Patent Publication Number: US-2023139325-A1

Title: Improving milk production and compositional characteristics with novel ruminococcus bovis

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of priority to U.S. Provisional Application No. 63/002,588, filed on Mar. 31, 2020, hereby incorporated by reference in its entirety. 
    
    
     FIELD 
     The present disclosure relates to isolated and biologically pure microorganisms that have applications, inter alia, in dairy production. The disclosed microorganisms can be utilized in their isolated and biologically pure states, as well as being formulated into compositions. Furthermore, the disclosure provides microbial ensembles, containing at least two members of the disclosed microorganisms, as well as methods of utilizing said microbial ensembles. Furthermore, the disclosure provides for methods of modulating the rumen microbiome. 
     STATEMENT REGARDING SEQUENCE LISTING 
     The sequence listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the sequence listing is ASBI_021_02WO_ST25.txt. The text file is ˜901 kb, was created on Mar. 31, 2021, and is being submitted electronically via EFS-Web. 
     BACKGROUND 
     The global population is predicted to increase to over 9 billion people by the year 2050 with a concurrent reduction in the quantity of land, water, and other natural resources available per capita. Projections indicate that the average domestic income will also increase, with the projected rise in the GDP of China and India. The desire for a diet richer in animal-source proteins rises in tandem with increasing income, thus the global livestock sector will be charged with the challenge of producing more milk using fewer resources. The Food and Agriculture Organization of the United Nations predict that 70% more food will have to be produced, yet the area of arable land available will decrease. It is clear that the food output per unit of resource input will have to increase considerably in order to support the rise in population. 
     Milk and milk components from lactating ruminants are predominantly utilized in the preparation of foodstuffs in many different forms. Nevertheless, milk and milk components find numerous alternative applications in non-food areas such as the manufacture of glues, textile fibers, plastic materials, or in the production of ethanol or methane. There have been many strategies to improve milk production and content in ruminants through nutritional modulations, hormone treatments, changes in animal management, and selective breeding; however, the need for more efficient production of milk and milk components per animal is required. 
     Identifying compositions and methods for sustainably increasing milk production and modulating milk components of interest while balancing animal health and wellbeing have become imperative to satisfy the needs of every day humans in an expanding population. Increasing the worldwide production of milk and further modulating desirable milk components by scaling up the total number of livestock on dairy farms would not only be economically infeasible for many parts of the world, but would further result in negative environmental consequences. 
     Thus, meeting global milk and milk component yield expectations, by simply scaling up current high-input agricultural systems—utilized in most of the developed world—is simply not feasible. 
     There is therefore an urgent need in the art for improved methods of increasing milk production and further increasing yield of desirable milk components. 
     SUMMARY OF THE DISCLOSURE 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a)  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and (b) a carrier suitable for oral ruminant administration. In some embodiments, the  Ruminococcus bovis  is deposited as TSD-225 or NCTC 14479. In some embodiments, the composition comprises: (a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or (b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the composition comprises: (a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 28; (b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; and/or (c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: (a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
     In some embodiments, the  Ruminococcus bovis  comprises one or more mutations in the whole genome. In some embodiments, the one or more mutations are selected from the group consisting of: (a) a G→T substitution at position 297 of SEQ ID NO: 2109; (b) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111; (c) a T→G substitution at position 307 of SEQ ID NO: 2111; (d) a −A deletion at position 300 of SEQ ID NO: 2113; (e) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115; (f) a +T insertion between positions 105-106 of SEQ ID NO: 2117; (g) a C→T substitution at position 298 of SEQ ID NO: 2119; (h) a C→A substitution at position 298 of SEQ ID NO: 2121; and (i) a +AC insertion between positions 43-44 of SEQ ID NO: 2123. 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a)  Ruminococcus bovis  comprising one or more mutations selected from the group consisting of: (i) a G→T substitution at position 297 of SEQ ID NO: 2109; (ii) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111; (iii) a T→G substitution at position 307 of SEQ ID NO: 2111; (iv) a −A deletion at position 300 of SEQ ID NO: 2113; (v) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115; (vi) a +T insertion between positions 105-106 of SEQ ID NO: 2117; (vii) a C→T substitution at position 298 of SEQ ID NO: 2119; (viii) a C→A substitution at position 298 of SEQ ID NO: 2121; and (ix) a +AC insertion between positions 43-44 of SEQ ID NO: 2123; and (b) a carrier suitable for oral ruminant administration. In some embodiments, the composition comprises: (a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or (b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the composition comprises: (a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 28; (b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; and/or (c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: (a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a)  Ruminococcus bovis  comprising a nucleic acid sequence selected from any one of SEQ ID NOs: 2110, 2112, 2114, 2116, 2118, 2120, 2122, or 2124; and (b) a carrier suitable for oral ruminant administration. In some embodiments, the composition comprises: (a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or (b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the composition comprises: (a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 28; (b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; and/or (c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: (a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a) a  Ruminococcus bovis  with the deposit accession number PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479; and (b) a carrier suitable for oral ruminant administration. In some embodiments, the composition comprises: (a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or (b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the composition comprises: (a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO; 28; (b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; and/or (c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: (a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
     In some embodiments, the ruminant is a cow. 
     In some embodiments, a ruminant administered the composition exhibits an increase in milk production that leads to an increase in milk yield or an increase in energy-corrected milk. 
     In some embodiments, a ruminant administered the composition exhibits an improved milk compositional characteristic selected from the group consisting of: an increase in milk fat(s), an increase in milk protein(s), an increase of carbohydrates in milk, an increase of vitamins in milk, an increase of minerals in milk, or combinations thereof. 
     In some embodiments, a ruminant administered the composition exhibits at least one improved phenotypic trait, selected from the group consisting of: an improved efficiency in feed utilization, improved digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in manure production, improved dry matter intake, an improved efficiency of nitrogen utilization, or combinations thereof. 
     In some embodiments, the composition is formulated to protect  Ruminococcus bovis  from external stressors prior to entering the gastrointestinal tract of the ruminant. In some embodiments, the composition is formulated to protect the  Ruminococcus bovis  from oxidative stress. In some embodiments, the composition is formulated to protect the  Ruminococcus bovis  from moisture. 
     In some embodiments, the composition is combined with food. In some embodiments, the composition is combined with cereal, starch, oilseed cake, or vegetable waste. In some embodiments, the composition is combined with hay, haylage, silage, livestock feed, forage, fodder, beans, grains, micro-ingredients, fermentation compositions, mixed ration, total mixed ration, or a mixture thereof. 
     In some embodiments, the composition is formulated as a solid, liquid, or mixture thereof. In some embodiments, the composition is dry. In some embodiments, the composition is formulated as a pellet, capsule, granulate, or powder. In some embodiments, the composition is encapsulated. In some embodiments, the composition is encapsulated in a polymer or carbohydrate. 
     In some embodiments, the composition is combined with water, medicine, vaccine, or a mixture thereof. 
     In some embodiments, the  Ruminococcus bovis  is present in the composition in an amount of at least 10 2  cells. 
     In some embodiments, the present disclosure provides a method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of any of the compositions disclosed herein. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits an increase in milk production that leads to a measured increase in milk yield. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits an increase in milk production and improved milk compositional characteristics that leads to a measured increase in energy-corrected milk. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits an improved milk compositional characteristic selected from the group consisting of: an increase in milk fat(s), an increase in milk protein(s), an increase of carbohydrates in milk, an increase of vitamins in milk, an increase of minerals in milk, or combinations thereof. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits at least a 1% increase in the average production of: milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits at least a 10% increase in the average production of: milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement exhibits at least a 20% increase in the average production of; milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement, further exhibits at least one improved phenotypic trait, selected from the group consisting of: an improved efficiency in feed utilization, improved digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in manure production, improved dry matter intake, an improved efficiency of nitrogen utilization, or combinations thereof. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement, further exhibits a shift in the microbiome of the rumen. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement, further exhibits a shift in the microbiome of the rumen, wherein a population of microbes present in the rumen before administration of the ruminant supplement increase in abundance after administration of the ruminant supplement. 
     In some embodiments, the ruminant administered the effective amount of the ruminant supplement, further exhibits: a shift in the microbiome of the rumen, wherein a population of microbes present in the rumen before administration of the ruminant supplement decrease in abundance after administration of the ruminant supplement. 
     In some embodiments, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits: a shift in the microbiome of the rumen, wherein a first population of microbes present in the rumen before administration of the ruminant supplement increase in abundance after administration of the ruminant supplement, and wherein a second population of microbes present in the rumen before administration of the ruminant supplement decrease in abundance after administration of the ruminant supplement. 
     In some embodiments, the present disclosure provides a composition comprising: (a) a  Ruminococcus bovis  with a deposit accession number of TSD-225 or NCTC 14479; (b) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (c) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (d) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
     In some embodiments, the present disclosure provides a composition that performs the same or better than recombinant bovine growth hormone for increasing milk production or improving milk compositional characteristics in a ruminant, wherein the composition comprises: (a)  Ruminococcus  bois comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and (b) a carrier suitable for oral ruminant administration. In some embodiments, the composition comprises: (a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or (b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the composition comprises: (a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 28; (b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; and/or (c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: (a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248; (b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or (c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347. 
    
