Patent Description:
The present invention relates generally to graft versus host disease (GVHD). More particularly, the present invention relates to a therapeutic composition for use in treating a graft versus host disease (GVHD) in a subject following bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT).

Despite continuing improvements in outcomes of patients undergoing allogeneic bone marrow transplant (allo BMT), GVHD continues to be a leading cause of mortality in this population'. Modern immune suppression strategies are only partially effective at preventing GVHD and simultaneously increase the risks for infections and disease recurrence. Strategies that reduce GVHD but leave immune function intact can thus potentially improve outcomes. One such strategy is to target the complex community of microbes that reside within our intestinal tracts, collectively termed the intestinal microbiota.

A relationship between the microbiota and GVHD has long been suspected but is still not well understood. Mice transplanted in germ-free conditions<NUM> or receiving gut-decontaminating antibiotics<NUM> develop less severe GVHD. Clinical studies initially suggested a benefit from near-total bacterial decontamination<NUM>,<NUM>, but later showed no clear benefit<NUM>-<NUM> and this approach was discontinued in the early <NUM><NUM>. Partial gut decontamination continues to be practiced but little is known regarding optimal antibiotics. One study found the addition of metronidazole to ciprofloxacin led to a significant reduction in acute GVHD, suggesting that anaerobic bacteria may contribute to GVHD pathogenesis<NUM>.

More recent studies, however, indicate that this approach may not be ideal. The administration of metronidazole during allo BMT was associated with expansion of vancomycin-resistant Enterococcus within the intestinal tract, which in some patients preceded enterococcal bacteremia<NUM>. Other studies have found that obligate anaerobes in the intestine, in particular Clostridial species, are important mediators of intestinal homeostasis and prevent inflammation by upregulating intestinal regulatory T cells<NUM>.

Recently it was reported that increased bacterial diversity at the time of engraftment was associated with improved overall survival following allo BMT and reduced transplant-related mortality<NUM>. The population studied, however, was heterogeneous and in particular included <NUM>% patients who received a T-cell depleted allograft. Recipients of this type of transplant are at much lower risk of developing GVHD. Likely because of inadequate numbers of patients and heterogeneity, it was not possible to determine the subcategories of non-relapse mortality associated with low diversity, which include GVHD, infection and organ failure. <CIT> discloses the treatment! prevention of rejection in organ transplantation, such as GVHD following bone marrow transplantation, using human commensal bacteria. <NPL> discloses that intestinal inflammation secondary to GVHD is associated with shifts in the composition of intestinal microbiota.

Thus the need exists for a treatment that exploits the relationship between intestinal microbiota and GVHD.

In an aspect, the invention provides therapeutic composition for use in treating a graft versus host disease (GVHD) in a subject following bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT), wherein the therapeutic composition comprises one or more purified populations of bacteria selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum, Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli, and combinations or mixtures thereof. In another aspect, the invention provides a therapeutic composition for use in preventing, reducing the likelihood of, and/or treating a graft versus host disease (GVHD) in a subject undergoing bone marrow or hematopoietic stem cell transplant, wherein the therapeutic composition comprises one or more purified populations of bacteria selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum, Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli, and combinations or mixtures thereof. In another aspect, the invention provides a method for screening a subject for risk of developing GVHD following bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT), the method comprising determining the abundance of a bacterial species of the order Clostridiales in a sample of fecal material from the subject, wherein the subject is at an increased risk for GVHD if the abundance of said Clostridiales in said sample of fecal material is less than the abundance of said Clostridiales in a sample of fecal material from a subject who is not at risk for developing GVHD, and wherein said Clostridiales species is selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum, Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli and combinations or mixtures thereof. The present disclosure is based on the observation that graft versus host disease correlates with major changes in intestinal microbiota that occur during bone marrow and/or hematopoietic stem cell transplant suggesting that commensal bacteria can be predictors and modulators of GVHD risk and severity.

The present disclosure therefore relates to methods and compositions for preventing the loss of or restoring mammalian bacterial gastrointestinal microbiota in a subject during bone marrow or hematopoietic stem cell transplant in order to prevent, reduce the severity or treat GVHD. The disclosure encompasses several approaches or a combination thereof for preventing loss of relevant bacteria in the first instance, for restoring bacteria in a subject that has sustained loss of protective bacteria and supporting the endogenous populations or the repopulated bacteria. The approaches include:.

The disclosure relates to a method for restoring gastrointestinal bacteria that has been lost, for example, as the result of exposure to antibiotics with high activity against anaerobes, comprising administering to a subject in need of such treatment, an effective amount of at least one bacteria from the order Clostridiales, or combinations thereof. The bacteria may be administered orally. Alternatively, bacteria can be administered rectally, for example, by enema.

The present disclosure relates to compositions for the reduction of graft versus host disease (GVHD) and GVHD-related mortality. It is based on the observation that there is a change in the microbiota of the gut that correlates with GVHD-related mortality. In particular, the presence of certain bacterial species including some organisms that ferment xylose, raffinose, cellobiose or melizitose is particularly effective in reducing GVHD-related mortality.

The disclosure relates to a method of reducing the risk of developing graft versus host disease (GVHD) and/or treating GVHD in a subject undergoing bone marrow transplant or hematopoietic stem cell transplant, the method comprising administering to the subject a therapeutically effective amount of a therapeutic composition comprising one or more bacteria from the order Clostridiales, wherein the composition.

Disclosed herein is a method for reducing the likelihood, incidence or severity of GVHD in a subject, the method comprising administering to the subject a composition comprising at least one species of the order Clostridiales. The organism may comprise a 16SrDNA with the nucleotide sequence of GenBank X94966, a nucleotide sequence selected from SEQ ID NOS: <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> and <NUM> or a sequence with about <NUM>% to <NUM>% identity to any of said sequences; for example about <NUM>-<NUM>%; in for example about <NUM>-<NUM>%. The therapeutic composition may comprise bacteria selected from genuses Blautia, Ruminococcus, Eubacterium, Holdemania, and Clostridium. The bacteria may be selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli and combinations or mixtures thereof.

The Blautia species may be Blautia producta.

Disclosed herein is a therapeutic composition comprising a Clostridiales species. The organism may comprise a 16SrDNA with the nucleotide sequence of GenBank X94966, a nucleotide sequence selected from SEQ ID NOS: <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> and <NUM> or a sequence with about <NUM>% to <NUM>% identity to any of said sequences; for ex-ampe about <NUM>-<NUM>%; for example about <NUM>-<NUM>%. The therapeutic composition may comprise bacteria selected from genuses, Blautia, Ruminococcus, Eubacterium, Holdemania, and Clostridium. The bacteria may be selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli and combinations or mixtures thereof.

Disclosed herein is a method for reducing the likelihood of or preventing GVHD, wherein a composition comprising at least one species of Clostridiales is administered to the subject from about <NUM> week to about <NUM> weeks before allo BMT, from about <NUM> day to about <NUM> weeks before all BMT, and from about <NUM>-<NUM> days before allo BMT.

A method for reducing the risk, incidence or severity of graft versus host disease (GVHD) in a subject undergoing a bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT), the method comprising administering to the subject a therapeutically effective amount of oral vancomycin or ampicillin when the subject has been treated for neutropenic fever with an intravenous antibiotic selected from the group consisting of metronidazole, piperacillin-tazobactam (pip-tazo), imipenem.

A method for reducing the risk of developing graft versus host disease (GVHD) in a subject following a bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT), the method comprising: determining the abundance of Akkermansia muciniphila in a sample of fecal material from the subject; and administering a therapeutically effective amount of an antibiotic selected from ampicillin and oral vancomycin to the subject when the abundance of Akkermansia muciniphila is above from <NUM>% to <NUM>%, wherein administration of the antibiotic reduces abundance of Akkermansia muciniphila and the risk of GVHD is reduced or eliminated. Abundance of Akkermansia muciniphila in said sample above <NUM>% may indicate risk of developing GVHD. The abundance of Akkermansia muciniphila is determined prior to transplant, following antibiotic treatment for transplant-related neutropenic fever or both.

In practicing the present invention, many conventional techniques in molecular biology, microbiology and bacteriology are used, techniques which are within the skill of the art.

With respect to terminology, the terms used herein are intended to be construed in accordance with their standard meaning as known to those of skill in the relevant art. The definition of some terms are given here for convenience.

"Patient" or "subject" as used herein refers to mammals and includes human and veterinary animals.

The terms "intestinal microbiota", "gut flora", and "gastrointestinal microbiota" are used interchangeably to refer to bacteria in the digestive tract.

The term "probiotic" refers to a substantially pure bacteria (i.e., a single isolate), or a mixture of desired bacteria, and may also include any additional components that can be administered to a mammal for restoring microbiota. Such compositions are also referred to herein as a "bacterial inoculant.

The term "prebiotic" refers to an agent that increases the number and/or activity of one or more desired bacteria. Non-limiting examples of prebiotics useful in the methods of the present disclosure include saccharides, such as xylose, raffinose, cellobiose and melizitose.

A "therapeutically effective amount" means the amount of a bacterial inoculant or a compound (e.g., a narrow spectrum antibiotic or anti-bacterial agent) that, when administered to a subject for treating a disorder or condition, is sufficient to effect such treatment.

