867 
                   Holdemania  sp900120005 
               
               
                   
                 −0.031492474 
                 AM51-8 sp900546435 
               
               
                   
                 −0.035434119 
                 Phil1 sp001940855 
               
               
                   
                 −0.038913964 
                   Schaedlerella  sp004556565 
               
               
                   
                 −0.044020829 
                   Lachnospira  sp900552795 
               
               
                   
                 −0.047515072 
                   Muricomes  sp900604355 
               
               
                   
                 −0.052967481 
                 
                   Prevotella 
                   buccae 
                 
               
               
                   
                 −0.071596115 
                   Longicatena  sp003433845 
               
               
                   
                 −0.0796651 
                 
                   Desulfovibrio 
                   fairfieldensis 
                 
               
               
                   
                 −0.100975915 
                   Lachnospira  sp003537285 
               
               
                   
                 −0.115966192 
                 
                   Butyricimonas 
                   faecihominis 
                 
               
               
                   
                 −0.172472377 
                   Blautia _A sp900551465 
               
               
                   
                 −0.187868969 
                 
                   Anaerotruncus 
                   massiliensis 
                 
               
               
                   
                 −0.19109635 
                 
                   Anaerofustis 
                   stercorihominis 
                 
               
               
                   
                 −0.206509093 
                 UMGS1688 sp900544575 
               
               
                   
                 −0.210914586 
                 
                   Bifidobacterium 
                   dentium 
                 
               
               
                   
                 −0.228226067 
                 
                   Bacteroides 
                   cutis 
                 
               
               
                   
                 −0.241407669 
                 F23-B02 sp001916715 
               
               
                   
                 −0.247678711 
                 COE1 sp001916965 
               
               
                   
                 −0.267182222 
                   Ruminococcus _E  bromii _B 
               
               
                   
                 −0.286160011 
                   Porphyromonas  sp001552775 
               
               
                   
                 −0.323514014 
                 UBA1691sp900544715 
               
               
                   
                 −0.335225188 
                 GCA-900066755 sp900066755 
               
               
                   
                 −0.340598662 
                   Eubacterium _G sp900548465 
               
               
                   
                 −0.35989301 
                   Limosilactobacillus   fermentum _A 
               
               
                   
                 −0.460367032 
                 
                   Mesosutterella 
                   massiliensis 
                 
               
               
                   
                 −0.475293296 
                 
                   Escherichia 
                   flexneri 
                 
               
               
                   
                 −0.542914883 
                   Enterococcus _B  faecium   
               
               
                   
                 −0.599141069 
                 CAG-521sp000437635 
               
               
                   
                 −0.675358406 
                   Phocaeicola  sp000436795 
               
               
                   
                 −0.774574761 
                 CAG-83 sp900550585 
               
               
                   
                   
               
            
           
         
       