    
     
       DESCRIPTION OF THE DRAWINGS 
         FIG.  1    shows a general workflow of one embodiment of the method for determining the absolute abundance of one or more active microorganism strains. 
         FIG.  2    shows a general workflow of one embodiment of a method for determining the co-occurrence of one or more, or two or more, active microorganism strains in a sample with one or more metadata (environmental) parameters, followed by leveraging cluster analysis and community detection methods on the network of determined relationships. 
         FIG.  3    depicts a schematic diagram that illustrates an example process flow for use with an exemplary microbe interaction analysis and selection system, including the determination of MIC scores discussed throughout the present disclosure. 
         FIG.  4    shows average nucleotide identity (ANI) between JE7A12 T  and phylogenetically related organisms as well as standing species in the genus  Ruminococcus . NCBI GenBank accession number appended to end of species label. 
         FIG.  5    shows the 16S phylogenetic position of JE7A12 T . Dendrogram; JE7A12 T  and the closest 25  Ruminococcus  16S sequences in the RDP database. The tree was constructed using the neighbor-joining method based on the comparison of 1500 nt long sequences. Bootstrap values, resulting from 500 replications, given at each branch point. 
         FIG.  6    shows the whole genome phylogenetic position of JE7A12 T . Closest cultured neighbors are shown with an asterisks. Branch length is appended to each branch. NCBI GenBank accession numbers in parentheses. 
         FIG.  7    shows a methylene blue stain of JE7A12 T  after 48 hours of incubation viewed at 1000× magnification. 
         FIG.  8    shows a Gram stain of JE7A12 T  after 48 hours of incubation viewed at 1000× magnification. 
         FIG.  9    shows milk yield in cows administered control, treatment 1, or treatment 2 over time. B indicates p≤0.05 for control versus treatment 2; and c indicates p≤0.05 for treatment 1 versus treatment 2. 
         FIG.  10    shows energy corrected milk (ECM) in cows administered control, treatment 1, or treatment 2 over time. B indicates p&lt;0.05 for control versus treatment 2; and c indicates p≤0.05 for treatment 1 versus treatment 2. 
         FIG.  11 A  shows percent fat in milk from cows administered control, treatment 1, or treatment 2 over time. C indicates p≤0.05 for treatment 1 versus treatment 2. 
         FIG.  11 B  shows pounds (lbs) of fat in milk from cows administered control, treatment 1, or treatment 2 over time. B indicates p&lt;0.05 for control versus treatment 2; and c indicates p&lt;0.05 for treatment 1 versus treatment 2. 
         FIG.  12 A  shows percent protein in milk from cows administered control, treatment 1, or treatment 2 over time. A indicates p≤0.05 for control versus treatment 1; and c indicates p&lt;0.05 for treatment 1 versus treatment 2. 
         FIG.  12 B  shows pounds (lbs) of protein in milk from cows administered control, treatment 1, or treatment 2 over time. B indicates p&lt;0.05 for control versus treatment 2; and c indicates p≤0.05 for treatment 1 versus treatment 2. 
         FIG.  13 A  shows percent lactose in milk from cows administered control, treatment 1, or treatment 2 over time. 
         FIG.  13 B  shows pounds (lbs) of lactose in milk in cows administered control, treatment 1, or treatment 2 over time. B indicates p&lt;0.05 for control versus treatment 2; and c indicates p&lt;0.05 for treatment 1 versus treatment 2. 
         FIG.  14 A  shows dry matter intake in cows administered control, treatment 1, or treatment 2 over time. B indicates p&lt;0.05 for control versus treatment 2; and c indicates p&lt;0.05 for treatment 1 versus treatment 2. 
         FIG.  14 B  shows feed efficiency (energy corrected milk to dry matter intake) in cows administered control, treatment 1, or treatment 2 over time. 
         FIG.  15 A  shows body weight of cows administered control, treatment 1, or treatment 2 over time. 
         FIG.  15 B  shows body condition of cows administered control, treatment 1, or treatment 2 over time. 
         FIG.  16 A  shows energy corrected milk (ECM) in cows administered control, treatment 1, or treatment over time. 
         FIG.  16 B  shows milk fat in cows administered control, treatment 1, or treatment over time. 
         FIG.  17 A  shows milk yield in cows administered control, treatment 1, or treatment over time. Post-peak signifies greater than 90 days in milk. 
         FIG.  17 B  shows energy corrected milk (ECM) in cows administered control, treatment 1, or treatment over time. Post-peak signifies greater than 90 days in milk. 
     