"Blautia", "Blautia-related" or "Blautia-like species" are Gram-stain-positive, non-motile bacteria that are obligate anaerobes found in the feces of humans and other mammals (Liu et al. Blautia species include, for example, Blautia producta (ATCCR <NUM>-DSM <NUM>, American Type Culture Collection, Manassas, VA). Blautia-like species include those with a 16SrDNA sequence with <NUM>% to <NUM>% sequence identity (ifor example <NUM>-<NUM>% identity) to the 16SrDNA of Blautia producta (GenBank X94966). A number of Blautia-related species are shown in Table <NUM> below by name (NCBI name) including the <NUM> rDNA sequence of each.

Though not a member of the order Clostridiales, Holdemania filiformis is a bacteria associated with less GVHD and therefore is intended to be encompassed by the disclosure as a potential therapeutic.

Antibiotics vary considerably in the strength of their activity against anaerobic commensals and are designated herein as either having high or low activity against anaerobes. Antibiotics with high activity against anaerobes include metronidazole, piperacillin-tazobactam (pip-taxo or P/T) and imipenem. Antibiotics with low activity against anaerobes include aztreonam, ceftazidime/cefepime, iv vancomycin, levofloxacin, ciprofloxacin, cefazolin, atovaquone and tmp-smx.

The relevant taxonomical characteristics of relevant strains of organisms may be confirmed with results obtained from <NUM> rDNA sequence analysis and the Analytical Profile Index (API®) bacterial identification system in addition to other conventional methods used in the art for bacterial identification.

For patients with hematologic malignancies such as leukemias, lymphomas and other related cancers, allogeneic blood marrow transplantation (allo BMT) or hematopoietic stem cell transplant (HSCT) is a critically important therapy that can produce cures when chemotherapy alone cannot. More than <NUM>,<NUM> patients undergo all BMT worldwide each year. A major risk of bone marrow/hematopoietic stem cell transplant continues to be graft-versus-host-disease (GVHD), which results from the donor immune system recognizing the transplant recipient's organs as foreign, leading to life-threatening inflammation. Developing strategies that reduce GVHD but leave global immune function intact should produce a major benefit for patients.

In the past, the use of broad-spectrum antibiotics in allo-HSCT recipients had been thought to be protective against GVHD. Broad-spectrum combinations were administered with the goal of complete gut decontamination, and this was associated with reduced GVHD in mouse models (<NUM>) and in some (<NUM>, <NUM>),though not all clinical studies (<NUM>-<NUM>). Similarly, the addition of metronidazole to ciprofloxacin resulted in reduced GVHD in a small randomized study (<NUM>), lending support to the hypothesis that intestinal bacteria contribute to GVHD pathophysiology.

A series of recent studies, however, have described a different association, in which allo-HSCT recipients who sustain more severe microbiota injury are more likely to develop severe GVHD (<NUM>, <NUM>, <NUM>, <NUM>). Microbiota injury has been observed in several ways, including expansion of commensal Enterococcus species (<NUM>), loss of overall diversity (<NUM>), reductions of commensals from the genus Blautia, a member of the order Clostridiales (<NUM>), and most recently low levels of indole, a byproduct of tryptophan metabolism produced by intestinal bacteria that can be quantified in the urine in the form of <NUM> indoxyl sulfate (<NUM>). Consistent with these reports, in the current study we demonstrate that use of antibiotics with a broader spectrum of activity, such as imipenem, leads to increased microbiota injury (especially loss of Clostridiales) and increased GVHD severity.

A full explanation has yet to be revealed for the seeming inconsistencies between early studies and more recent studies, but one possible contribution could be the rise of antibiotic-resistant bacteria including resistant enterococci, which can make successful gut decontamination difficult to achieve. Increases in the frequency of colonization with resistant organisms have been observed in allo-HSCT recipients over time (<NUM>). A recent study found that gut decontamination was unsuccessful in nearly half of patients where it was attempted. Interestingly, successfully decontaminated patients had a much lower incidence of acute GVHD compared to unsuccessfully decontaminated patients (<NUM>).

In this study, we demonstrate that different antibiotics used to treat neutropenic fever have different effects on intestinal microbiota composition, both in patients and in mouse models. We also identified several important changes produced by imipenem treatment in mice with GVHD, including severity of GVHD in the colon, inflammatory changes, and breakdown of the protective colonic mucus barrier.

One promising approach to reducing the risk, incidence and severity of GVHD is targeting the complex community of microbes that reside within the human intestinal tract, collectively termed the intestinal microbiota. While a relationship between the microbiota and GVHD has been suspected for many years, it remains imperfectly understood. Gut decontamination with antibiotics is practiced at some but not all centers, and there is no consensus regarding ideal choice of antibiotic coverage.

Disclosed herein are results demonstrating that the abundance of bacteria belonging to the taxa Clostridiales including the genus Blautia, a commensal commonly found in the intestinal tract of humans, predicts for protection from life-threatening GVHD in all transplant patients. Furthermore, in murine models, introducing a species of Blautia of murine origin reduces GVHD severity. Not wishing to be bound by theory, it appears to do so by inducing regulatory T cells with generation of short-chain fatty acid metabolic byproducts (SCFA).

Additional studies characterizing the natural history of Clostridiales and Blautia abundance in all BMT/HSCT recipients demonstrated that the vast majority of patients begin with abundant amounts of endogenous populations of these organisms, but many lose them in a dramatic fashion during the transplantation. Interestingly, loss of Blautia correlates strongly with reductions in oral nutritional intake in both humans and mice.

Nutritional intervention strategies to support Clostridiales/Blautia abundance following all BMT/HSCT may provide one method to mitigate GVHD. It has been shown in murine models that these nutritional approaches can successfully prevent loss of Clos-tridialeslBlautia as well as reduce severity of GVHD. These results identified the microbiota as a potent therapeuteic target that can be recruited to significantly reduce GVHD.

The relationship between intestinal microbiota composition and graft-versus-host disease (GVHD) after allo BMT or HSCT is not well understood. Intestinal bacteria have traditionally been thought to contribute to GVHD, but recent animal studies in non-transplant settings have identified populations of obligately anaerobic intestinal commensals with anti-inflammatory properties.

In one study, the fecal bacterial composition of <NUM> patients was evaluated from day <NUM> after BMT. Increased bacterial diversity was associated with reduced GVHD-related mortality. Furthermore, harboring increased amounts of bacteria belonging to the genus Blautia was associated with reduced GVHD lethality in this cohort and confirmed in another independent cohort of <NUM> patients. Blautia abundance was also associated with improved overall survival. Evaluating the abundance of Blautia with respect to clinical factors, it was found that loss of Blautia was associated with two clinical factors: <NUM>) treatment with antibiotics that inhibit anaerobic bacteria and <NUM>) receiving total parenteral nutrition (TPN) for longer durations. Increased abundance of commensal bacteria belonging to the Blautia genus is associated with reduced lethal GVHD and improved overall survival.

In another study, <NUM> patients were retrospectively examined for neutropenic fever following allogeneic hematopoietic stem cell transplantation (allo-HSCT). It was found that administering antibiotics with increased activity against anaerobes, including piperacillin-tazobactam (pip/tazo) or imipenem-cilastatin (imipenem), was associated with increased GVHD-related mortality, compared to administering antibiotics, such as aztreonam or cefepime, with reduced activity against anaerobes. Stool microbiota composition analysis demonstrated that pip/tazo and imipenem administration were associated with more severe loss of members of the bacterial order Clostridiales. Experiments in mouse models demonstrated similar flora changes with these antibiotics. Moreover, modeling antibiotic treatment in mice with GVHD recapitulated aggravated mortality with imipenem compared to aztreonam.

The present disclosure describes methods to reduce the likelihood, incidence or severity of, to prevent or otherwise treat GVHD by preventing the loss of or reestablishing certain Clostridiales populations in the gut.

IThe disclosure encompasses a method for reducing the risk, incidence or severity of graft versus host disease (GVHD) in a subject undergoing a bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT) by taking steps to prevent the loss of beneficial activity, for example, by avoiding the use, when possible of antibiotics that are damaging with respect to anaerobes. The method may comprise selecting/administering to the subject in need thereof an antibiotic with reduced activity for anaerobic bacteria selected from the group consisting of intravenous vancomycin, ceftriaxone, ceftazidime, cefepime, aztreonam, trimethoprim-sulfamethoxazole, ciprofloxacin, levofloxacin and atovaquone.

Restoration of microbiota may be achieved by administering to a subject in need thereof a therapeutically effective amount of a probiotic composition comprising an effective amount of at least one bacterial strain, or a combination of several strains, from the taxa Clostridiales wherein the composition (i) stimulates growth and/or activity of bacteria which are protective against GVHD and/or (ii) inhibits growth and/or activity of bacteria which are over-represented in GVHD. Support for protective bacteria can be provided in the form of a nutritional supplement or prebiotic, in some cases, saccharides fermented by the beneficial bacteria. Inhibition of over-represented bacteria, for example, Akkermansia by administering an antibiotic that will ablate those organisms and prevent the "crowding out" of the beneficial Clostridial species is also contemplated by the disclosure.