     
                     TABLE 39                  Linear discriminant analysis (LDA) effect size method (LEfSe) was used to       classify microbes (GTDB database) enriched in cancer or control. Analysis was       conducted on 322 cancer samples and 96 control samples. LEfSe first identifies       features that are statistically different among various populations using the non-       parametric factorial Kruskal-Wallis (KW) sum-rank test; It then performs additional       pairwise tests to assess whether these differences are consistent with respect to       population subclasses using the unpaired Wilcoxon rank-sum test. Lastly, LEfSe uses       LDA to estimate the effect size of each differentially abundant feature. A total of 135       species were enriched in cancer patients and 189 species were enriched in healthy individuals.                                             LDA                   Enrichment   score   p-value       taxID   Organism Name   Group   (log10)   (Kruskal-Wallis test)               17568     Blautia _A   Cancer   2.13760   0.0010911377336           sp900120195                   17532     Blautia coccoides     Cancer   2.39200   0.000968237855956       17534     Blautia hansenii     Cancer   2.61227   0.0216950428348       17535     Blautia hominis     Cancer   2.00955   0.0132436138036       17536   Blautia sp000432195   Cancer   2.64642   6.48111804063e−05       38844     Streptococcus  mutans   Cancer   2.19809   0.000766810025194       21762     Eisenbergiella tayi     Cancer   2.09239   0.0257014664011       18508   CAG-273 sp000437855   Cancer   2.19293   0.00149432368338       22144     Escherichia     Cancer   2.24534   0.000447045218029           sp000208585                   20468     Coprococcus eutactus     Cancer   2.35758   0.00917122961097       17540     Blautia  sp003287895   Cancer   2.62746   1.36005693245e−05       17547     Blautia  sp900556555   Cancer   2.05367   0.0264114231619       17148     Bacteroides     Cancer   2.10570   0.00282381576978             bouchesdurhonensis                     15906     Anaerostipes     Cancer   2.01922   0.00114807012388           sp000508985                   14115   43-108 sp001915545   Cancer   2.64298   1.11878531695e−06       36509     Ruminococcus _H   Cancer   2.33650   0.00895450765663           sp900549945                   15832     Anaerobutyricum     Cancer   2.23321   0.0225920389673             hallii _A                   36428     Ruminococcus _A   Cancer   2.53016   0.00139750682718           sp000432335                   25300     Hungatella     Cancer   2.20734   2.41051912452e−07           sp005845265                   31012     Oscillibacter welbionis     Cancer   2.97773   0.000181598180603       23244     Fusobacterium _B   Cancer   2.05886   0.00968800303448           sp900541465                   21884     Enterocloster     Cancer   2.53945   6.46879345659e−10             aldenensis                     26966     Longicatena innocuum     Cancer   2.62342   0.000826173225832       38939     Streptococcus     Cancer   2.54944   0.000251671138383           sp000187445                   20690     Cronobacter sakazakii     Cancer   2.00001   0.00176581732956       20055     Clostridium _Q   Cancer   2.60684   4.89158492686e−09             symbiosum                     15178     Agathobacter     Cancer   2.00539   0.0481413837296           sp000434275                   21731     Eggerthella lenta     Cancer   2.94523   0.006101347123       38891     Streptococcus     Cancer   2.42213   2.6511957776e−05             parasanguinis _D                   38889     Streptococcus     Cancer   2.56043   0.000319467593934             parasanguinis _B                   38888     Streptococcus     Cancer   2.33233   9.51509478653e−05             parasanguinis _A                   38887     Streptococcus     Cancer   2.35117   0.00071108799438             parasanguinis                     22512     Faecalimonas     Cancer   2.23748   0.012095387025           sp900556835                   19869     Citrobacter freundii     Cancer   2.07185   0.00906080909617       23068     Flavonifractor     Cancer   2.96730   2.14986779138e−09           sp000508885                   33819     Providencia rettgeri _D   Cancer   2.20376   0.00955245042142       17543     Blautia  sp900541955   Cancer   2.50204   0.0173404800143       32690     Phocaeicola dorei     Cancer   3.66861   0.000216406212684       32695     Phocaeicola plebeius     Cancer   2.44370   0.00392932331679       32699     Phocaeicola sartorii     Cancer   2.18940   0.00108006311504       18772   CAG-83 sp001916855   Cancer   2.01482   0.00380931699685       17198     Bacteroides     Cancer   2.48723   0.0172953376659           sp900557355                   17196     Bacteroides     Cancer   2.44481   0.00508686372198           sp900556215                   17191     Bacteroides     Cancer   2.18952   4.52735545739e−05           sp900066265                   44733     Veillonella atypica     Cancer   2.18847   0.0402708440438       27993     Mediterraneibacter     Cancer   3.55674   0.0496897855081             torques                     38890     Streptococcus     Cancer   2.20714   0.000599054128583             parasanguinis _C                   21757     Eisenbergiella     Cancer   2.18135   0.00915828126624           sp900539715                   17157     Bacteroides faecis     Cancer   2.61898   0.000484436396227       15918     Anaerotruncus     Cancer   2.22604   0.00133142885356             colihominis                     38951     Streptococcus     Cancer   2.92682   0.00217861964326           sp001556435                   18579   CAG-45 sp900066395   Cancer   2.49950   0.00574455333834       17554     Blautia _A   Cancer   3.19213   2.23528859735e−06           sp000433815                   21497     Dorea scindens     Cancer   2.79558   2.09572874651e−05       26866     Limosilactobacillus     Cancer   2.34117   0.0103155939811             fermentum                     17205     Bacteroides     Cancer   3.21745   0.00012372735459             xylanisolvens                     21888     Enterocloster     Cancer   3.08276   3.13138339085e−12             clostridioformis                     21886     Enterocloster bolteae     Cancer   2.81644   2.15012098387e−ll       18199     Butyricimonas     Cancer   2.14057   4.33439876776e−05             faecihominis                     41906   UBA1691   Cancer   3.44725   2.33522633211e−10           sp900544375                   25980     Klebsiella variicola     Cancer   2.09542   0.0155919157839       21889     Enterocloster     Cancer   2.54158   2.41667650124e−07             clostridioformis _A                   36521     Ruthenibacterium     Cancer   2.77271   8.80361828788e−05             lactatiformans                     26241     Lachnospira     Cancer   2.04108   0.0461403001471           sp000436535                   15835     Anaerobutyricum     Cancer   2.11887   0.0181255372277           sp900016875                   21501     Dorea  sp000433535   Cancer   3.18022   8.50501585649e−07       15033     Acutalibacter     Cancer   2.20583   2.07942112135e−05           sp900543555                   17156     Bacteroides     Cancer   2.00310   0.00578699520994             faecichinchillae                     17150     Bacteroides     Cancer   2.30080   1.18027718738e−06             caecimuris                     44095   UBA9502   Cancer   2.56934   0.000419156172297           sp900538475                   32688     Phocaeicola coprocola     Cancer   3.05308   0.0168486380976       39618     Succiniclasticum     Cancer   2.14647   0.0262474166286           sp900544275                   17197     Bacteroides     Cancer   2.67332   0.0181020544302           sp900556625                   18198     Butyricimonas faecalis     Cancer   2.54767   2.02297766283e−06       36434     Ruminococcus _B   Cancer   3.40611   