    
    
     BUDAPEST TREATY ON THE INTERNATIONAL RECOGNITION OF THE DEPOSIT OF MICROORGANISMS FOR THE PURPOSE OF PATENT PROCEDURES 
     Some microorganisms described in this application were deposited with the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Culture Collection (NRRL®), located at 1815 N. University St., Peoria, Ill. 61604, USA. Some microorganisms described in this application were deposited with the Bigelow National Center for Marine Algae and Microbiota, located at 60 Bigelow Drive, East Boothbay, Me. 04544, USA. Some microorganisms described in this application were also deposited with the American Type Culture Collection (ATCC®), located at 10801 University Blvd., Manassas, Va. 20110, USA. Some microorganisms described in this application were deposited with the National Collection of Type Cultures operated by the Public Health England, located at Porton Down, Salisbury, SP4 0JG, United Kingdom. 
     The deposits were made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure and/or type strain rules and procedures. The deposit accession numbers for the Budapest Treaty deposits and type strains are provided in Table 2. The depository, accession numbers, and corresponding dates of deposit for the microorganisms described in this application are separately provided in Table 4. 
     In Table 1, the closest predicted hits for taxonomy of the microbes are listed in columns 2, and 5. Column 2 is the top taxonomic hit predicted by BLAST, and column 5 is the top taxonomic hit for genus+species predicted by BLAST. Table 3 shows the top taxonomic hit predicted by BLAST. The compositions of the present disclosure may contain any one, or any combination, of the microbes listed below in Table 1 and Table 3. The microbes of Table 1 and Table 3 may be administered as a single microbial product and/or as a microbial consortia comprising a combination of microbes from Table 1 and Table 3. 
     The strains designated in the tables below have been deposited in the labs of Native Microbials, Inc. since at least before the date of filing of the present application and before the date of deposit with the noted depository institutions. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Microbes of the present disclosure, including bacteria (1-89) and fungi (90-123). 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 BLAST 
                   
                   
                   
                   
                   
               
               
                   
                   
                   
                   
                 Taxonomic 
               
               
                   
                 BLAST 
                 Blast 
                   
                 Top Hit 
                 Blast 
               
               
                 Predicted Taxa of 
                 Taxonomic 
                 % 
                 Query 
                 w/Genus + 
                 % 
                 Query 
                 Strain 
                 Sequence 
                 MIC 
               
               
                 Isolated Microbes 
                 Top Hit 
                 Ident. 
                 Cover 
                 Species 
                 Identity 
                 Cover 
                 Designation 
                 Identifier 
                 Score 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                 
                   Ruminococcus bovis 
                 
                 Clostridiaceae 
                 96% 
                 100%  
                 
                   Ruminococcus 
                 
                 91% 
                 82% 
                 Ascusb_5 
                 SEQ ID 
                 0.85694 
               
               
                 sp. nov. 
                 bacterium 
                   
                   
                 
                   bromii 
                 
                   
                   
                   
                 NO: 1 
               
               
                 
                   Ruminococcus bovis 
                 
                 Clostridiaceae 
                 96% 
                 100%  
                 
                   Ruminococcus 
                 
                 91% 
                 82% 
                 Ascusb_5 
                 SEQ ID 
                 0.85694 
               
               
                 sp. nov. 
                 bacterium 
                   
                   
                 
                   bromii 
                 
                   
                   
                   
                 NO: 2108 
               
               
                 
                   Ruminococcus 
                 
                 Rumen bacterium 
                 93% 
                 84% 
                 
                   Ruminococcus 
                 
                 91% 
                 82% 
                 Ascusb_7 
                 SEQ ID 
                 0.97384 
               
               
                 (Genus) 
                   
                   
                   
                 
                   bromii 
                 
                   
                   
                   
                 NO: 2 
               
               
                   Clostridium  IV 
                 Rumen bacterium 
                 89% 
                 97% 
                 
                   Intestinimonas 
                 
                 85% 
                 100%  
                 Ascusb_26 
                 SEQ ID 
                 0.82051 
               
               
                 (Cluster) 
                 NK4A214 
                   
                   
                 
                   butyriciproducens 
                 
                   
                   
                   
                 NO: 3 
               
               
                   Roseburia  (Genus) 
                 Lachnospiraceae 
                 89% 
                 100%  
                 
                   Pseudobutyrivibrio 
                 
                 89% 
                 96% 
                 Ascusb_27 
                 SEQ ID 
                 0.87214 
               
               
                   
                 bacterium 
                   
                   
                 
                   ruminis 
                 
                   
                   
                   
                 NO: 4 
               
               
                   Hydrogenoanaero - 
                 Lachnospiraceae 
                 87% 
                 93% 
                 
                   Roseburia 
                 
                 86% 
                 93% 
                 Ascusb_32 
                 SEQ ID 
                 0.81269 
               
               
                   bacterium  (Genus) 
                 bacterium 
                   
                   
                 
                   inulinivorans 
                 
                   
                   
                   
                 NO: 5 
               
               
                   Clostridium  XIVa 
                 
                   Eubacterium 
                 
                 92% 
                 100%  
                 
                   Eubacterium 
                 
                 92% 
                 100%  
                 Ascusb_79 
                 SEQ ID 
                 0.82765 
               
               
                 (Cluster) 
                 
                   ventriosum 
                 
                   
                   
                 
                   ventriosum 
                 
                   
                   
                   
                 NO: 6 
               
               
                 
                   Saccharofermentans 
                 
                 Rumen bacterium 
                 87% 
                 100%  
                 
                   Faecalibacterium 
                 
                 91% 
                 76% 
                 Ascusb_82 
                 SEQ ID 
                 0.93391 
               
               
                 (Genus) 
                   
                   
                   
                 
                   prausnitzii 
                 
                   
                   
                   
                 NO: 7 
               
               
                 
                   Saccharofermentans 
                 
                 
                   Saccharofermentans 
                 
                 100%  
                 99% 
                 
                   Saccharofermentans 
                 
                 83% 
                 92% 
                 Ascusb_102 
                 SEQ ID 
                 0.82247 
               
               
                 (Genus) 
                 sp. 
                   