The method to reduce the likelihood or severity of GVHD may comprise administering to a subject in need thereof a therapeutically effective amount of a composition comprising one or more bacterial species from the taxa Clostridiales, for example, a Blautia species/isolate that has been shown to reduce GVHD.

Bacterial strains administered according to the methods of the present disclosure can comprise live bacteria. One or several different bacterial inoculants can be administered simultaneously or sequentially (including administering at different times). Such bacteria can be isolated from microbiota and grown in culture using known techniques.

Administration of a bacterial composition can be accomplished by any method known in the art likely to introduce the organisms into the desired location. The bacteria may be administered orally. Alternatively, bacteria can be administered rectally for example, by enema.

The dosage of the bacterial inoculant or compound of the disclosure will be apparent to the skilled artisan. It is contemplated that a variety of doses will be effective to achieve colonization of the gastrointestinal tract with the desired bacterial inoculant, e.g. <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, <NUM><NUM>, and <NUM><NUM> CFU for example, can be administered in a single dose. Lower doses can also be effective, e.g., <NUM><NUM>, and <NUM><NUM> CFU. Subsequent inoculations, when necessary are envisioned.

Organisms contemplated for administration to restore the gastrointestinal microbiota include those shown in Table <NUM> below.

Species for use in the method described herein may include Blautia producta (ATCCR <NUM>-DSM <NUM>, American Type Culture Collection, Manassas, VA) or those indicated by an asterisk in Table <NUM> below. New Blautia isolates are being identified every year; in some instances isolates of other genuses are being recategorized as Blautia. So, for example, Blautia-like or Blautia-related species may include Ruminococcus obeum, Ruminococcus faecis; Ruminococcus lactaris, etc. (see Table <NUM> below).

To assess the association with GVHD-related mortality (or any other outcome), a script was utilized that calculates the association of the log-transformed abundance of each bacteria with the time to event of the outcome of interest, using a Cox proportional hazards test. This has the advantage of taking into consideration the time that passes before the event for each patient. The other major advantage is that the Cox proportional hazards test result can be readily adjusted to account for effects of other potential clinical factors that could confound. In this case, we performed the univariate analysis, as well as a multivariate analysis adjusting for type of transplant (cord blood vs. peripheral blood vs. bone marrow) and conditioning intensity.

Data was analyzed at the operational taxonomic unit (OTU) level. The nucleotide sequence information for each specific <NUM> rRNA was BLASTed against the NCBI <NUM> database to give the names.

In general, Blautia and Blautia-related species (including species from the genuses, Ruminococcus, Lactococcus, Anaerostipes, Holdemania, and) are Gram-stain-positive, non-motile bacteria that are obligate anaerobes found in the feces of humans and other mammals (Liu et al. Bacteria shown to have an association with GVHD, whether beneficial or detrimental are shown in Table <NUM> with those associated with lower risk or incidence of GVHD indicated by *.

Blautia and Blautia-like species, particularly those strains with a 16SrRNA sequence that closely matches that of the 16SrRNA sequence (GenBank X94966) of Blautia producta or any of SEQ ID NOS: <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM>, <NUM> and <NUM> (for example, with <NUM>% to <NUM>% sequence identity or <NUM>-<NUM>% identity) are suitable for use in the disclosed methods.

The abundance of bacteria from the taxa Clostridiales, which includes Blautia, has also been shown to be predictive for reduced GVHD-related mortality in some patients. Interestingly, several of <NUM> clostridial isolates tested (for characterization, see <NPL>) are very close relatives and therefore, may be useful in practicing the method disclosed herein.

Methods for determining whether a Blautia or Blautia-like species or isolate is suitable for use in the present disclosure may include determining the percent identity of the 16SrRNA of a species/isolate with the 16SrRNA sequence of Blautia producta (GenBank X94966) or any of SEQ ID NOS: <NUM>-<NUM>; methods for doing so are well known in the art.

Blautia species for use in the present disclosure include those Blautia and Blautia-like species that ferment certain sugars, for example, xylose, raffinose, cellobiose and melizitose. Provision of nutritional supplements comprising these sugars may be suitable for administration to a subject as a prebiotic strategy for reducing GVHD.

One or more different bacterial inoculants can be administered simultaneously or sequentially (including administering at different times). Bacterial strains administered according to the methods of the present disclosure can comprise live bacteria, frozen bacteria, bacterial spores or a combination thereof. Such bacteria can be isolated from an appropriate microbiota source or obtained from a cell repository (such as the American Type Culture Collection/ATCC) and grown in culture using known techniques.

Delivery of Blautia species to a subject to reduce the likelihood, incidence, severity or otherwise prevent or treat GVHD may be accomplished using any oral delivery system suitable for administering live microorganisms to an individual in need thereof, for example, as described in <CIT>. Such a delivery system may comprise a probiotic agent that comprises at least one species of live Blautia microorganisms that have been shown to correlate with reduced GVHD; optionally, at least one additional agent for example, intestinal motility agents; and a delivery vehicle, wherein the oral delivery vehicle releases the probiotic agent to the distal small intestine of the individual. A Blautia isolate may be administered in combination with a sugar that it is known to ferment.

Oral delivery may be achieved via a vehicle selected from the group consisting of pills, tablets, caplets, capsules, soft gels, and coated probiotic granules, that will release the probiotic agent in the distal small intestine. The disclosure further provides for oral delivery wherein the probiotic agent is present, and is in a dosage form selected from immediate release, delayed release, extended release which is released in the distal small intestine, and targeted release which is targeted to be released in the distal small intestine.

In one study, subjects analyzed retrospectively for impact of antibiotics on clinical outcomes consisted of <NUM> adult patients undergoing all-HSCT at Memorial Sloan Kettering Cancer Center (MSKCC) from <NUM> to <NUM>. Patients who received conventional grafts (non-T cell depleted) were included in this study; patients who received ex-vivo T cell depleted grafts or peri-transplant alemtuzumab were excluded. Stool specimens were collected and stored weekly over the course of the transplant hospitalization. The study was approved by the Institutional Review Board at MSKCC. All study patients provided written informed consent for biospecimen collection and analysis.

GVHD was diagnosed clinically, confirmed pathologically by biopsy whenever possible, and classified according to historical consensus criteria as described previously (see <NPL>). These criteria were applied to GVHD with purely acute features that occurred after day <NUM>. Cases of GVHD were further categorized by treatment with or without systemic steroids (prednisone or methylprednisolone, <NUM>/kg daily or higher). Cause of death was determined using a standard algorithm where outcomes were prioritized in the following order: <NUM>) primary disease recurrence, <NUM>) graft failure, <NUM>) GVHD, <NUM>) infection, and <NUM>) organ failure; thus in patients without disease recurrence or graft failure, those who were being treated for GVHD at the time of death were considered to have succumbed to GVHD-related mortality, including those who died from infections. Disease risk was determined according to the ASBMT RFI <NUM> Disease Classification. Conditioning intensity was assigned based on previously established working definitions.

Stool samples from patients were stored at <NUM> for <<NUM> before freezing at - <NUM>. Ileal and large intestinal samples from mice were frozen at -<NUM>. DNA was extracted using one of two methods, which give similar results.

For each stool specimen, DNA was extracted using a phenol-chloroform extraction technique (see <NPL>) or using Power Soil DNA isolation kit (MO BIO Laboratories).

For each stool specimen, DNA was extracted and purified. Samples were analyzed using the <NUM> GS FLX Titanium platform to sequence the V1-V3 region of the bacterial <NUM> rRNA gene or were alternatively analyzed using the Illumina MiSeq platform to sequence the V4-V5 region of the <NUM> rRNA gene. Sequence data were compiled and processed using mothur version <NUM> and QIIME version <NUM>. <NUM>, screened and filtered for quality. Operational taxonomic units (OTUs) were classified to the species level using a modified form of the Greengenes reference database. Principal component analysis was performed upon a weighted and normalized Unifrac distance matrix of OUT abundance in R software. Data from this study has been stored in the NCBI Sequence Read Archive (url: ncbi.

Phylogenetic abundance comparisons were performed in order to identify biomarkers of GVHD-related mortality using linear discriminant analysis (LDA) effect size (LEfSe) analysis27, using a logarithmic LDA cutoff of <NUM>.

All antibodies were obtained from BD Biosciences-Pharmingen. For cell analysis of surface markers, cells were stained for <NUM> minutes at <NUM> in PBS with <NUM>% BSA (PBS/BSA) after Fc block, washed, and resuspended in DAPI in PBS/BSA. Cell surface staining was followed by intracellular staining with the eBioscience kit per the manufacturer's instructions. Dead cells were excluded with LIVE/DEAD Fixable Dead Cell Stain kit (Invitrogen). All flow cytometry was performed on an LSR II (BD Biosciences) and analyzed with FlowJo (TreeStar Software).