0.00343207293924             gnavus                     36436     Ruminococcus _C   Cancer   2.59013   3.11571237196e−06             callidus                     37769     Sellimonas intestinalis     Cancer   2.90188   0.0010421172501       14650     Acidaminococcus     Cancer   2.84483   5.37086074804e−06             intestini                     38929     Streptococcus     Cancer   2.93889   0.0133708816272             salivarius                     31909     Parabacteroides     Cancer   3.49346   0.00845055659135             distasonis                     26428     Lawsonibacter     Cancer   2.27921   0.00119563602136           sp900066825                   15902     Anaerostipes caccae     Cancer   2.59029   1.32175359294e−05       22142     Escherichia flexneri     Cancer   3.07841   0.000448573849446       39003     Streptococcus     Cancer   2.91268   1.23303428895e−06             vestibularis                     17204     Bacteroides uniformis     Cancer   3.76744   0.00767040878452       22082     Erysipelatoclostridium     Cancer   3.10882   4.49001877438e−05             ramosum                     17179     Bacteroides rodentium     Cancer   2.36982   0.000809140186422       25979     Klebsiella     Cancer   2.50337   0.0209044295048             quasivariicola                     38737     Streptococcus     Cancer   2.56735   0.0450278679091             anginosus _C                   19879     Citrobacter youngae     Cancer   2.10125   0.0268286601359       32689     Phocaeicola     Cancer   2.39012   8.788249368e−06             coprophilus                     33237     Prevotella     Cancer   2.05312   0.00100376799716           sp000257925                   23067     Flavonifractor plautii     Cancer   2.95190   2.03840497779e−09       22140     Escherichia     Cancer   2.72638   0.000178346031215             dysenteriae                     21898     Enterocloster     Cancer   2.07701   0.0133349033913           sp900541315                   21890     Enterocloster     Cancer   2.05837   5.58379720897e−08             lavalensis                     17201     Bacteroides     Cancer   3.50101   0.0235802219915             thetaiotaomicron                     38946     Streptococcus     Cancer   2.35186   3.7304387141e−05           sp000448565                   26964     Longicatena     Cancer   2.71146   0.000140435878             caecimuris                     31921     Parabacteroides     Cancer   2.04037   0.000627513743016           sp900155425                   21401     Dialister  sp900343095   Cancer   2.42134   0.0326132648947       18336   CAG-103 sp900543625   Cancer   2.23674   0.000902041176381       17180     Bacteroides salyersiae     Cancer   2.66579   2.13189055395e−05       18337   CAG-1031   Cancer   2.57987   0.000146355127079           sp000431215                   21512     Dorea  sp900543415   Cancer   2.70565   3.39380545885e−10       32682   Phill2 sp002633275   Cancer   2.31286   0.00199992224058       22509     Faecalimonas     Cancer   2.27491   0.0151214093109           sp900550975                   22186     Eubacterium _G   Cancer   2.14863   0.000467276332765             ventriosum                     22513     Faecalimonas     Cancer   2.77402   0.0436444293568             umbilicata                     32208     Parasutterella     Cancer   2.31846   0.0356205438601           sp000980495                   32727     Phocaeicola vulgatus     Cancer   3.87915   0.0142224019801       18334   CAG-103 sp900317855   Cancer   2.18662   0.0252397542571       26805     Ligilactobacillus     Cancer   2.50862   0.000565702472295             salivarius                     17147     Bacteroides     Cancer   2.02458   0.000193059075288             acidifaciens                     33256     Prevotella     Cancer   2.00053   0.0228785615692           sp001275135                   32637     Phascolarctobacterium     Cancer   3.07562   0.00859527040104             faecium                     19917     Clostridioides difficile     Cancer   2.14826   0.000396856053418       17574     Blautia _A   Cancer   2.00426   0.00105097878926           sp900547615                   18469   CAG-217 sp900547275   Cancer   2.17756   0.0150594036026       18461   CAG-194 sp000432915   Cancer   2.41211   0.0114380924628       17578     Blautia _A   Cancer   2.09782   8.7672215879e−05           sp900551465                   31913     Parabacteroides     Cancer   2.32757   7.57370993477e−07             johnsonii                     36435     Ruminococcus _B   Cancer   2.32731   0.000138031227462           sp900544395                   17188     Bacteroides     Cancer   2.09073   0.00116767135794           sp003545565                   18649   CAG-492 sp000434335   Cancer   2.02629   0.000100614508133       41907   UBA1691   Cancer   2.86541   7.87326411749e−07           sp900544715                   17160     Bacteroides fragilis     Cancer   2.62172   0.0152421440534       31910     Parabacteroides     Cancer   2.20437   0.0138650485607             distasonis _A                   17186     Bacteroides     Cancer   2.21447   0.00117561051251           sp002491635                   17189     Bacteroides     Cancer   2.61541   4.67903060213e−07           sp003865075                   20471     Coprococcus     Cancer   2.05457   8.85142109464e−08           sp000433075                   17167     Bacteroides     Cancer   2.99981   0.0304061339071             intestinalis                     17168     Bacteroides     Cancer   2.49123   0.011609802117             intestinalis _A                   21894     Enterocloster     Cancer   2.40734   0.00141864996401           sp001517625                   17154     Bacteroides cutis     Cancer   2.12726   0.038819131362       36679   SFFH01 sp900542445   Control   2.41059   3.30021813163e−06       36440     Ruminococcus _C   Control   3.20407   1.2103932064e−08           sp000980705                   41347   UBA11524   Control   2.03222   0.00829874351407           sp000437595                   20338     Collinsella     Control   2.08313   1.11217975236e−08           sp900556415                   22089     Erysipelatoclostridium     Control   2.42399   1.1132866617e−06           sp900544435                   22087     Erysipelatoclostridium     Control   2.25783   2.64720533759e−10           sp003024675                   20324     Collinsella     Control   2.21598   1.04125747668e−08           sp900554905                   22085     Erysipelatoclostridium     Control   2.96769   4.21528595137e−ll           sp000752095                   20321     Collinsella     Control   2.00425   0.000781585095622           sp900554645                   36447     Ruminococcus _D   Control   3.39071   6.09724921548e−06             bicirculans                     18401   CAG-1427   Control   2.05861   0.000239442448034           sp000435675                   15198     Agathobaculum     Control   2.45929   0.00687534588514           sp900625105                   17538     Blautia  sp001304935   Control   2.76252   0.00021477069236       44369   UMGS1241   Control   2.48651   0.000229158432302           sp900549955                   26970     Longicatena     Control   2.04471   0.0253206102387           sp900411325                   15193     Agathobaculum     Control   2.72460   2.55177393509e−06           sp003481705                   22497     Faecalibacterium     Control   2.45021   0.00114034752317           sp900539885                   15191     Agathobaculum     Control   2.40050   9.30926345453e−05             butyriciproducens                     18588   CAG-460 sp900544625   Control   2.45197   0.00302957091049       36473     Ruminococcus _E   Control   2.36465   0.0116416270466           sp003438075                   25246     Holdemanella     Control   2.39373   5.39071908999e−06           sp900551285                   25245     Holdemanella     Control   2.13257   0.010514300225           