                   
                 
                   acetigenes 
                 
                   
                   
                   
                 NO: 8 
               
               
                 
                   Butyricicoccus 
                 
                   Clostridium  sp. 
                 87% 
                 100%  
                 
                   Ruminococcus 
                 
                 86% 
                 99% 
                 Ascusb_89 
                 SEQ ID 
                 0.74361 
               
               
                 (Genus) 
                   
                   
                   
                 
                   flavefaciens 
                 
                   
                   
                   
                 NO: 9 
               
               
                 
                   Papillibacter 
                 
                 Rumen bacterium 
                 91% 
                 99% 
                 
                   Clostridium 
                 
                 88% 
                 82% 
                 Ascusb_111 
                 SEQ ID 
                 0.82772 
               
               
                 (Genus) 
                 NK4A214 
                   
                   
                 
                   saccharolyticum 
                 
                   
                   
                   
                 NO: 10 
               
               
                 
                   Ruminococcus 
                 
                 Ruminococcaceae 
                 100%  
                 94% 
                 
                   Clostridium 
                 
                 85% 
                 99% 
                 Ascusb_119 
                 SEQ ID 
                 0.8263 
               
               
                 (Genus) 
                   
                   
                   
                 
                   lentocellum 
                 
                   
                   
                   
                 NO: 11 
               
               
                   Hydrogenoanaero - 
                 Rumen bacterium 
                 85% 
                 98% 
                 
                   Ruminococcus 
                 
                 85% 
                 100%  
                 Ascusb_145 
                 SEQ ID 
                 0.81161 
               
               
                   bacterium  (Genus) 
                 NK4B29 
                   
                   
                 
                   flavefaciens 
                 
                   
                   
                   
                 NO: 12 
               
               
                 
                   Pelotomaculum 
                 
                 
                   Faecalibacterium 
                 
                 86% 
                 93% 
                 
                   Faecalibacterium 
                 
                 86% 
                 82% 
                 Ascusb_205 
                 SEQ ID 
                 0.81461 
               
               
                 (Genus) 
                 sp. 
                   
                   
                 
                   prausnitzii 
                 
                   
                   
                   
                 NO: 13 
               
               
                 
                   Saccharofermentans 
                 
                 Bacterium 
                 99% 
                 91% 
                 
                   Saccharofermentans 
                 
                 90% 
                 79% 
                 Ascusb_232 
                 SEQ ID 
                 0.81428 
               
               
                 (Genus) 
                 MA3003 
                   
                   
                 
                   acetigenes 
                 
                   
                   
                   
                 NO: 14 
               
               
                 Lachnospiraceae 
                 Bacterium 
                 95% 
                 93% 
                 
                   Blautia luti 
                 
                 88% 
                 92% 
                 Ascusb_252 
                 SEQ ID 
                 0.8196 
               
               
                 incertae sedis (Family) 
                 VCD3003 
                   
                   
                   
                   
                   
                   
                 NO: 15 
               
               
                 
                   Butyricicoccus 
                 
                 Ruminococcaceae 
                 91% 
                 77% 
                 
                   Clostridium 
                 
                 83% 
                 99% 
                 Ascusb_268 
                 SEQ ID 
                 0.74813 
               
               
                   sensu stricto  (Genus) 
                 bacterium 
                   
                   
                 
                   lentocellum 
                 
                   
                   
                   
                 NO: 16 
               
               
                 Lachnospiraceae 
                 Bacterium 
                 96% 
                 92% 
                 
                   Coprococcus catus 
                 
                 88% 
                 100%  
                 Ascusb_374 
                 SEQ ID 
                 0.76214 
               
               
                 incertae sedis (Family) 
                 YAB2006 
                   
                   
                   
                   
                   
                   
                 NO: 17 
               
               
                 
                   Anaeroplasma 
                 
                 
                   Anaeroplasma 
                 
                 97% 
                 100%  
                 
                   Anaeroplasma 
                 
                 97% 
                 100%  
                 Ascusb_411 
                 SEQ ID 
                 0.76213 
               
               
                 (Genus) 
                 
                   varium 
                 
                   
                   
                 
                   varium 
                 
                   
                   
                   
                 NO: 18 
               
               
                 
                   Clostridium sensu 
                 
                 Clostridiales 
                 100%  
                 93% 
                 
                   Clostridium 
                 
                 81% 
                 91% 
                 Ascusb_546 
                 SEQ ID 
                 0.83869 
               
               
                   stricto  (Genus) 
                 bacterium 
                   
                   
                 
                   stercorarium 
                 
                   
                   
                   
                 NO: 19 
               
               
                 
                   Butyricicoccus 
                 
                 Clostridiales 
                 88% 
                 91% 
                 
                   Aminiphilus 
                 
                 80% 
                 77% 
                 Ascusb_672 
                 SEQ ID 
                 0.74829 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   circumscriptus 
                 
                   
                   
                   
                 NO: 20 
               
               
                 
                   Butyricicoccus 
                 
                 Clostridiales 
                 89% 
                 89% 
                 
                   Aminiphilus 
                 
                 97% 
                 27% 
                 Ascusb_765 
                 SEQ ID 
                 0.74111 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   circumscriptus 
                 
                   
                   
                   
                 NO: 21 
               
               
                 
                   Rikenella 
                 
                   Bacteroides  sp. 
                 93% 
                 64% 
                 
                   Alistipes shahii 
                 
                 93% 
                 64% 
                 Ascusb_812 
                 SEQ ID 
                 0.73874 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 22 
               
               
                 
                   Tannerella 
                 
                 
                   Alistipes shahii 
                 
                 86% 
                 100%  
                 
                   Alistipes shahii 
                 
                 86% 
                 100%  
                 Ascusb_1295 
                 SEQ ID 
                 0.8365 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 23 
               
               
                 
                   Howardella 
                 
                 Clostridiales 
                 85% 
                 100%  
                 
                   Oscillibacter 
                 
                 89% 
                 41% 
                 Ascusb_1763 
                 SEQ ID 
                 0.75083 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   valericigenes 
                 