Antibiotics used during transplant hospitalization were divided into those that included significant activity against anaerobic bacteria (pip/tazo, ticarcillin clavulanate, imipenem, meropenem, metronidazole, oral vancomycin and clindamycin), and those with reduced activity (intravenous vancomycin, ceftriaxone, ceftazidime, cefepime, aztreonam, trimethoprim-sulfamethoxazole, ciprofloxacin, levofloxacin, atovaquone (<NUM>).

As per our institutional practice, patients received ciprofloxacin prophylaxis, and those undergoing more intense conditioning than nonmyeloablative regimens also received intravenous vancomycin prophylaxis starting day -<NUM> through day <NUM> (<NUM>). Antibiotic prophylaxis against Pneumocystis jiroveci (trimethoprim sulfamethoxazole, aerosolized pentamadine, or atovaquone) was given at the discretion of the transplant physician.

For each stool specimen, DNA was purified using a phenol-chloroform extraction technique with mechanical disruption (bead-beating) based on a previously described protocol (<NUM>). Samples were analyzed using the <NUM> GS FLX Titanium platform to sequence the V1-V3 region of the bacterial <NUM> rRNA gene or were alternatively analyzed using the Illumina MiSeq platform to sequence the V4-V5 region of the <NUM> rRNA gene. Sequence data were compiled and processed using mothur version <NUM> (<NUM>), screened and filtered for quality (<NUM>). Operational taxonomic units (OTUs) were classified to the species level (<NUM>) using a modified form of the Greengenes reference database (<NUM>). Principal component analysis was performed upon a weighted and normalized Unifrac (<NUM>) distance matrix of OTU abundance in R software. Data from this study has been stored in the NCBI Sequence Read Archive (see url: www.

Mice were sacrificed on day <NUM> after receiving a total of three times of antibiotics treatment. The distal colon was removed and pooled (n = <NUM>; both for aztreonam and imipenem treatement groups), followed by RNA isolation using TrizolLS. RNA was prepared using RiboMinus (LifeTechnologies). The library was sequenced using the Ion Proton System (LifeTechnologies). Aligned RNA was analyzed for fold change. Differential gene expression was assessed in imipenem vs. aztreonam treated mice.

Paired-end raw reads from shotgun sequencing were trimmed using Trimmo-matic <NUM> (<NUM>) using a maximum mismatch of <NUM>, minimum terminal base score of <NUM>, and the Illumina TruSeq adapter sequences. The remaining clipped reads were taxonomically assigned using Kraken (<NUM>). Briefly, trimmed and filtered reads were taxonomically classified by k-mer resemblance to bacterial, viral and fungal k-mer profiles generated from the NCBI Genome and Chromosome collections (accessed November <NUM>, <NUM>). Unclassified reads were further interrogated with BLAST (nt database, March <NUM>, <NUM>) and non-microbial reads were discarded. Functional analysis was conducted on quality filtered reads using HUMAnN v0. <NUM> (<NUM>), which determines the abundance of genes and pathways in a given metagenomic community. To identify those functional categories that were differentially represented between the aztreonam and imipenem-treated subject samples, we employed LEfSe (<NUM>); a validated tool that identifies differentially abundant biomarkers such as genes, pathways or organisms between microbial communities.

Recipients were sacrificed on day <NUM> and <NUM> long segments of colon together with fecal content were carefully collected and soaked into a water-free Methanol-Carnoy's fixative (<NUM>% dry methanol, <NUM>% chloroform and <NUM>% acetic acid) (<NUM>) overnight. The tissues were then washed in methanol, embedded in paraffin, and then <NUM> sections were placed on glass slides. Slides were deparaffinized, and stained with standard Periodic acid-Schiff method, and assessed by light microscope (<NUM>).

Formalin-fixed colons from recipients were stained with anti-mouse CD3 antibody A0452 (DAKO), pSTAT3 antibody <NUM> (Cell Signaling), CD11b antibody ab133357 (Abcam), B220 antibody <NUM> (BD Pharmingen), versus isotype control. Immunofluorescence secondary staining was performed with AF488 for pSTAT3 and B220, and AF594 for CD3 and CD11b. Pieces of colon with fecal material were fixed in Carnoy and bacterial FISH (EUB338) (<NUM>) and immunostainings were done with MUC2C3 antiserum and DNA by Hoechst <NUM> (Life technologies) as previously described (<NUM>, <NUM>).

Female C57BL/<NUM>, C57BL/<NUM>/Ly5. <NUM>, and 129S1/SvlmJ mice were obtained from the Jackson Laboratory (Bar Harbor, Maine, USA). Mice used for experiments were <NUM>-<NUM> weeks old. Mice were treated with a gut-decontaminating antibiotic cocktail (ampicillin and vancomycin) to mimic microbiota injury that occurs in allo BMT patients. Mice were then exposed to a myeloablative dose of total body irradiation (TBI, <NUM> Gy from a 137Cs source as a split dose with a <NUM>-hour interval between doses) and then transplanted by intravenous injection with bone marrow and purified splenic T cells from fully MHC-mismatched B10. BR mice (H2k into H2b). Donor mice were euthanized by asphyxiation using carbon dioxide, and spleens, femurs, and tibias were removed aseptically. Donor BM was obtained by flushing of tibia and femora with cold tissue culture media. Donor BM was T cell depleted (TCD) by incubation with <NUM>µg anti-Thy-<NUM> per <NUM> BM cells for <NUM> minutes at <NUM>, followed by incubation with <NUM>µL of low-TOX-M rabbit complement per <NUM><NUM> BM cells for <NUM> minutes at <NUM>, so that GVHD could be reproducibly induced by simultaneous injection of T cell-depleted BM and donor splenic T cells in experimental mice. Splenic T cells were purified with anti-CD5 MACS beads (Miltenyi). The BM cells (<NUM> × <NUM><NUM> per recipient) and splenic T cells (<NUM> × <NUM> per recipient) were transplanted by tail vein injection.

Entire stool specimens are collected and homogenized in <NUM>-<NUM> volumes of <NUM>% peptone using a sterile stainless steel blender with <NUM>-<NUM> volumes of peptone. Approximately <NUM> gram of the specimen is serially diluted (<NUM>-fold) in pre-reduced, anaerobically sterilized (PRAS) dilution blanks (Anaerobe Systems). A separate ~<NUM> gram aliquot is weighed, dried in a vacuum overnight, and re-weighed in order to calculate counts on a dry-weight basis. To select for Clostridiales bacteria, including Blautia species, <NUM>µL of the homogenized stool sample dilution series is plated on Brain-Heart Infusion blood agar (SBA, Becton Dickinson) supplemented with <NUM>µg/mL trimethoprim (Sigma Chemical) and <NUM>µg/mL sulfamethoxazole (Sigma), Brucella Blood Agar (BAP, Anaeobe Systems), CDC ANA blood agar, (BBL Microbiology Systems), and egg yolk agar (EYA, Anaerobe Systems) (<NPL>). To select for spore-formers, the dilutions may be heated at <NUM>-<NUM> for <NUM>-<NUM> minutes and plated in the same manner as the non-heated homogenized stool samples. After <NUM> days of growth at <NUM> in an anaerobic chamber, single colonies are selected. The colony purification process is repeated by restreaking select single colonies, growing as described above, and selecting again for single colonies. Single colonies are frozen in <NUM>%-<NUM>% glycerol in <NUM> cryotubes and stored at -<NUM>.

C57BL/<NUM> mice purchased from The Jackson Laboratory (Bar Harbor, Maine) were treated with oral vancomycin and ampicillin. Following decontamination, mice were housed in autoclaved conditions (caging, bedding, water and food) to eliminate nearly all endogenous Clostridia present within the flora of mice. Mice were then treated by gavage with either a liquid suspension of cultured Enterococcus faecalis as a control, or a Blautia isolate. Mice were then exposed to a myeloablative dose of total body irradiation (TBI, <NUM> Gy) and then transplanted by intravenous injection with bone marrow and purified T cells from fully MHC-mismatched B10. BR mice (H2k into H2b). Effects on intestinal pathology and overall survival were evaluated as described. Mice colonized by Blautia, compared to those harboring Enterococcus, were protected from GVHD, with improved survival (Figure <NUM>).

Mice were monitored daily for survival and weekly for GVHD clinical scores (see <NPL>). Small intestine, large intestine, and liver samples were evaluated histologically for evidence of GVHD and scored as previously described (see <NPL>).

The small intestinal lumens of adult mice are rinsed with ice-cold water and segmented. Crypts are eluted by first turning the segments inside out and then shaking them in PBS containing <NUM> EDTA and lacking Ca2+ and Mg2+. The eluted villi and crypts are pelleted at 700xg, resuspended in PBS, and transferred to siliconized microfuge tubes using capillary pipettes. The crypts are resuspended in iPIPES buffer (<NUM> PIPES (pH <NUM>) and <NUM> NaCl) in preparation of exposure to secretory stimuli.