sp900547815                   25244     Holdemanella     Control   2.16423   0.000129153396687           sp003458715                   18402   CAG-1427   Control   2.02925   0.00989909203149           sp000436075                   20131     Collinsella     Control   2.50700   9.18497857285e−06             aerofaciens _G                   22491     Faecalibacterium     Control   2.61316   1.05261675827e−06             prausnitzii _J                   17200     Bacteroides stercoris     Control   3.05136   0.042749136853       18416   CAG-1427   Control   2.27099   0.0267898981999           sp900556585                   41454   UBA1191   Control   2.21447   9.43642971559e−06           sp900545775                   22490     Faecalibacterium     Control   2.65573   1.19439741311e−05             prausnitzii _l                   20339     Collinsella     Control   2.31396   1.12520743428e−05           sp900556445                   23770   GCA-900066135   Control   2.13602   2.91176542674e−08           sp900543575                                             17575     Blautia _A   Control   2.61892   1.33647845585e−07           sp900548245                   18784   CAG-83 sp900547745   Control   2.05677   0.000783754622785       17344     Bifidobacterium     Control   3.89216   0.0472240909999             adolescentis                     25848   KLE1615 sp900066985   Control   2.60806   1.08359063226e−05       17562     Blautia _A   Control   2.06312   0.000228185017914           sp900066145                   32723     Phocaeicola     Control   2.61412   0.032610595599           sp900553715                   41455   UBA1191   Control   2.50874   8.12599169877e−05           sp900549125                   21661   ER4 sp000765235   Control   2.34673   0.000662818789913       18331   CAG-103 sp000432375   Control   2.87783   5.58314397621e−07       37771     Sellimonas     Control   2.51538   0.0307760188802           sp002161525                   18338   CAG-110 sp000434635   Control   2.74437   6.44929544018e−05       24117     Gemmiger     Control   2.05341   4.66989314069e−05           sp900539695                   24112     Gemmiger formicilis     Control   2.44504   0.00333770203037       33197     Prevotella copri _A   Control   2.65431   0.0283791459871       24118     Gemmiger     Control   2.16137   1.2620604518e−05           sp900540595                   44359   UMGS1071   Control   2.09882   0.000974900001284           sp900542375                   21409     Dialister  sp900555245   Control   2.63436   0.00333770203037       22173     Eubacterium _F   Control   2.36858   3.51840365919e−05           sp003491505                   21500     Dorea  sp000433215   Control   2.33715   1.97114808776e−08       19946     Clostridium saudiense     Control   2.17730   0.0230705246422       19949     Clostridium     Control   2.05791   0.00616715858917           sp000435835                   17560     Blautia _A   Control   2.33260   2.52783279408e−06           sp003478765                   17563     Blautia _A   Control   2.88048   0.00298338599418           sp900066165                   17566     Blautia _A   Control   2.55805   5.85243145116e−06           sp900066355                   41419   UBA11774   Control   2.48337   0.0450169284476           sp003507655                   17559     Blautia _A   Control   2.26051   0.00340034813393           sp003477525                   21493     Dorea longicatena     Control   3.31604   5.28875486139e−09       17565     Blautia _A   Control   2.75595   9.24085724755e−11           sp900066335                   18785   CAG-83 sp900548615   Control   2.00739   0.00287952903975       18783   CAG-83 sp900545585   Control   2.51557   4.66505048711e−06       17413     Bifidobacterium     Control   2.50849   0.00126433385994           sp002742445                                             15188     Agathobacter     Control   2.36342   0.000411600171088           sp900550845                   15183     Agathobacter     Control   2.45178   0.00017678701388           sp900546625                   15181     Agathobacter     Control   2.82123   0.000142395876762           sp900317585                   15186     Agathobacter     Control   2.34044   0.0348666029549           sp900549895                   18651   CAG-492 sp900553225   Control   2.53389   0.000269274517967       19908     Cloacibacillus     Control   2.01540   0.0327228894077             porcorum                     18241     Butyrivibrio _A   Control   2.37277   0.00126177720823             crossotus                     18243     Butyrivibrio _A   Control   2.29993   0.000757328088867           sp900543865                   20287     Collinsella     Control   2.10823   5.77069184548e−06           sp900551365                   44382   UMGS1375   Control   2.31480   0.00204908177496           sp900066615                   14550     Acetatifactor     Control   2.28979   0.00350713933387           sp900066365                   17230     Barnesiella     Control   2.45687   0.00109479017124             intestinihominis                     17558     Blautia _A   Control   2.11266   1.13585564617e−09           sp003474435                   27982     Mediterraneibacter     Control   3.12051   3.79965372336e−09             faecis                     44383   UMGS1375   Control   2.10198   1.99431838413e−06           sp900551235                   17549     Blautia _ Amassiliensis     Control   3.35483   9.0678522457e−06       44304   UCG-010 sp003150115   Control   2.07626   1.93454349489e−08       40350     Terrisporobacter     Control   2.27319   0.0201956139629           sp900557165                   17555     Blautia _A   Control   2.77455   1.50755393035e−07           sp000436615                   17550   Blautia_ A   obeum     Control   3.28966   5.87804863778e−05       17551   Blautia_ A   obeum _B   Control   2.10105   0.00117560721128       18491   CAG-269 sp003525075   Control   2.94816   1.10382253131e−06       30848     Odoribacter laneus     Control   2.42804   0.02830176635       17564     Blautia _A   Control   2.57852   3.49087257679e−ll           sp900066205                   15043     Adlercreutzia     Control   2.07439   0.0164550857066             celatus _A                   36088     Roseburia     Control   2.43035   0.0265096583225             inulinivorans                     20185     Collinsella     Control   2.45893   1.78086972764e−07           sp900541475                   22483     Faecalibacterium     Control   2.53717   1.48409829345e−07             prausnitzii _A                   14374   AM51-8 sp003478275   Control   2.04747   0.001001970988       21494     Dorea longicatena _B   Control   3.01526   4.84949138423e−07       18771   CAG-83 sp000435975   Control   2.58227   0.00441888019065       18673   CAG-533 sp000434495   Control   2.22485   0.00514615742321       18475   CAG-245 sp000435175   Control   2.22165   0.0435372051499       15831     Anaerobutyricum hallii     Control   3.09528   0.00014746116909       15836     Anaerobutyricum     Control   2.70371   0.000916439523968           sp900554965                   22482     Faecalibacterium     Control   3.19093   2.18287972068e−06             prausnitzii                     20276     Collinsella     Control   2.08412   7.91309114891e−05           sp900550185                   20272     Collinsella     Control   2.49443   1.41645935111e−08           sp900549455                   24122     Gemmiger     Control   2.36155   4.05221257543e−06           sp900554145                   44754     Veillonella     Control   2.24720   0.0330231957551           sp900556785                   36477     Ruminococcus _E   Control   3.37778   0.0144137210572           sp003526955                   21892     Enterocloster     Control   2.38993   0.00857107906373           sp000431375                   18445   CAG-177 sp003538135   Control   2.07697   0.000716445637701       