                   
                   
                   
                 NO: 24 
               
               
                 
                   Prevotella 
                 
                 Bacteroidetes 
                 97% 
                 95% 
                 
                   Odoribacter 
                 
                 77% 
                 86% 
                 Ascusb_1780 
                 SEQ ID 
                 0.89749 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   splanchnicus 
                 
                   
                   
                   
                 NO: 25 
               
               
                 
                   Butyricimonas 
                 
                 Bacteroidetes 
                 95% 
                 99% 
                 
                   Tannerella forsythia 
                 
                 83% 
                 92% 
                 Ascusb_1801 
                 SEQ ID 
                 0.89664 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                   
                   
                   
                   
                 NO: 26 
               
               
                 
                   Clostridium sensu 
                 
                 Bacterium 
                 96% 
                 93% 
                   Hydrogenoanaero - 
                 84% 
                 86% 
                 Ascusb_1833 
                 SEQ ID 
                 0.73989 
               
               
                   
                   
                   
                   
                 
                   bacterium 
                 
               
               
                   stricto  (Genus) 
                 XBB3002 
                   
                   
                 
                   saccharovorans 
                 
                   
                   
                   
                 NO: 27 
               
               
                 
                   Clostridium sensu 
                 
                 
                   Clostridium 
                 
                 98% 
                 100%  
                 
                   Clostridium 
                 
                 98% 
                 100%  
                 Ascusb_3138 
                 SEQ ID 
                 0.76524 
               
               
                   stricto  (Genus) 
                 
                   butyricum 
                 
                   
                   
                 
                   butyricum 
                 
                   
                   
                   
                 NO: 28 
               
               
                 
                   Saccharofermentans 
                 
                 Rumen bacterium 
                 87% 
                 99% 
                 
                   Faecalibacterium 
                 
                 90% 
                 76% 
                 Ascusb_6589 
                 SEQ ID 
                 0.76539 
               
               
                 (Genus) 
                 NK4A214 
                   
                   
                 
                   prausnitzii 
                 
                   
                   
                   
                 NO: 29 
               
               
                 Lachnospiraceae 
                 
                   Roseburia 
                 
                 90% 
                 100%  
                 
                   Roseburia 
                 
                 90% 
                 100%  
                 Ascusb_7921 
                 SEQ ID 
                 0.86201 
               
               
                 incertae sedis (Family) 
                 
                   intestinalis 
                 
                   
                   
                 
                   intestinalis 
                 
                   
                   
                   
                 NO: 30 
               
               
                 
                   Succinivibrio 
                 
                 
                   Succinivibrio 
                 
                 95% 
                 99% 
                 
                   Succinivibrio 
                 
                 95% 
                 99% 
                 Ascusb_11 
                 SEQ ID 
                 0.50001 
               
               
                 (Genus) 
                 
                   dextrinosolvens 
                 
                   
                   
                 
                   dextrinosolvens 
                 
                   
                   
                   
                 NO: 2045 
               
               
                 
                   Prevotella 
                 
                 Bacterium 
                 100%  
                 93% 
                 
                   Prevotella 
                 
                 91% 
                   
                 Ascusb_36 
                 SEQ ID 
                 0.55431 
               
               
                 (Genus) 
                 MB2027 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2046 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 100%  
                 99% 
                 
                   Prevotella 
                 
                 100%  
                   
                 Ascusb_67 
                 SEQ ID 
                 0.49156 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2047 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 97% 
                 100%  
                 
                   Prevotella 
                 
                 97% 
                 100%  
                 Ascusb_87 
                 SEQ ID 
                 0.59635 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2048 
               
               
                 
                   Ruminobacter 
                 
                   Ruminobacter  sp. 
                 92% 
                 99% 
                 
                   Ruminobacter 
                 
                 92% 
                 100%  
                 Ascusb_101 
                 SEQ ID 
                 0.75099 
               
               
                 (Genus) 
                   
                   
                   
                 
                   amylophilus 
                 
                   
                   
                   
                 NO: 2049 
               
               
                 
                   Syntrophococcus 
                 
                 
                   Blautia producta 
                 
                 91% 
                 100%  
                 
                   Blautia producta 
                 
                 91% 
                 100%  
                 Ascusb_104 
                 SEQ ID 
                 0.70044 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 2050 
               
               
                 
                   Succinivibrio 
                 
                 
                   Succinivibrio 
                 
                 96% 
                 99% 
                 
                   Succinivibrio 
                 
                 96% 
                 99% 
                 Ascusb_125 
                 SEQ ID 
                 0.44408 
               
               
                 (Genus) 
                 
                   dextrinosolvens 
                 
                   
                   
                 
                   dextrinosolvens 
                 
                   
                   
                   
                 NO: 2051 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 
                   Butyrivibrio 
                 
                 99% 
                 100%  
                 
                   Butyrivibrio 
                 
                 99% 
                 100%  
                 Ascusb_149 
                 SEQ ID 
                 0.50676 
               
               
                 (Genus) 
                 
                   fibrisolvens 
                 
                   
                   
                 
                   fibrisolvens 
                 
                   
                   
                   
                 NO: 2052 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 99% 
                 99% 
                 
                   Prevotella 
                 
                 99% 
                 99% 
                 Ascusb_159 
                 SEQ ID 
                 0.5744 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2053 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 96% 
                 99% 
                 
                   Prevotella 
                 
                 96% 
                 99% 
                 Ascusb_183 
                 SEQ ID 
                 0.50204 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2054 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 99% 
                 100%  
                 
                   Prevotella 
                 
                 99% 
                 100%  
                 Ascusb_187 
                 SEQ ID 
                 0.56688 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2055 
               
               
                 
                   Prevotella 
                 
                 Bacterium XBB2006 
                 100%  
                 94% 
                 
                   Prevotella albensis 
                 
                 87% 
                 97% 
                 Ascusb_190 
                 SEQ ID 
                 0.56183 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 2056 
               
               
                 Lachnospiraceae 
                 Lachnospiraceae 
                 91% 
                 100%  
                 
                   Roseburia 
                 
                 89% 
                 100%  
                 Ascusb_199 
                 SEQ ID 
                 0.62487 
               
               
                 incertae sedis (Family) 
                 bacterium 
                   
                   
                 
                   inulinivorans 
                 
                   
                   
                   
                 NO: 2057 
               
               
                 
                   Syntrophococcus 
                 
                 
                   Ruminococcus 
                 
                 95% 
                 100%  
                 
                   Ruminococcus 
                 
                 95% 
                 100%  
                 Ascusb_278 
                 SEQ ID 
                 0.51235 
               