Crypts are incubated in <NUM>µl of iPIPES containing <NUM> bacterial (Clostridiales) CFU per crypt for <NUM> at <NUM>. Cellular components are pelleted by brief centrifugation, and supernatants transferred to sterile microfuge tubes and stored at -<NUM>. This method may be scaled up using up to ~<NUM> crypts in <NUM> iPIPES (plus or minus Clostridiales bacteria). Crypts are pelleted and <NUM>µL of the supernatants are analyzed for bactericidal activity against Clostridiales and Enterococcus bacteria in liquid culture or on agar plates. Proteins are extracted from the rest of the supernatant as well as the crypts using <NUM>% acetic acid. Total protein extracted from each fraction was resolved by AU-PAGE and subjected to western blot analysis using anti-cryptdin-<NUM> as follows. Proteins from AU-PAGE are transferred to a nitrocellulose membrane. The membrane is then blocked with <NUM>% skim milk, incubated sequentially with anti-rabbit mouse cryptdin-<NUM> (<NUM>:<NUM>), horseradish peroxidase-conjugated anti-rabbit IgG (<NUM>:<NUM>,<NUM>) and chemilumi-nescent substrate (SuperSignal, Pierce, Rockland, IL), and visualized (<NPL>).

Quantitative PCR (qPCR) of bacterial <NUM> rRNA genes was performed on tissue samples using DyNAmo SYBR Green qPCR kit (Finnzymes) and <NUM> of the universal bacterial primer 8F (<NUM>'-AGAGTTTGATCCTGGCTCAG-<NUM>' SEQ ID NO: <NUM>) and the broad-range bacterial primer 338R (<NUM>'-TGCTGCCTCCCGTAGGAGT-<NUM>' SEQ ID NO: <NUM>). Standard curves were prepared by serial dilution of the PCR blunt vector (Invitrogen) containing <NUM> copy of the <NUM> rRNA gene.

Short-chain fatty acids (SCFA) are produced by many bacteria as a byproduct of carbohydrate fermentation. SCFA have been found to be important modulators of the immune system. They are abundantly produced by Blautia and related bacteria from the Class Clostridia. To evaluate how Blautia and related bacteria mediate suppression of GVHD, fecal pellets were collected to quantify SCFA levels, particularly acetate, propionate, or butyrate. SCFAs, creatines, and hydroxy-SCFAs were quantified by alkalinizing stool samples, obtaining fingerprints of the metabolic composition of the sample using 1D <NUM> NMR on a Bruker Avance-<NUM> Spectrometer, and analyzing with supervised multivariate statistical methods using Chenomx NMR Suite software.

Preliminary experiments were done to test the impact of administration of SCFA on murine GVHD. A significant benefit of propionate given via drinking water (data not shown), or butyrate given via drinking water or via enema (data not shown) was not observed while a notable benefit with administration of acetate via drinking water was. Sodium acetate (<NUM>) will be delivered via the drinking water of mice beginning <NUM> weeks prior to BMT. Mice will then be irradiated and transplanted with continued supplementation of sodium acetate. Outcomes that will be evaluated in mice include GVHD clinical scores, survival, and day <NUM> and <NUM> tissue pathology. Kaplan-Meier curves will display the overall survival for the two groups. In addition, the area under the curve (AUC) will summarize the weekly total GVHD score from the time of infusion to week <NUM> for each mouse. Mice will be euthanized to evaluate for pathological evidence of GVHD, as well as to quantify and characterize large intestinal Tregs and alloreactive effector T cells by flow cytometry on days <NUM> and <NUM>.

An intestinal epithelial crypt culture system as previously described (<NPL>). <NUM> crypts per well were suspended in liquefied growth factor reduced Matrigel (Corning) (<NUM>% Advanced DMEM / F12 medium (Gibco); <NUM>% growth factor reduced Matrigel) at <NUM>. Then, they were plated in pre-warmed delta-surface Nunc <NUM>-well plates in <NUM>µL drops for small intestine, 30ul drops for large intestine, each containing approximately <NUM>-<NUM> crypts. After the Matrigel drops polymerized, 500ul complete crypt culture medium was added to small intestine crypt cultures (ENR-medium: advanced DMEM/F12 (Sigma), <NUM> L-glutamine (Sigma), <NUM> HEPES (Sigma), 100U/ml penicillin/100µg/ml streptomycin (Sigma), <NUM> N-acetyl cysteine (Sigma), <NUM> × B27 supplement (Invitrogen,), <NUM> × N2 supplement (Invitrogen), 50ng/ml mEGF (Peprotech), 100ng/ml mNoggin (Peprotech) and <NUM>% human R-spondin-<NUM> conditioned medium of hR-spondin-<NUM>-transfected HEK 293T cells. In some experiments evaluating budding hR-spondin-<NUM> was lowered to <NUM>-<NUM>%. Large intestine crypts were cultured in WENR-medium containing <NUM>% of Wnt3a conditioned medium in addition to the aforementioned proteins and <NUM>% Bovine serum Albumin (Sigma). For large intestine cultures <NUM> SB202190 (Sigma, Cat. S7067) and ALK5 inhibitor (A83-<NUM>, Tocris) were added to the WENR. All plates were incubated at <NUM>/<NUM>% CO2 and the media was replaced every <NUM>-<NUM> days. Control wells were left untreated, and where applicable, treatment wells received different concentrations of bacterial metabolites along with medium changes. Crypts were passaged at day <NUM> by mechanically disrupting them with a seropipet, washing away the Matrigel by spinning down the crypts in excess medium, and replating them after reconstitution of the pellet in liquefied Matrigel.

Utilizing Blautia isolate of C57BL/<NUM> origin, as well as a Lactobacillus johnsonii of C57BL/<NUM> origin, the ability of these bacteria to ferment a variety of sugars was evaluated using pH and optical density to evaluate bacterial growth in media lacking glucose. Lactobacillus johnsonii was evaluated because this bacteria expands in the setting of calorie restriction at the expense of Clostridia, and is thus presumably a direct competitor for nutrients in the murine intestine. Two sugars that are fermented by Blautia and not by Lactobacillus: rhamnose and xylose were identified from this analysis.

C57BL/<NUM> mice were inoculated orally with a murine Blautia isolate known to ferment xylose. Some mice were then administered xylose in the drinking water (<NUM>/L) beginning <NUM> days prior to BMT with B10. BR BM and T cells. These mice receiving xylose exhibited an expansion of Blautia, measured by <NUM> deep sequencing, in the intestinal flora despite the presence of GVHD on day <NUM> after BMT (<FIG>). Interestingly, long-term administration of xylose also led to improved survival of mice with GVHD.

A further study shows the growth of strains from a clostridial mix, in BHI media without glucose to which various sugars are added. Glucose gave the best results and was able to support the growth of <NUM> of the total <NUM> strains. Glucose, however would have limited benefit since it likely doesn't give a selective advantage to the beneficial bacteria. Raffinose was able to support <NUM> strains, while cellobiose appeared to support <NUM> strains not supported by raffinose. A mixture of raffinose and cellobiose can be administered to a subject to provide support for at least a portion of the beneficial bacteria.

Bacterial metabolites including SCFAs, creatines, and hydroxy-SCFAs will be quantified by obtaining fingerprints of the metabolic composition of the sample using 1D <NUM> NMR on a Bruker Avance-<NUM> Spectrometer, and analyzing with supervised multivariate statistical methods using Chenomx NMR Suite software.

From studying the effects of calorie restriction on intestinal microbiota composition it was observed that obligate anaerobes (Clostridia, Bacteroidetes) are reduced in abundance while facultative anaerobes (Lactobacillales, Proteobacteria) expand. Production of free radicals by E. coli in the setting of starvation has been described previously (<NPL>. Experiments were designed to examine in vitro if Lactobacillus johnsonii could suppress the growth of our murine Blautia isolate under starvation conditions, and to further investigate if production of free radicals could be a contributing factor. Specifically, Blautia was cultured either alone, or with L. johnsonii, and it was observed that L. johnsonii indeed suppressed the growth of Blautia, but failed to do so if additional media was added to prevent starvation (<FIG>). The effects of media that had supported the growth of L. johnsonii to plateau phase were further investigated following sterile filtration. Lacto-conditioned media had no effect on the growth of Lactobacillus when mixed with fresh media in a <NUM>:<NUM> ratio, but could suppress the growth of Blautia, indicating that under starvation conditions, Lactobacillus releases substances that suppress the growth of Blautia but not itself. It was then examined if reducing agents could rescue Blautia from Lacto-conditioned-media-mediated suppression. L-cysteine, ascorbic acid, and sodium thioglycolate were all found to be able to support Blautia growth in the presence of Lacto-conditioned media. Together, these results suggest that Lactobacillus may develop a competitive advantage over Blautia in the setting of limited nutrients due to production of free radicals, which are selectively damaging to obligately anaerobic bacteria due to a lack of protective enzymes including glutathione transferases, catalases, and superoxide dismutases.

Blautia was cultured in liquid PY medium alone, or supplemented with glucose or xylose (<NUM>/L), for <NUM> hours. Media was centrifuged and the supernatant was evaluated for levels of SCFA.

Antibiotics used during transplant hospitalization were divided into those that included significant activity against anaerobic bacteria (piperacillin-tazobactam, ticarcillin-clavulanate, imipenem-cilastatin, meropenem, metronidazole, oral vancomycin and clindamycin), and those with reduced activity (intravenous vancomycin, ceftriaxone, ceftazidime, cefepime, aztreonam, trimethoprim-sulfamethoxazole)<NUM>.