40005   TF01-11 sp001414325   Control   2.66655   0.000363496777214       17366     Bifidobacterium     Control   2.20765   0.0114038100379             catenulatum                     26235     Lachnospira eligens _B   Control   2.56502   0.0154865827583       36087     Roseburia intestinalis     Control   3.09407   0.0279857822864       23215     Fusicatenibacter     Control   3.44159   2.62500713715e−06             saccharivorans                     19959     Clostridium     Control   2.64288   0.000134946507533           sp900540255                   30930   Olsenella_E   Control   2.10495   9.32929729361e−05           sp003150175                   18510   CAG-273 sp003507395   Control   3.10648   7.55800913874e−06       36438     Ruminococcus _C   Control   2.50387   0.00215829381827           sp000437175                   17579     Blautia _A   Control   2.07825   5.77555977528e−12           sp900551715                   18631   CAG-485sp900541835   Control   2.21771   0.00687270499319       20052     Clostridium _Q   Control   2.13420   5.46070638709e−05           sp003024715                   18846   CAG-964 sp000435335   Control   2.16784   0.0427477385672       21907     Enterococcus faecalis     Control   2.55268   0.000973238270192       17233     Barnesiella     Control   2.22322   0.00884314924177           sp003150885                   17404     Bifidobacterium     Control   2.66841   0.00855402261808             ruminantium                     29933     Negativibacillus     Control   2.17199   0.0422015141754           sp000435195                   18346   CAG-110 sp003525905   Control   2.33171   0.00175739825879       20478     Coprococcus _A   Control   2.31292   1.03016482881e−08           sp900548825                   40012   TF01-11 sp003529475   Control   2.55554   2.41121115527e−08       18426   CAG-170 sp000432135   Control   2.41207   0.000193772855899       22237     Eubacterium _R   Control   2.42086   0.00209914829707           sp000433975                   22498     Faecalibacterium     Control   2.93189   8.29721553513e−07           sp900539945                   22499     Faecalibacterium     Control   2.40470   0.000272278325887           sp900540455                   22484     Faecalibacterium     Control   3.14427   3.49956264954e−08             prausnitzii _C                   44737     Veillonella dispar _A   Control   2.58590   0.011756073445       22199     Eubacterium _I   Control   2.44993   0.000781473771325             ramulus                     20133     Collinsella     Control   2.42591   4.45271353249e−07             aerofaciens _I                   23216     Fusicatenibacter     Control   2.62476   0.00684254308783           sp900543115                   18577   CAG-45 sp000438375   Control   2.02767   0.0318370090133       36437     Ruminococcus _C   Control   2.14431   8.48212740565e−05           sp000433635                   30995     Oscillibacter     Control   2.10314   0.000287891879703           sp001916835                   18843   CAG-95 sp900066375   Control   2.50108   0.00140687944173       18482   CAG-269 sp000437215   Control   2.72572   0.028711054205       15903     Anaerostipes hadrus     Control   3.45161   4.07263251646e−05       44517   UMGS743   Control   2.14080   0.00458547437347           sp900545085                   36674   SFEL01 sp004557245   Control   2.08035   1.95437989749e−05       15904     Anaerostipes     Control   3.04152   7.21486613455e−09             hadrus _A                   44405   UMGS1491   Control   2.24642   0.000330918704025           sp900554775                   36508     Ruminococcus _H   Control   2.95780   0.000800746402152           sp003531055                   15468     Alistipes  sp000434235   Control   2.30490   0.0124196560779       18511   CAG-273 sp003534295   Control   2.70758   0.0159319228906       20477     Coprococcus _ Acatus     Control   2.29379   1.01475697641e−06       20167     Collinsella     Control   2.39447   9.35633056563e−09           sp900540895                   36429     Ruminococcus _A   Control   2.42518   7.23070236119e−05           sp000437095                   20473     Coprococcus     Control   2.25740   1.14391166168e−08           sp900066115                   25571     Intestinibacter     Control   2.27861   0.0497710656561           sp900540355                   17226     Bariatricus comes     Control   3.17691   4.0099294784e−10       36096     Roseburia     Control   2.24323   0.0231106169811           sp900552665                   24113   Gemmiger qucibialis   Control   3.16098   2.99842836046e−05       22496   Faecalibacterium   Control   2.23613   1.90744603181e−07           sp003449675                                             43535   UBA7182   Control   2.09576   1.84717329358e−07           sp003481535                   24119     Gemmiger     Control   2.56966   1.80894410074e−07           sp900540775                   36431     Ruminococcus _A   Control   2.66427   5.49451308118e−08           sp003011855                   18480   CAG-269 sp000431335   Control   3.04994   6.96985807634e−06       18484   CAG-269 sp001915995   Control   2.01969   0.025830997993       18485   CAG-269 sp001916005   Control   2.10988   3.25915762025e−07       18648   CAG-492 sp000434015   Control   2.21000   1.30539446398e−07       26240     Lachnospira     Control   2.55618   0.000628363206244           sp000436475                   18679   CAG-536 sp000434355   Control   2.82212   0.00456621092046       15176     Agathobacter rectalis     Control   3.41921   0.000310178035846       21491     Dorea formicigenerans     Control   2.80870   5.93297276419e−06       26245     Lachnospira     Control   2.56136   0.0023267608224           sp003451515                   18509   CAG-273 sp000438355   Control   2.76462   0.0305438756183       20345     Collinsella     Control   2.00151   2.5548792017e−07           sp900557455                   20342     Collinsella     Control   3.12583   9.53488707721e−05           sp900556605                   25241     Holdemanella biformis     Control   2.52660   0.00128748752692       36078     Romboutsia     Control   2.47361   0.000416035368085             timonensis                     18438   CAG-170 sp900556635   Control   2.15669   2.45053105973e−05       28004     Megasphaera     Control   2.70507   0.0488599018113           sp000417505                   22488     Faecalibacterium     Control   2.98235   1.81752622445e−05             prausnitzii _G                   22489     Faecalibacterium     Control   2.77389   3.98763445095e−06             prausnitzii _H                   18433   CAG-170 sp900545925   Control   2.09412   1.07072435143e−06       20469     Coprococcus     Control   2.96335   0.00490028391811             eutactus _A                   19952     Clostridium     Control   2.47249   9.76605249819e−06           sp001916075                   33438     Prevotella     Control   2.63503   0.0105872123676           sp900551275                   27983     Mediterraneibacter     Control   2.82901   3.28992544736e−05             lactaris                     17358     Bifidobacterium     Control   2.90693   0.00395513293096             bifidum                     22277     Evtepia  sp004556345   Control   2.09867   0.000584164019016       40011   TF01-11 sp003524945   Control   2.99299   0.0106460099673       22486     Faecalibacterium     Control   2.31452   6.15296343593e−06             prausnitzii _E                   26247     Lachnospira     Control   2.63101   0.0141817065492           sp900316325                    
A composite score was then assigned to each organism, accounting for both their correlations to immune markers and fold change between cancer and control cohorts (Tables 40, and 41). The score is defined as the geometric mean of three metrics: fold change between cancer and control samples, CD3+ correlation, and CD3+CD56+ correlation.
 