               
                 (Genus) 
                 
                   gnavus 
                 
                   
                   
                 
                   gnavus 
                 
                   
                   
                   
                 NO: 2058 
               
               
                 
                   Ruminobacter 
                 
                   Ruminobacter  sp. 
                 100%  
                 99% 
                 
                   Ruminobacter 
                 
                 99% 
                 100%  
                 Ascusb_329 
                 SEQ ID 
                 0.4754 
               
               
                 (Genus) 
                   
                   
                   
                 
                   amylophilus 
                 
                   
                   
                   
                 NO: 2059 
               
               
                 
                   Butyrivibrio 
                 
                   Butyrivibrio  sp. 
                 100%  
                 100%  
                 
                   Butyrivibrio 
                 
                 99% 
                 98% 
                 Ascusb_368 
                 SEQ ID 
                 0.60727 
               
               
                 (Genus) 
                   
                   
                   
                 
                   hungatei 
                 
                   
                   
                   
                 NO: 2060 
               
               
                   Clostridium _XlVa 
                 
                   Eubacterium 
                 
                 100%  
                 96% 
                 
                   Eubacterium 
                 
                 100%  
                 96% 
                 Ascusb_469 
                 SEQ ID 
                 0.66345 
               
               
                 (Cluster) 
                 
                   oxidoreducens 
                 
                   
                   
                 
                   oxidoreducens 
                 
                   
                   
                   
                 NO: 2061 
               
               
                 
                   Prevotella 
                 
                 Rumen bacterium 
                 99% 
                 99% 
                 
                   Prevotella brevis 
                 
                 91% 
                 100%  
                 Ascusb_530 
                 SEQ ID 
                 0.44804 
               
               
                 (Genus) 
                 NK4A111 
                   
                   
                   
                   
                   
                   
                 NO: 2062 
               
               
                 
                   Prevotella 
                 
                   Prevotella  sp. 
                 100%  
                 93% 
                 
                   Prevotella copri 
                 
                 100%  
                 93% 
                 Ascusb_728 
                 SEQ ID 
                 0.55431 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 2063 
               
               
                 Lachnospiraceae 
                 
                   Eubacterium 
                 
                 99% 
                 100%  
                 
                   Eubacterium 
                 
                 99% 
                 100%  
                 Ascusb_756 
                 SEQ ID 
                 0.72136 
               
               
                 incertae sedis (Family) 
                 
                   ruminantium 
                 
                   
                   
                 
                   ruminantium 
                 
                   
                   
                   
                 NO: 2064 
               
               
                 
                   Roseburia 
                 
                 Lachnospiraceae 
                 89% 
                 93% 
                 [ Clostridium ] 
                 89% 
                 91% 
                 Ascusb_810 
                 SEQ ID 
                 0.65527 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   xylanovorans 
                 
                   
                   
                   
                 NO: 2065 
               
               
                 Lachnospiraceae 
                 
                   Lachnospira 
                 
                 99% 
                 100%  
                 
                   Lachnospira 
                 
                 99% 
                 100%  
                 Ascusb_817 
                 SEQ ID 
                 0.46512 
               
               
                 incertae sedis (Family) 
                 
                   pectinoschiza 
                 
                   
                   
                 
                   pectinoschiza 
                 
                   
                   
                   
                 NO: 2066 
               
               
                 
                   Butyrivibrio 
                 
                 
                   Butyrivibrio 
                 
                 98% 
                 99% 
                 
                   Butyrivibrio 
                 
                 98% 
                 99% 
                 Ascusb_826 
                 SEQ ID 
                 0.65357 
               
               
                 (Genus) 
                 
                   fibrisolvens 
                 
                   
                   
                 
                   fibrisolvens 
                 
                   
                   
                   
                 NO: 2067 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 
                   Pseudobutyrivibrio 
                 
                 100%  
                 95% 
                 
                   Pseudobutyrivibrio 
                 
                 97% 
                 100%  
                 Ascusb_880 
                 SEQ ID 
                 0.52295 
               
               
                 (Genus) 
                 sp. 
                   
                   
                 
                   ruminis 
                 
                   
                   
                   
                 NO: 2068 
               
               
                 
                   Turicibacter 
                 
                 
                   Sinimarinibacterium 
                 
                 87% 
                 69% 
                 
                   Sinimarinibacterium 
                 
                 87% 
                 69% 
                 Ascusb_913 
                 SEQ ID 
                 0.55141 
               
               
                 (Genus) 
                 
                   flocculans 
                 
                   
                   
                 
                   flocculans 
                 
                   
                   
                   
                 NO: 2069 
               
               
                 Lachnospiraceae 
                 Bacterium 
                 100%  
                 91% 
                 
                   Butyrivibrio 
                 
                 90% 
                 100%  
                 Ascusb_974 
                 SEQ ID 
                 0.53487 
               
               
                 incertae sedis (Family) 
                 FB3002 
                   
                   
                 
                   fibrisolvens 
                 
                   
                   
                   
                 NO: 2070 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 
                   Pseudobutyrivibrio 
                 
                 97% 
                 99% 
                 
                   Pseudobutyrivibrio 
                 
                 97% 
                 99% 
                 Ascusb_1069 
                 SEQ ID 
                 0.55299 
               
               
                 (Genus) 
                 
                   ruminis 
                 
                   
                   
                 
                   ruminis 
                 
                   
                   
                   
                 NO: 2071 
               
               
                 
                   Anaerolinea 
                 
                 Chloroflexi 
                 88% 
                 99% 
                 
                   Anaerolinea 
                 
                 90% 
                 57% 
                 Ascusb_1074 
                 SEQ ID 
                 0.50893 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   thermophila 
                 
                   
                   
                   
                 NO: 2072 
               
               
                 
                   Roseburia 
                 
                 Lachnospiraceae 
                 98% 
                 99% 
                 
                   Eubacterium rectale 
                 
                 94% 
                 100%  
                 Ascusb_1293 
                 SEQ ID 
                 0.61745 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 2073 
               
               
                 
                   Propionibacterium 
                 
                 
                   Propionibacterium 
                 
                 100%  
                 100%  
                 
                   Propionibacterium 
                 
                 100%  
                 100%  
                 Ascusb_1367 
                 SEQ ID 
                 0.54046 
               
               
                 (Genus) 
                 
                   acnes 
                 
                   
                   
                 
                   acnes 
                 
                   
                   