As per institutional practice, patients received ciprofloxacin prophylaxis, and those undergoing conditioning more intense then nonmyeloablative regimens also received intravenous vancomycin prophylaxis starting day -<NUM> through day <NUM><NUM>. Antibiotic prophylaxis against Pneumocystis jiroveci (trimethoprim-sulfamethoxazole, aerosolized pentamadine, or atovaquone) was given at the discretion of the transplant physician.

The incidence of acute GVHD and GVHD-related mortality was estimated using cumulative incidence functions, treating relapse and death unrelated to GVHD as competing events, and compared across factors using Gray's test. Overall survival probabilities were estimated using Kaplan-Meier methodology and compared using the logrank test. Comparisons of bacterial abundance were performed using the Mann-Whitney U for unpaired tests. For mouse experiments, data were presented as mean ± SEM. Survival curves were analyzed with the Mantel-Cox log-rank test. For other comparisons, nonpar-ametric Mann-Whitney U test was used. In all analyses statistical significance was defined as P < <NUM> based on a <NUM>-sided test. Statistical analyses were performed using R version <NUM>. <NUM> (The R Foundation for Statistical Computing, Vienna, Austria) and GraphPad Prism version <NUM> for Machintosh, (GraphPad Software, San Diego, California, USA).

Our group recently reported that increased bacterial diversity at the time of engraftment was associated with improved overall survival following allo BMT and reduced transplant-related mortality, but in that heterogeneous patient population we were unable to determine if diversity was associated with reduced GVHD<NUM>. For the current study, we began by asking if bacterial flora diversity could predict for lethal GVHD in a more uniform population of patients at high risk for developing GVHD. We utilized banked stool samples collected from patients who underwent allo BMT at our center. We identified a cohort of <NUM> patients who, following conventional allo BMT without T cell depletion, had provided a stool sample following BMT infusion and prior to hospital discharge (collected day <NUM>-<NUM>, median day <NUM>; clinical characteristics summarized in Table <NUM>). We analyzed the flora composition of these stool samples by sequencing regions V1-V3 of the <NUM> rRNA gene using the <NUM> platform, and followed patients clinically for development of GVHD-related mortality.

We ranked patients by the median Shannon diversity index into two equal groups and found that increased bacterial diversity was indeed associated with reduced GVHD lethality (<FIG>, p=<NUM>). To identify bacterial subsets associated with either increased or decreased GVHD-related mortality, we compared the abundances of bacterial genera from patients who did or did not die from GVHD by linear discriminant analysis (LDA) effect size (LEfSe)<NUM> as a hypothesis-generating approach. We found that bacteria belonging to the genus Blautia were most significantly associated with reduced GVHD-related mortality (<FIG>, p=<NUM>). The Blautia genus notably includes anaerobic intestinal commensal organisms within the bacterial class Clostridia<NUM>,<NUM>.

We evaluated Blautia abundance as a predictive factor for GVHD-related mortality, stratifying patients by the median Blautia abundance of <NUM>%, and found that a higher abundance of Blautia was associated with reduced GVHD-related mortality (<FIG>, p=<NUM>). We repeated this analysis in a subsequent cohort of <NUM> patients (clinical characteristics summarized in Table <NUM>).

Despite differences in sequence methodology including analysis of V4-V5 of the <NUM> rRNA gene and using the MiSeq platform, this independent cohort demonstrated similar results, with a median Blautia abundance that was again <NUM>% and confirmation of an association between Blautia abundance with less GVHD lethality (<FIG>, p=<NUM>). Evaluating the combined cohorts, we found that Blautia abundance was strongly predictive of improved overall survival following allo BMT. This was largely driven by reduced GVHD-related mortality and to a lesser degree reduced relapse-related mortality (p=<NUM>), with no difference in non-GVHD treatment-related mortality (<FIG>). Similar results were obtained when cohorts were analyzed separately (data not shown). Adjusting for the two most readily modifiable risk factors for acute GVHD, graft source and conditioning intensity, we found that Blautia abundance maintained an association with reduced GVHD-related mortality (HR <NUM> [<NUM>-<NUM>], p=<NUM>). Regarding relapse-related mortality, an adjusted model factoring in disease risk and graft source demonstrated a reduction in the association with Blautia abundance (p=<NUM>).

We also evaluated the association of GVHD-related mortality with other bacteria. Because increased Enterococcus may be associated with GVHD<NUM>, we evaluated if Enterococcus, or potentially beneficial bacteria (Lactobacillus and Bacteroides) were associated with GVHD-related mortality in our patient population. We also evaluated Veil-lonella, which was predicted by LEfSe analysis of the first patient flora cohort to be associated with increased GVHD-related mortality (p=<NUM>). Our results indicate that none of these bacterial taxa were predictive of GVHD-related mortality in the combined cohorts (<FIG>).

We also asked if bacterial subtypes related to Blautia could be predictive of reduced lethal GVHD. Bacteria from the genus Blautia are classified as follows: family-Lachnospiraceae, order - Clostridiales, class - Clostridia, and phylum - Firmicutes<NUM>. Analyzing patients by abundance of bacteria from Lachnospiraceae, Clostridiales, and Clostridia all demonstrated associations with a reduced incidence of lethal GVHD, suggesting that members of Blautia, and potentially its relatives, contribute a protective effect against lethal GVHD (data not shown). At the species level, three Blautia taxa were associated with reduced GVHD-related mortality, similar to results at the genus level.

Having identified Blautia as a promising biomarker of GVHD-related mortality, we asked if it also correlated with reduced clinical acute GVHD. Our results indicate that Blautia abundance could be associated with a reduced incidence of acute GVHD grades <NUM>-<NUM> though this did not reach statistical significance (p=<NUM>); there was no association with acute GVHD grades <NUM>-<NUM> (<FIG>). Blautia abundance did, however, predict for reduced development of acute GVHD requiring treatment with systemic corticosteroids (p=<NUM>), suggesting that loss of Blautia is associated with acute GVHD that will not respond to topical corticosteroids alone. Regarding classical acute GVHD target organs, increased Blautia abundance was not linked to skin GVHD or upper gut GVHD (<FIG>). It trended towards being associated with reduced lower gut GVHD (p=<NUM>) and was associated with reduced liver GVHD (p=<NUM>) though the number of events was small.

We further examined the associations between Blautia abundance and GVHD outcomes while adjusting for clinical risk factors. After adjusting for the two most readily modifiable risk factors for acute GVHD, graft source and conditioning intensity, we found that Blautia abundance maintained an association with reduced GVHD leading to treatment with systemic steroids (HR <NUM> [<NUM>-<NUM>], p=<NUM>) and mortality (HR <NUM> [<NUM>-<NUM>], p=<NUM>). The limited number of events in our patient population precluded adjusting for additional factors. Corroborating this analysis, we found that in patients grouped by conditioning intensity, Blautia remained predictive for protection against lethal GVHD in patients with nonmyeloablative conditioning (<FIG>, p=<NUM>) and trended towards being associated with protection in patients receiving myeloablative and reduced intensity conditioning, (p=<NUM> and p=<NUM>). In patients grouped by graft source, those that received peripheral blood stem cell grafts showed a strong association between Blautia abundance and reduced lethal GVHD (<FIG>, p=<NUM>), while those receiving cord blood stem cell grafts trended towards showing this association (p=<NUM>). Together, these results suggest that studies of larger cohorts of patients could demonstrate an association between Blautia abundance and reduced GVHD lethality across different conditioning intensities and graft sources.

To determine if Blautia abundance provides additional prognostic information, we investigated potential associations between Blautia abundance and known risk factors for acute GVHD<NUM>-<NUM>. We found that conditioning intensity, patient age, performance status, donor/patient gender, CMV status and disease risk were not associated with Blautia abundance (Table <NUM>). While limited by small number, patients of an Asian or Hispanic background appeared to have lower abundance of Blautia. Finally, evaluating Blautia abundance and graft source also showed no association. In summary, our analysis indicates that Blautia abundance does not appear to be associated with known risk factors for acute GVHD.

To better understand the heterogeneity in Blautia abundance in our patient population, we attempted to identify determinants of Blautia abundance. An analysis of all stool samples from both flora cohorts showed that a large majority of patients had relatively large amounts of Blautia upon admission for transplant hospitalization, with a median abundance of ><NUM> (<NUM>%) (<FIG>). In many patients, however, Blautia levels rapidly dropped during the course of hospitalization. As would be expected, we found that patients who were not exposed to antibiotics with anaerobic coverage were more likely to have increased levels of Blautia (<FIG>).

Due to nausea and mucositis following conditioning, allo BMT patients commonly experience a prolonged period of significantly reduced oral intake and are treated with supplementary TPN. We used duration of TPN supplementation as an indicator of oral nutrition and examined for associations with Blautia abundance. Interestingly, patients with TPN use of less than <NUM> days duration (indicating delayed, interrupted or discontinued TPN therapy since initiation of TPN is considered on day <NUM> and stool samples were on average collected on day <NUM>), had increased levels of Blautia (<FIG>). TPN duration was associated with loss of Blautia even in patients that avoided treatment with anaerobe-active antibiotics (<FIG>). Together these results indicate that anaerobic antibiotic therapy and poor oral nutritional intake both appear to mediate suppression of Blautia in the intestinal tract.