Table 40 (illustrated as  FIG.  49   ). Microbe rankings were based on classified species results using the GTDB database with a mean abundance of at least 0.005% with significant differences between cancer and control cohorts for inclusion into the therapeutic (inverse p value, Mann Whitney U test). For each classified species hit, CD3+ and CD3+CD56+ correlations are included in the table as per the linear mixed model analysis or set to zero if the mixed model correlation is negative or if the Spearman correlation was not significant enough to necessitate mixed model analysis. The cancer and control fold change, CD3+ correlation, and CD3+CD56+ correlation for each OSU were converted to percentile scores, and a combined score for each species level hit was generated by computing the geometric mean of each of the three percentiles.
 
Table 41 (illustrated as  FIG.  50   ). Microbe rankings were based on classified species results using the GTDB database with a mean abundance of at least 0.005% with significant differences between cancer and control cohorts for inclusion into the therapeutic (LDA score, LEfSe). For each classified species hit, CD3+ and CD3+CD56+ correlations are included in the table as per the linear mixed model analysis or set to zero if the mixed model correlation is negative or if the Spearman correlation was not significant enough to necessitate mixed model analysis. The cancer and control fold change, CD3+ correlation, and CD3+CD56+ correlation for each OSU were converted to percentile scores, and a combined score for each species level hit was generated by computing the geometric mean of each of the three percentiles.
 