                   
                 NO: 2074 
               
               
                   Clostridium _XIVa 
                 Lachnospiraceae 
                 88% 
                 100%  
                 
                   Pseudobutyrivibrio 
                 
                 86% 
                 97% 
                 Ascusb_1632 
                 SEQ ID 
                 0.46826 
               
               
                 (Cluster) 
                 bacterium 
                   
                   
                 
                   ruminis 
                 
                   
                   
                   
                 NO: 2075 
               
               
                 
                   Olsenella 
                 
                 Coriobacteriaceae 
                 98% 
                 100%  
                 
                   Olsenella profusa 
                 
                 97% 
                 100%  
                 Ascusb_1674 
                 SEQ ID 
                 0.51533 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                   
                   
                   
                   
                 NO: 2076 
               
               
                 
                   Streptococcus 
                 
                 
                   Streptococcus 
                 
                 95% 
                 82% 
                 
                   Streptococcus 
                 
                 95% 
                 82% 
                 Ascusb_1786 
                 SEQ ID 
                 0.48678 
               
               
                 (Genus) 
                 
                   dentirousetti 
                 
                   
                   
                 
                   dentirousetti 
                 
                   
                   
                   
                 NO: 2077 
               
               
                   Clostridium _XlVa 
                   Butyrivibrio  sp. 
                 99% 
                 96% 
                 
                   Butyrivibrio 
                 
                 93% 
                 100%  
                 Ascusb_1812 
                 SEQ ID 
                 0.64367 
               
               
                 (Cluster) 
                   
                   
                   
                 
                   proteoclasticus 
                 
                   
                   
                   
                 NO: 2078 
               
               
                   Clostridium _XlVa 
                 Bacterium 
                 99% 
                 91% 
                 
                   Butyrivibrio 
                 
                 96% 
                 99% 
                 Ascusb_1850 
                 SEQ ID 
                 0.57807 
               
               
                 (Cluster) 
                 DAZ2002 
                   
                   
                 
                   hungatei 
                 
                   
                   
                   
                 NO: 2079 
               
               
                 
                   Roseburia 
                 
                 Lachnospiraceae 
                 95% 
                 99% 
                 
                   Eubacterium 
                 
                 89% 
                 100%  
                 Ascusb_1879 
                 SEQ ID 
                 0.45014 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   oxidoreducens 
                 
                   
                   
                   
                 NO: 2080 
               
               
                   Clostridium _IV 
                 Ruminococcaceae 
                 87% 
                 99% 
                 
                   Ruminococcus 
                 
                 85% 
                 91% 
                 Ascusb_2090 
                 SEQ ID 
                 0.75266 
               
               
                 (Cluster) 
                 bacterium 
                   
                   
                 
                   bromii 
                 
                   
                   
                   
                 NO: 2081 
               
               
                   Clostridium _XICa 
                 Bacterium 
                 99% 
                 99% 
                 
                   Clostridium 
                 
                 85% 
                 90% 
                 Ascusb_2124 
                 SEQ ID 
                 0.4673 
               
               
                 (Cluster) 
                 MA2020 
                   
                   
                 
                   algidixylanolyticum 
                 
                   
                   
                   
                 NO: 2082 
               
               
                 Lachnospiracea 
                 Bacterium 
                 94% 
                 94% 
                 
                   Eubacterium 
                 
                 91% 
                 100%  
                 Ascusb_2198 
                 SEQ ID 
                 0.55249 
               
               
                 incertae sedis (Family) 
                 YSB2008 
                   
                   
                 
                   ruminantium 
                 
                   
                   
                   
                 NO: 2083 
               
               
                 Erysipelotrichaceae 
                 
                   Catenisphaera 
                 
                 90% 
                 91% 
                 
                   Catenisphaera 
                 
                 90% 
                 91% 
                 Ascusb_2511 
                 SEQ ID 
                 0.50619 
               
               
                 incertae sedis (Family) 
                 
                   adipataccumulans 
                 
                   
                   
                 
                   adipataccumulans 
                 
                   
                   
                   
                 NO: 2084 
               
               
                 
                   Solobacterium 
                 
                 Erysipelotrichaceae 
                 92% 
                 99% 
                 
                   Solobacterium 
                 
                 91% 
                 100%  
                 Ascusb_2530 
                 SEQ ID 
                 0.53735 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   moorei 
                 
                   
                   
                   
                 NO: 2085 
               
               
                 Lachnospiraceae 
                 
                   Eubacterium 
                 
                 95% 
                 100%  
                 
                   Eubacterium 
                 
                 95% 
                 100%  
                 Ascusb_2597 
                 SEQ ID 
                 0.52028 
               
               
                 incertae sedis (Genus) 
                 
                   ruminantium 
                 
                   
                   
                 
                   ruminantium 
                 
                   
                   
                   
                 NO: 2086 
               
               
                   Clostridium _XlVa 
                 
                   Butyrivibrio 
                 
                 99% 
                 100%  
                 
                   Butyrivibrio 
                 
                 99% 
                 100%  
                 Ascusb_2624 
                 SEQ ID 
                 0.55465 
               
               
                 (Cluster) 
                 
                   proteoclasticus 
                 
                   
                   
                 
                   proteoclasticus 
                 
                   
                   
                   
                 NO: 2087 
               
               
                 
                   Ralstonia 
                 
                   Ralstonia  sp. 94 
                 100%  
                 99% 
                 
                   Ralsonia insidiosa 
                 
                 99% 
                 100%  
                 Ascusb_2667 
                 SEQ ID 
                 0.52371 
               
               
                 (Genus) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 2088 
               
               
                   Clostridium _XlVa 
                   Butyrivibrio  sp. 
                 97% 
                 94% 
                 
                   Butyrivibrio 
                 
                 95% 
                 100%  
                 Ascusb_2836 
                 SEQ ID 
                 0.43374 
               
               
                 (Cluster) 
                   
                   
                   
                 
                   proteoclasticus 
                 
                   
                   
                   
                 NO: 2089 
               
               
                 
                   Eubacterium 
                 
                 Eubacteriaceae 
                 84% 
                 100%  
                 
                   Casaltella 
                 
                 87% 
                 82% 
                 Ascusb_3003 
                 SEQ ID 
                 0.56301 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                 
                   massiliensis 
                 
                   
                   
                   
                 NO: 2090 
               
               
                 