In this study we began with finding that in allo BMT recipients, the bacterial genus from stool samples most associated with reduced GVHD-related mortality was Blautia, in two independent cohorts. Patients with more Blautia also showed a reduced incidence of acute GVHD requiring treatment with systemic corticosteroids and improved overall survival. To demonstrate these associations, we ranked patients by their Blautia abundance and stratified by the median value, which happened to be <NUM>% in both cohorts.

Surprisingly, despite the association with GVHD-related mortality, Blautia abundance did not distinguish the incidence of acute GVHD grades <NUM>-<NUM>, which is known to identify patients less likely to respond to steroids, leading to poor survival<NUM>. However, it is known that there is a subpopulation of patients initially presenting with grade <NUM> acute GVHD who nevertheless fare poorly that may be identified by novel GVHD grading systems<NUM> or by novel biomarkers<NUM>. Further investigation in additional patient cohorts may determine if Blautia abundance can similarly add to the prognostic utility of clinical acute GVHD grading.

The abundance of bacteria from the class Clostridia, which includes Blautia, has also been shown to be predictive for reduced GVHD-related mortality in our patients. Interestingly, several of the <NUM> clostridial isolates are very close relatives of members of the genus Blautia, including one strain with a <NUM> sequence that most closely matches that of the <NUM> sequence (GenBank X94966) of species Blautia producta (ATCCR <NUM>-DSM <NUM>, American Type Culture Collection, Manassas, VA), which was predictive for reduced GVHD lethality in our patient cohort. A beneficial anti-inflammatory association of Blautia has also been observed in other clinical settings, including colorectal cancer<NUM>, inflammatory pouchitis following ileal pouch-anal anastomosis<NUM>, and liver cirrhosis<NUM>.

In a second study, We began by asking if treatment with antibiotics that target anaerobic bacteria is associated with clinical differences in GVHD-related mortality. Allo-HSCT patients at our center receive a prophylactic regimen of antibiotics,
including a short course of trimethoprim-sulfamethoxazole to prevent Pneumocystis jiroveci pneumonia, as well as intravenous vancomycin and ciprofloxacin throughout the period of neutropenia. Notably, we have found that this regimen usually results in only mild perturbations to the composition of the intestinal microbiota (<NUM>). Later in the course of allo-HSCT, patients who develop neutropenic fever are treated with empiric antibiotics, the selection of which can vary due to a history of medication allergies or patient-specific considerations. Some patients who develop persistent fevers, abdominal symptoms, or have microbiological evidence of infection with a resistant bacterium may receive second-line antibiotics that are often more active against anaerobes. Finally, allo- HSCT patients are also commonly diagnosed with and treated for Clostridium difficile colitis during the allo-HSCT hospitalization, which rapidly leads to loss of anaerobic intestinal commensals (<NUM>, <NUM>).

We retrospectively identified a cohort of <NUM> adult patients allo-HSCT patients consecutively transplanted at our center from <NUM> to <NUM> that met our inclusion criteria of being at standard risk for GVHD (i.e. no ex vivo T-cell depletion) and receiving treatment for neutropenic fever. Patients who received second-line antibiotics or received antibiotics that treat Clostridium difficile colitis (metronidazole either intravenously or orally, or vancomycin orally) were excluded. The remaining <NUM> patients were classified as receiving antibiotics that were more active against anaerobes (predominately piperacillin-tazobactam (pip/tazo) and imipenem-cilastatin (imipenem)), or receiving treatment with antibiotics less active against anaerobes (predominately cefepime and aztreonam) (<NUM>); clinical characteristics are provided in Table <NUM>. We found that <NUM> patients who received antibiotics with anaerobic activity had a significantly increased incidence of GVHD-related mortality in the first year following allo-HSCT (<FIG>, p=<NUM>). Univariate analyses for previously identified GVHD risk factors demonstrated no significant association with GVHD-related mortality in this data set (Table <NUM>), suggesting that the type of antibiotic exposure may be a novel predictor of GVHD-related mortality. We also performed a multivariate analysis evaluating the association of type of antibiotic exposure with GVHD related mortality while adjusting for GVHD risk factors associated with GVHD related mortality in our patient group using a significance criteria of p<<NUM>. We found that type of antibiotic exposure remained significant after adjusting for donor/HLA match (p=<NUM>) (Table <NUM>). These results support the possibility that selecting antibiotics that preserve anaerobic commensals may reduce the risk of GVHD. An alternative hypothesis would be that patients with a history of allergies to penicillins (and are thus more likely to receive cephalosporins or aztreonam instead of penicillins and carbapenems) may be protected against GVHD, though this seems to have less biological plausibility.

HSCT patients were on intestinal bacterial composition. In <NUM>, our center began to prospectively collect weekly stool samples from patients undergoing allo-HSCT. From this specimen bank, we identified paired stool samples collected from patients prior to as well as following initiation of specific antibiotics during the course of allo-HSCT. Representative cases of patients treated for neutropenic fever, as well as of patients who did not require therapeutic antibiotics (but did receive prophylactic antibiotics), are shown in <FIG>, B to G. Using <NUM> rRNA gene deep sequencing, we evaluated the effects of these antibiotics on microbial composition. We focused on changes in abundance of Clostridiales, a predominant order of anaerobic gram-positive commensal bacteria that includes many species associated with intestinal health (<NUM>, <NUM>, <NUM>).

We found that patients often demonstrated loss of Clostridiales and this temporally coincided with beginning treatment with imipenem, pip/tazo, or metronidazole, while treatment with aztreonam often led to relative preservation of Clostridiales abundances (<FIG>, B to G). Quantifying the change in Clostridiales abundance before and after starting specific antibiotics, we found that patients treated with imipenem, pip/tazo and metronidazole all had significantly lower abundances of Clostridiales compared to those treated with aztreonam (Fig. <NUM>).

To further explore causality and mechanisms of the effects of antibiotics with anaerobic activity on GVHD, we turned to experiments in mice. We first treated healthy C57BL/<NUM> mice with antibiotics either with increased activity against anaerobic bacteria (pip/tazo, imipenem, and metronidazole) or with reduced activity (aztreonam and cefepime). Mice were treated by subcutaneous (SC) injections of each antibiotic twice a day for two days (<NUM>/kg for pip/tazo and <NUM>/kg for others) and stool samples were collected, followed by <NUM> rRNA gene amplification and sequence analysis. We found that systemic treatment with imipenem or metronidazole significantly reduced the abundance of Clostridiales and increased that of Enterococcus, while treatment with aztreonam or cefepime spared Clostridiales (<FIG>). Interestingly, treatment with pip/tazo resulted in no amplifiable bacterial DNA after two days of treatment, indicating near-complete decontamination in mice (data not shown).

We next investigated the effects of antibiotic treatment in a clinically relevant MHC-matched minor antigen-mismatched allo-HSCT model (C57BL/<NUM> into 129S1). We chose not to administer prophylactic antibiotics such as IV vancomycin or ciprofloxacin, which minimally perturb the intestinal microbiota composition, and focused on comparing the effects of aztreonam, which spared Clostridiales in both patients and mice, with imipenem, which depleted Clostridiales in both patients and mice, when given in the first weeks after allo-HSCT similar to the frequent clinical scenario of post-transplant fever/neutropenia. Lethally irradiated 129S1 recipients were transplanted with C57BL/<NUM> T-cell depleted bone marrow (TCD-BM) cells and <NUM> × <NUM> C57BL/<NUM> splenic T cells. Control recipients received TCD-BM only. Recipients were treated with either aztreonam or imipenem SC three times per week starting on day <NUM> after allo-HSCT. Remarkably, we observed significantly increased mortality in imipenem-treated recipients within <NUM> weeks of starting treatment (<FIG>). Control recipients without T-cell transfer (no GVHD control) showed <NUM>% survival, indicating that antibiotic treatment itself did not have adverse effects on BM engraftment or survival after myeloablative irradiation. These results were reproducible in three consecutive and independent experiments. Histological examination of GVHD target organs on day <NUM> after allo-HSCT (<NUM> days after starting antibiotic therapy) revealed that increased GVHD pathology was present in mice treated with imipenem. Interestingly, this was localized to the colon (<FIG> and <FIG>) while other common GVHD target organs, including the skin, liver and small intestine, showed no significant differences in the degree of inflammation and damage. <NUM> rRNA gene sequencing of stool samples from mice with GVHD followed by principal component analysis indicated that aztreonam and imipenem therapy led to distinct patterns of microbiota composition (<FIG>). The taxa that best explained the differences between these groups, as assessed by linear discriminate analysis of effect size (LEfSe) (<NUM>) are depicted in <FIG>, E and F. Transplanted mice treated with imipenem showed a loss of Clostridiales, corroborating our results in patients and untransplanted mice.