     Machine Learning for Live Biotherapeutic Design 
     The top 6 scoring organisms from Table 40 is selected for screening in simulated microbial mixes. Each combination of 4 organisms from the top 6 (listed in Table 42, below) is evaluated in silico using the trained machine learning model. For the cancer samples in the model, relative species abundances for the four organisms in the putative mix are increased in silico by a certain amount (here 0.5%). This simulates in silico the physical action of adding microbes to the gut microbiome. Classification is then performed using the machine learning model to estimate the probability that each augmented sample is a cancer sample. The hypothesis is that combinations of microbes that make cancer samples appear more like control samples according to the model are better candidates for therapeutic mixes. Each putative mix is scored by its mean predicted cancer probability across all the augmented cancer samples, with lower mean predicted cancer probabilities corresponding to notionally better therapeutic candidates. All of the exemplary live biotherapeutic compositions (exemplary microbial combinations) are then validated experimentally as described in Examples 18 and 19. 
     
       
         
           
               
             
               
                 TABLE 42 
               
             
            
               
                   
               
               
                 The top 6 scoring organisms using LEfSe from Table  
               
               
                 40 have been selected for screening in simulated 
               
               
                 microbial mixes. All possible combinations of 4  
               
               
                 organisms from the top 6 are shown. 
               
            
           
           
               
               
               
            
               
                   
                   
                 Organism Name 
               
               
                   
                   
               
               
                   
                 Mix 1 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                 Mix 2 
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                 Mix 3 
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 4 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                 Mix 5 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 6 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 7 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269sp000431335 
               
               
                   
                 Mix 8 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                 Mix 9 
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 10 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 11 
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 12 
                   Blautia _A  obeum   
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                   Faecalibacterium prausnitzii _C 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 13 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 14 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
                 CAG-269 sp000431335 
               
               
                   
                 Mix 15 
                   Erysipelatoclostridium  sp000752095 
               
               
                   
                   
                   Blautia _A  obeum   
               
               
                   
                   
                   Dorea longicatena _B 
               
               
                   
                   
                 
                   Mediterraneibacter faecis 
                 
               
               
                   
                   
               
            
           
         
       
     
     Example 26—Therapeutic Effect of Fecal Microbiota Transplant (FMT) on Influenza Infection with Antibiotic Pretreatment 
     In previous experiments performed by Persephone Biosciences and other researchers, Fecal Material Transplant (FMT) from responder and non-responder patients to mice with ectopicly introduced tumors and treated with anti-PD-1 immunotherapy agents showed that the mice receiving responder FMT showed greater immunotherapy-induced tumor shrinkage than those receiving FMT from non-responder patients. As there could be immunological similarities between the responses against tumors and viral infection, the immunological effects of healthy control and non-responsive cancer patient FMTs on mice challenged with lethal doses of influenza A/California/04/2009 (H1N1) virus was investigated. Mortality, weight loss, mean day of death, lung virus titers, lung pathology scores and weights and lung cytokine concentrations were the primary endpoints. 
     Female 6-week-old BALB/c mice were obtained from Charles River Laboratories (Wilmington, Mass.) for this experiment. The mice were quarantined for 3 days before use and maintained on Teklad Rodent Diet (Harlan Teklad) and tap water at the Laboratory Animal Research Center of Utah State University (USU). A total of 82 mice were randomized into 4 groups of 18 mice per group with 10 mice used as normal controls for weight gain (Table 43). During week 1 of the study, mice were treated with antibiotic mix aliquots by oral (PO) administration of 0.1 ml daily for five days. The antibiotic mix aliquots contained 1 mg/mL each of ampicillin, gentamicin, metronidazole, neomycin, and 0.5 mg/mL vancomycin. 
     
       
         
           
               
             
               
                 TABLE 43 
               
             
            
               
                   
               
               
                 Experimental design for viral infection challenge experiment. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Number 
                   
                   
                   
               
               
                   
                 Mice per 
                 FMT 
                   
                   
               
               
                 Group 
                 Group 
                 Treatment 
                 Virus 
                 Observations 
               
               
                   
               
               
                 1 
                 18 
                 Healthy 
                 A/CA/04/2009 
                 9 animals observed for weight loss and 
               
               
                   
                   
                 Control 
                 (H1N1pdm) 
                 mortality for 14 days post-virus exposure. 
               
               
                 2 
                 18 
                 Non 
                   
                 9 animals per group sacrificed on day 3 
               
               
                   
                   
                 Responder 
                   
                 post-infection for lung virus titers, lung 
               
               
                   
                   
                   
                   
                 weights, lung scores, and lung cytokine concentrations. 
               
               
                 3 
                 18 
                 Healthy 
                 No Virus 
                 9 animals observed for weight loss and 
               
               
                   
                   
                 Control 
                   
                 mortality for 14 days post-virus exposure. 
               
               
                 4 
                 18 
                 Non 
                   
                 9 animals per group sacrificed on day 3 
               
               
                   
                   
                 Responder 
                   
                 post-infection for lung virus titers, lung 
               
               
                   
                   
                   
                   
                 weights, lung scores, and lung cytokine concentrations. 
               
               
                 5 
                 10 
                 No FMT 
                 No Virus 
                 Normal controls for weight gain. 
               
               
                   
               
            
           
         
       
     
     On Week 2 of the study, mice were then given FMT treatments every day for five days by PO administration of a 0.2 ml volume of FMT preparation. Two fecal sample sets, each representing a single fecal donation from two test subjects, were used to create FMT preparations for the study. One of these (PBT-138) was donated by a subject at late stage non-small cell lung cancer who had failed to respond to Keytruda as Non-Responder, or NR). The other sample set, (PBT-208) was donated by a subject in good health and without history of cancer or cancer-related disease or complications (hereto referred as Healthy Control, or HC). Two groups of 18 mice each were provided the NR-FMT, while two groups of 18 mice each were provided the HC-FMT. Upon receipt, fecal material was homogenized with anoxic phosphate-buffered saline (PBS) containing 1 g/L cysteine and 30% glycerol in an anaerobic chamber with an atmosphere of 5% hydrogen, 10% carbon dioxide, and 85% nitrogen, then frozen in 1.2 mL aliquots and stored at −80° C. Prior to the experiment, FMT aliquots were thawed in the anaerobic chamber, combined, and diluted 10-fold in PBS containing 0.5 g/L cysteine and 15% glycerol. The solution was stirred on ice for 10 minutes until homogenous, then poured through 100 micron mesh filters to remove gross particulates. Aliquots of 15 ml were pipetted into fresh appropriately labeled 50 ml conical tubes and kept upright on ice. The headspace atmosphere of each tube was then exchanged for 100% argon by introducing a stream of filtered argon into the top of the tube for 10 seconds, after which the tube was tightly recapped. These single-use aliquots were stored at −80° C., and removed immediately prior to administering to the mice. FMT treatments were continued twice weekly for weeks 3, 4, and 5 of the study. 
     At the beginning of week 6 of the study, 2 treatment groups of mice, one representing HC-FMT and the other representing NR-FMT, were challenged with mouse-adapted influenza A/California/04/2009 (H1N1) (A/CA/04/2009; H1N1pdm) via intranasal route. The virus was received from Dr. Elena Govorkova, Department of Infectious Diseases, St. Jude Children&#39;s Research Hospital, Memphis Tenn. The virus was adapted to replication in the lungs of BALB/c mice by 9 sequential passages in mice. Virus was plaque purified in Madin-Darby Canine Kidney (MDCK) cells and a virus stock was prepared by growth in embryonated chicken eggs and then MDCK cells. For challenge, mice were anesthetized by intraperitoneal (IP) injection of ketamine/xylazine (50 mg/kg/5 mg/kg) prior to challenge by the intranasal route with approximately 1×103 (3×LD50) cell culture infectious doses (CCID50) of virus per mouse in a 90 μl inoculum volume. Nine mice per treatment group were euthanized 72 hours after influenza infection for evaluation of lung virus titers and cytokine concentrations. The remaining nine mice per group were weighed prior to influenza challenge then every day thereafter to assess the effects of FMT on preventing weight loss due to virus infection. All mice were observed for morbidity and mortality through day 14 post-influenza challenge. 
     Post-Infection Effects on Survival and Body Weight 
     Nine of eighteen mice per group are inspected for viability and weighed daily for fourteen days after the date of viral infection. Mice from all four groups remained viable until day six post infection, after which mice from the infected groups start to succumb ( FIG.  51   ). The daily percent survival of mice in the two infected groups (HC-FMT or NR-FMT) steadily decreased until day 10; mice are either found dead upon inspection or are humanely euthanized due to their adverse physical condition. One of 9 mice (11%) given the HC-FMT survived the infection, and one of nine mice (11%) given the NR1-FMT survived the infection. No statistically significant differences in survival curves were observed. All mice in the two uninfected groups remain viable until final euthanasia at day fourteen (data not shown). Mouse body weights ( FIG.  52   ) in the infected groups steadily decreased after the initial day of infection until day 7 post infection, corresponding to reduction of viability within the groups. After this time, mice treated with HC-FMT were observed to maintain higher body weights than mice treated with NR-FMT. No significant change in body weights is observed for mice in the two FMT-treated but uninfected groups. 
     Lung Pathology after Viral Infection 
     Three days after the day of viral infection, nine of eighteen mice from all four groups were sacrificed and their lungs removed for inspection and analyses. Virus titer was determined from homogenized mouse lung samples by end-point dilution in 96-well microplates of Madin Darby Canine Kidney (MDCK) cells. Briefly, log 10 dilutions of lung homogenate samples were prepared in minimum essential media (MEM) containing 10 units/ml trypsin, 1 μg/ml EDTA, and 50 μg/ml gentamicin (infection media). Confluent 96-well microplates of MDCK cells were prepared 24 hours prior to use and then washed to remove fetal bovine serum from the plates and replaced with infection media immediately prior to addition of lung homogenate dilutions. The plates were incubated for 6 days in a 37° C. incubator with 5% CO 2  and evaluated by visual observation of cytopathic effect (CPE). A 50% cell culture infectious dose (CCID 50 ) was calculated using the Reed-Muench method. No significant difference was observed by Welch&#39;s t-test for viral titers determined for lungs from infected HC-FMT or NR-FMT treated mice ( FIG.  53   ), while lungs from uninfected mice were not analyzed for viral titer. Visual scores of lung pathogenesis also did not differ significantly between the two infected groups ( FIG.  54   ), with little or no differences observed in degree of pathogenesis. Lungs removed from uninfected mice are all judged to have a “zero”, or healthy, lung score evaluation (data not shown). The weight of lungs removed from infected mice treated with NR-FMT were as a group higher than infected mice treated with HC-FMT ( FIG.  55   ). Higher relative lung weights in infected NR-FMT mice than infected HC-FMT mice could reflect higher levels of inflammation in the lungs of mice in the NR-FMT treated group (Hurst, B. L., Evans, W. J., Smee, D. F., Van Wettere, A. J. &amp; Tarbet, E. B. Evaluation of antiviral therapies in respiratory and neurological disease models of Enterovirus D68 infection in mice.  Virology  526, 146-154 (2019)). 
     Cytokine Concentrations in Lung Tissue 
     Lung tissue from FMT-treated, infected or uninfected mice, are subjected to analysis for concentrations of a variety of cytokines that are relevant immunological markers for viral infection and anti-tumor response. Lung homogenates were evaluated for concentrations of the following cytokines using a multi-plex cytokine kit (Quansys Biosciences, Logan, Utah) according to the manufacturer&#39;s instructions: Interleukins (IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-10, IL-12p70, IL-17), Monocyte Chemoattractant Protein 1 (MCP-1), Interferon gamma (IFN-γ), Tumor Necrosis Factor alpha (TNFα), Macrophage Inflammatory Protein 1α (MIP-1α), Granulocyte-Macrophage Colony-Stimulating-Factor (GM-CSF), and Regulated on Activation, Normal T-cell Expressed and Secreted (RANTES). Concentrations of each of these cytokines in all four treatment groups are presented in  FIGS.  56 - 59   . 
     Concentrations of IL-1α, IL-1β, IL-6, Il-17, MCP-1, IFN-g, TNFα, MIP-1a, and RANTES are significantly increased in influenza-infected mice compared to uninfected mice, as expected as a result of influenza infection (Khanna, M., Rajput, R., Kumar, B., Kumari, A. &amp; Saxena, L. Influenza virus Induced Cytokine Responses: An Evaluation of Host-Pathogen Association. (2014); Brydon, E. W. A., Morris, S. J. &amp; Sweet, C. Role of apoptosis and cytokines in influenza virus morbidity. FEMS Microbiology Reviews 29, 837-850 (2005)). The cytokines/chemokines IL-12p70, IL-2, TNFα, and IFN-γ are all increased in infected HC-FMT treated mice compared to infected NR-FMT treated mice, and are indicative of a T helper cell 1 (Th1) type of immune response. IL-12p70 is one of two subunits of the heterodimeric cytokine IL-12. IL-12 is secreted by antigen presenting cells like dendritic cells to differentiate naïve T cells to Th1 type helper T cells, that then secrete IL-2, TNFα, and IFN-γ as a result (Zundler, S. &amp; Neurath, M. F. Interleukin-12: Functional activities and implications for disease.  Cytokine and Growth Factor Reviews  26, 559-568 (2015)). IL-12 mediated immune responses resulting from viral infection are critical for enhancing cytotoxic activity of Natural Killer (NK) cells and CD8+ cytotoxic T lymphocytes, and IL-12 induced INF-g can switch Th17 type T helper cells to Th-1 T helper cells against virus infected cells (Guo, Y., Cao, W. &amp; Zhu, Y. Immunoregulatory functions of the IL-12 family of cytokines in antiviral systems.  Viruses  11, (2019)). These results suggest that the NR-FMT treatment of infected mice comparatively inhibits proper Th1 type immunoresponses. 
     The cytokines IL-3, IL-4 and IL-5 are both increased in concentration in lungs from HC-FMT treated mice compared to lungs from NR-FMT treated mice. IL-4 and IL-5 are characteristic of a Th2 type of immunoresponse, as IL-4 helps differentiate naïve T cells to Th2 type T helper cells; IL-4 is then produced by differentiated Th2 type cells to autostimulate their own proliferation. IL-5 produced by Th2 cells encourages B cells to produce IgA against gastrointestinal infections. IL-3 is produced by both Th1 and Th2 cells, and promotes neutrophil production which are among the first innate immune cells to be recruited during viral infection (Lamichhane, P. P. &amp; Samarasinghe, A. E. The Role of Innate Leukocytes during Influenza Virus Infection.  J. Immunol. Res.  2019, (2019)). 
     The cytokine IL-17 is significantly elevated in lungs of infected HC-FMT treated mice compared to infected NR-FMT treated mice. IL-17 is produced by Th17 helper T cells after maturation in response to costimulation by IL-6 and Tumor Growth Factor beta (TGFβ, not measured in this study) produced from Dentritic Cells. IL-17 induces production of IL-6, GM-CSF and IL-1β, all three of which are shown to be elevated to different levels in infected HC-FMT mice. IL-17 hinders viral infection by enhancing Th1 type immune responses, and has a critical role in activation and survival of CD8+ cytotoxic T cells, as well as B cell maturation and migration into lung in response to influenza infection (Ma, W. T., et al. The protective and pathogenic roles of IL-17 in viral infections: Friend or foe?  Open Biology  9, (2019)). 
     Both IL-3 and GM-CSF stimulation are negatively associated with Severe Acute Respiratory Illness (SARI) due to severe influenza disease (Wong, S.-S. et al. Severe Influenza Is Characterized by Prolonged Immune Activation: Results From the SHIVERS Cohort Study, doi:10.1093/infdis/jix571), although GM-CSF can itself be a marker for inflammation (Hamilton, J. A. Cytokines Focus GM-CSF in inflammation.  Journal of Experimental Medicine  217, (2019)). GM-CSF is itself elevated in lungs of infected HC-FMT treated mice compared to infected NR-FMT treated mice and is important for stimulating production of granulocytes like neutrophils, eosinophils and basophils, as well as monocytes that go on to mature into macrophages and dendritic cells in infected tissues (Hamilton, J. A. Cytokines Focus GM-CSF in inflammation.  Journal of Experimental Medicine  217, (2019)). 
     IL-1β is elevated in lungs of infected HC-FMT treated mice compared to lungs from infected NR-FMT treated mice. IL-1β is a pyrogen, fever producer and a master proinflammatory cytokine. It is induced in lung upon influenza infection, along with IL-6, IL-12, and TNFα (Kim, K. S., et al. Induction of interleukin-1 beta (IL-1β) is a critical component of lung inflammation during influenza A (H1N1) virus infection.  J. Med. Virol.  87, 1104-1112 (2015)), and has been demonstrated in IL-1β receptor knock out mice to be important for survival after influenza infection (Schmitz, N., Kurrer, M., Bachmann, M. F. &amp; Kopf, M. Interleukin-1 Is Responsible for Acute Lung Immunopathology but Increases Survival of Respiratory Influenza Virus Infection.  J. Virol.  79, 6441-6448 (2005)). MIP-1α is elevated in infected HC-FMT treated mice compared to infected NR-FMT treated mice. MIP-1α is a chemotactic cytokine secreted by macrophages and is important in recruiting inflammatory cells to infection sites and in maintaining effector immune responses (Bhavsar, I., Miller, C. S. &amp; A1-Sabbagh, M. Macrophage Inflammatory Protein-1 Alpha (MIP-1 alpha)/CCL3: As a biomarker. in  General Methods in Biomarker Research and their Applications  1-2, 223-249 (Springer International Publishing, 2015). MIP-1α is produced in response to IL-12, and is important for NK cell response to influenza infection (Kay, A. W. et al. Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy, doi:10.1073/pnas.1416569111). 
     Comparison of Microbiobial Taxa of Donor Feces Used to Produce HC-FMT and NR-FMT 
     Whole genome sequencing was performed on the donor FMT samples as described in Example 24. The bacterial populations differ significantly in HC and NR fecal samples ( FIG.  60   ). The microbial population within the fecal sample used to produce the HC-FMT is dominated by Gram-positive Ruminocococcaceae famil genera and species, Clostridiaceae family species like CAG-269 and CAG-110, as well as Lachnospiraceae family bacteria such as  Faecalibacterium prausnitzii, Blautia wexlerae , and  Anaerostipes hadrus . Lachnospiraceae and Ruminococcaceae family bacteria produce fermentation products like short chain fatty acids (SCFAs) that exert anti-inflammatory effects on the immune system (Pascal, M. et al. Microbiome and allergic diseases.  Frontiers in Immunology  9, (2018)). Conversely, the microbial population within the NR donor fecal sample is more dominated by Gram-negative species like  Bacteroides  that produce lipopolysaccharides that can promote inflammation (Hakansson, A. &amp; Molin, G. Gut microbiota and inflammation.  Nutrients  3, 637-687 (2011)), and  Fusobacterium  species that associate with gastrointestinal disorders like Irritable Bowel Disease (IBD) (Liu, L. et al.  Fusobacterium nucleatum  Aggravates the Progression of Colitis by Regulating M1 Macrophage Polarization via AKT2 Pathway.  Front. Immunol.  10, 1324 (2019)) and is considered a causal agent for colorectal cancer (Wu, J., Li, Q. &amp; Fu, X.  Fusobacterium nucleatum  Contributes to the Carcinogenesis of Colorectal Cancer by Inducing Inflammation and Suppressing Host Immunity.  Translational Oncology  12, 846-851 (2019)). 
     References (Example 9) 
     
         
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     A number of embodiments of the invention have been described. Nevertheless, it can be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.