Interestingly, an expansion of Akkermansia muciniphila was observed consistently in six experiments in these animals (<FIG>, G and H). We evaluated the effects of imipenem treatment on T-cell infiltration and STAT3 phosphorylation in the colon of mice with GVHD and found increased numbers of T cells infiltrating the colon, both by flow cytometry and by histology, with significantly higher levels of phosphorylated STAT3 seen in T cells in situ by fluorescent microscopy, supporting the notion that elevated levels of IL-<NUM> participated in the recruitment and activation of donor T-cells, which likely contributed to aggravated GVHD specifically in the colon. In mice with GVHD, imipenem treatment led to an expansion of Akkermansia muciniphila, a common commensal bacteria found in the intestinal tract of humans, mice and other animals. Notably, this bacterium is unusual in its ability to utilize mucin as a source of carbon and nitrogen (<NUM>). Breakdown of the colonic mucus layer has been observed following mono-colonization of germ-free mice with Akkermansia muciniphila, suggesting that Akkermansia muciniphila can degrade mucin in vivo as well as in vitro (<NUM>). What the effects of Akkermansia muciniphila are on intestinal homeostasis, however, is less clear and likely setting-dependent. In a murine obesity model, treatment with Akkermansia muciniphila resulted in improvement of metabolic disorders and reduced systemic levels of endotoxins, suggesting that in this setting Akkermansia muciniphila improved intestinal barrier function (<NUM>). However, a gnotobiotic murine model of Salmonella typhimurium infection showed that presence of Akkermansia muciniphila led to aggravated intestinal inflammation that was attributed to colonic mucus disruption (<NUM>). Our examination of the colon in imipenem-treated animals demonstrated a nearly complete effacement of the mucus layer. We also detected the presence of bacteria in the colonic lamina propria beyond the disrupted mucus layer, which is in agreement with the mucus layer providing a critical first line of defense against invasion of the intestinal mucosa (<NUM>). Why Akkermansia expands in the colon of transplanted mice treated with imipenem is unclear; to our knowledge, Akkermansia isolates have not been noted to be resistant to imipenem or other related antibiotics. Competitive interactions between Akkermansia and Clostridiales have also to our knowledge not been described, though studies have seen similar expansions of Akkermansia following treatment of mice with other antibiotics that inhibit Clostridiales, such as clindamycin (<NUM>). These results suggest that selecting antibiotics with a more limited spectrum of activity (especially against anaerobes) can prevent microbiota injury and reduce GVHD.

Clostridiales have notably been identified as major producers of short-chain fatty acids (SCFA) (<NUM>, <NUM>), which are bacterial fermentation products that play an important role in maintaining colonic homeostasis and health (<NUM>, <NUM>). Surprisingly, despite large differences in the abundances of Clostridiales, we observed no significant changes in the levels of SCFA in the colon comparing samples from recipients treated with aztreonam or imipenem (data not shown).

In order to acquire greater resolution of the bacterial composition between aztreonam- and imipenem-treated subject samples, we performed metagenomics shotgun sequencing with stool collected on day <NUM> after allo-HSCT. Our findings revealed that, concordant with the <NUM> sequencing results, imipenem but not aztreonam treatment resulted in an increased abundance of Akkermansia muciniphilia (<FIG>). However, as the largest percentage of reads from the analysis were determined to be unclassified, it is possible that additional significant differences in bacterial species composition exist between the two antibiotic-treatment types. Metagenomic shotgun sequencing analysis also revealed differences in gene content between microbiota samples from mice treated with aztreonam and imipenem, depicted by principal component analysis of gene orthologs (<FIG>). LEfSe analysis of gene pathways indicated that the microbiota genes in mice treated with imipenem were enriched for processes including lipopolysaccharide synthesis, and relatively depleted in several processes including D-alanine metabolism (data not shown). Interestingly, lipopolysaccharide is well-known for inducing a pro-inflammatory cascade in many disease processes including GVHD (<NUM>), while reductions in D-alanine content of lipotechoic acid can enhance the anti-inflammatory properties of Lactobacilli (<NUM>, <NUM>).

As mentioned above, we detected an increase in Akkermansia muciniphila in the flora of imipenem-treated mice using <NUM> rRNA deep sequencing (<FIG>). This bacterium has the ability to degrade mucus as a carbohydrate source (<NUM>, <NUM>). Utilizing our metagenomic shotgun sequencing results, we asked if genes predicted to encode for secretory mucolytic enzymes were differentially present in mice treated with each antibiotic. The identification and characterization of bacterial mucolytic enzymes is still a young field, but a recent study examined the whole genomic sequence of Akkermansia muciniphila ATCC BAA-<NUM>, isolated from human feces (<NUM>). The authors identified two strong candidates for mucus degradation: Amuc_0953, a sulfatase, and Amuc_2164, a glycosyl hydrolase, which both contained predicted secretory signal peptide cleavage sites as well as predicted mucin-binding domains. We quantified the presence of sequences with homology to these two genes and found that both were markedly enriched in samples from imipenem-treated mice (<FIG>). We then sought to characterize the mucus layer of the colon in antibiotic-treated transplanted mice. Using Periodic acid-Schiff staining, we observed a marked reduction in the thickness of the mucus layer in recipients treated with imipenem on day <NUM> compared to aztreonam-treated recipients (<FIG>, H and I). No differences in the numbers of mucus-producing goblet cells between aztreonam and imipenem-treated recipients were seen suggesting that mucus production was not impaired (<FIG>). Moreover, by utilizing a general bacterial <NUM> rRNA probe (EUB338) (<NUM>) coupled with Muc2 staining, we directly visualized the inner mucus layer in the colon of antibiotic-treated recipients and confirmed a dramatic thinning of the mucus layer of mice treated with imipenem. Strikingly, we also histologically observed dissemination of bacteria past the colonic epithelial barrier in imipenem-treated mice (<FIG>), while this was not seen in aztreonam treated mice. Taken together, these results indicate that imipenem treatment mayexacerbate GVHD through a combination of factors including compromised barrier function with thinning of the protective mucus layer and reduced numbers of colonic B cells, increased infiltration with granulocytes, elevated levels of IL-<NUM>, and increased numbers and activation of donor effector CD4+ T cells.

One question that arises is how the abundance of Blautia and other related bacteria as early as day <NUM> after allo BMT could biologically impact on acute GVHD and GVHD-related mortality, which can occur months, and in the case of mortality, years, after allo BMT. There are precedents however; serum cyclosporine concentrations in the first week following allo BMT predicted for onset of acute GVHD, even though onset of acute GVHD largely occurred after day <NUM><NUM>. Similarly, serum levels of the biomarker ST2 predicted for steroid-refractory GVHD and levels as early as day <NUM> were associated with <NUM>-month mortality without relapse<NUM>. Together, these studies suggest that conditions early post-BMT may affect the initiation of GVHD and dictate the eventual severity of the course of GVHD, though this can take months to fully manifest, perhaps due to partial containment of inflammation by ongoing administration of immune suppressants in the forms of GVHD prophylaxis and therapy.

Interestingly, while our results suggest that Blautia is associated with reduced GVHD, increased abundance of Blautia was not associated with increased relapse-related mortality. This suggests that Blautia may be linked with primarily localized anti-inflammatory effects, a possibility supported by our finding of a lack of an association with skin GVHD. Together, these data suggest that targeting the microbiota may allow for reduced GVHD without simultaneously compromising graft-versus-tumor effects. Indeed, we found an association of Blautia abundance with reduced relapse-related mortality, although this association was lost after adjusting for disease risk and graft source. Examining more thoroughly the impact of the microbiota on relapse would require further study.

Characterizing the abundance of Blautia in our patients over the course of their transplant hospitalization, we found that most patients initially had relatively large amounts of Blautia, but in many patients Blautia species were then dramatically lost. We identified two potential risk factors associated with loss of Blautia, including receiving antibiotics with anaerobic coverage and requiring longer treatment duration of TPN. The finding of reduced Blautia with antibiotic administration is not surprising, but the association with prolonged TPN was unexpected. While conditioning intensity and duration of TPN necessity are known to be associated<NUM>, we found no significant association between conditioning intensity and Blautia abundance (data not shown). This suggests that poor oral nutrition may be a more likely contributor to loss of Blautia than more intense conditioning. This explanation is corroborated by findings in mouse models that myeloablative conditioning is associated with only mild perturbations in flora composition, in comparison to larger perturbations characterized by loss of Clostridiales seen in both mice and humans with the onset of GVHD, a potent inducer of anorexia<NUM>. A pattern of loss of members of Clostridiales, including Roseburia, Faecalibacterium, Ruminococcus and Blautia species, can similarly be observed in volunteers placed on high-protein and low-carbohydrate diets<NUM> or on diets derived entirely from animal products<NUM>.

Claim 1:
A therapeutic composition for use in treating a graft versus host disease (GVHD) in a subject following bone marrow transplant (BMT) or hematopoietic stem cell transplant (HSCT), wherein the therapeutic composition comprises one or more purified populations of bacteria selected from the group consisting of Ruminococcus obeum, Clostridium hathewayi, Eubacterium desmolans, Dorea longicatena, Ruminococcus lactaris (Blautia producta), Eubacterium contortum, Ruminococcus faecis, Holdemania filiformis, Clostridium sordelli, and combinations or mixtures thereof.