                   Lachnobacterium 
                 
                 Rumen bacterium 
                 89% 
                 98% 
                 
                   Eubacterium 
                 
                 90% 
                 91% 
                 Ascusb_3504 
                 SEQ ID 
                 0.52856 
               
               
                 (Genus) 
                   
                   
                   
                 
                   xylanophilum 
                 
                   
                   
                   
                 NO: 2091 
               
               
                 
                   Acholeplasma 
                 
                 
                   Acholeplasma 
                 
                 86% 
                 72% 
                 
                   Acholeplasma 
                 
                 86% 
                 72% 
                 Ascusb_3881 
                 SEQ ID 
                 0.4402 
               
               
                 (Genus) 
                 
                   brassicae 
                 
                   
                   
                 
                   brassicae 
                 
                   
                   
                   
                 NO: 2092 
               
               
                 
                   Selenomonas 
                 
                 
                   Mitsuokella 
                 
                 91% 
                 97% 
                 
                   Mitsuokella 
                 
                 91% 
                 97% 
                 Ascusb_4728 
                 SEQ ID 
                 0.4761 
               
               
                 (Genus) 
                 
                   jalaludinii 
                 
                   
                   
                 
                   jalaludinii 
                 
                   
                   
                   
                 NO: 2093 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 98% 
                 100%  
                 
                   Prevotella 
                 
                 98% 
                 100%  
                 Ascusb_4934 
                 SEQ ID 
                 0.56204 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2094 
               
               
                   Clostridium _XlVa 
                   Butyrivibrio  sp. 
                 99% 
                 99% 
                 
                   Butyrivibrio 
                 
                 97% 
                 100%  
                 Ascusb_4959 
                 SEQ ID 
                 0.42892 
               
               
                 (Cluster) 
                   
                   
                   
                 
                   fibrisolvens 
                 
                   
                   
                   
                 NO: 2095 
               
               
                 
                   Succinivibrio 
                 
                 
                   Succinivibrio 
                 
                 86% 
                 84% 
                 
                   Succinivibrio 
                 
                 86% 
                 84% 
                 Ascusb_5525 
                 SEQ ID 
                 0.51758 
               
               
                 (Genus) 
                 
                   dextrinosolvens 
                 
                   
                   
                 
                   dextrinosolvens 
                 
                   
                   
                   
                 NO: 2096 
               
               
                 
                   Ruminobacter 
                 
                   Ruminobacter  sp. 
                 100%  
                 99% 
                 
                   Ruminobacter 
                 
                 99% 
                 100%  
                 Ascusb_12103 
                 SEQ ID 
                 0.52909 
               
               
                 (Genus) 
                   
                   
                   
                 
                   amylophilus 
                 
                   
                   
                   
                 NO: 2097 
               
               
                 
                   Sharpea 
                 
                 Lachnospiraceae 
                 97% 
                 100%  
                 
                   Sharpea azabuensis 
                 
                 100%  
                 91% 
                 Ascusb_14245 
                 SEQ ID 
                 0.61391 
               
               
                 (Genus) 
                 bacterium 
                   
                   
                   
                   
                   
                   
                 NO: 2098 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 87% 
                 97% 
                 
                   Prevotella 
                 
                 87% 
                 97% 
                 Ascusb_14945 
                 SEQ ID 
                 0.80101 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2099 
               
               
                 
                   Prevotella 
                 
                   Prevotella  sp. 
                 88% 
                 89% 
                 
                   Prevotella 
                 
                 87% 
                 945 
                 Ascusb_17461 
                 SEQ ID 
                 0.44777 
               
               
                 (Genus) 
                 DJF 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2100 
               
               
                 
                   Prevotella 
                 
                 Bacterium 
                 100%  
                 93% 
                 
                   Prevotella 
                 
                 91% 
                 99% 
                 Ascusb_20083 
                 SEQ ID 
                 0.52538 
               
               
                 (Genus) 
                 MB2027 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2101 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 99% 
                 100%  
                 
                   Prevotella 
                 
                 99% 
                 100%  
                 Ascusb_20187 
                 SEQ ID 
                 0.59156 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2102 
               
               
                 
                   Prevotella 
                 
                 
                   Prevotella 
                 
                 100%  
                 100%  
                 
                   Prevotella 
                 
                 100%  
                 100%  
                 Ascusb_20539 
                 SEQ ID 
                 0.4912 
               
               
                 (Genus) 
                 
                   ruminicola 
                 
                   
                   
                 
                   ruminicola 
                 
                   
                   
                   
                 NO: 2103 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 93% 
                 100%  
                 
                   Neocallimastix 
                 
                 84% 
                 100%  
                 Ascusf_11 
                 SEQ ID 
                 0.81719 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 31 
               
               
                 
                   Candida xylopsoc 
                 
                 
                   Pichia kudriavzevii 
                 
                 100%  
                 100%  
                 
                   Pichia kudriavzevii 
                 
                 100%  
                 100%  
                 Ascusf_15 
                 SEQ ID 
                 0.76088 
               
               
                 (Genus + Species) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 32 
               
               
                 
                   Orpinomyces 
                 
                   Orpinomyces  sp. 
                 100%  
                 100%  
                 
                   Neocallimastix 
                 
                 86% 
                 100%  
                 Ascusf_22 
                 SEQ ID 
                 0.76806 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 33 
               
               
                 
                   Orpinomycs 
                 
                 
                   Neocallimastix 
                 
                 86% 
                 80% 
                 
                   Neocallimastix 
                 
                 86% 
                 80% 
                 Ascusf_23 
                 SEQ ID 
                 0.85707 
               
               
                 (Genus) 
                 
                   frontalis 
                 
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 34 
               
               
                 
                   Orpinomyces 
                 
                   Orpinomyces  sp. 
                 95% 
                 100%  
                 
                   Neocallimastix 
                 
                 86% 
                 100%  
                 Ascusf_24 
                 SEQ ID 
                 0.85292 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 35 
               
               
                 
                   Candida apicol 
                 
                 
                   Candida apicola 
                 
                 100%  
                 100%  
                 
                   Candida apicola 
                 
                 100%  
                 100%  
                 Ascusf_25 
                 SEQ ID 
                 0.70561 
               
               
                 (Genus + Species) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 36 
               
               
                 
                   Candida rugosa 
                 
                 
                   Candida 
                 
                 100%  
                 100%  
                 
                   Candida 
                 
                 100%  
                 100%  
                 Ascusf_38 
                 SEQ ID 
                 0.78246 
               
               
                 (Genus + Species) 
                 
                   akabanensis 
                 
                   
                   
                 
                   akabanensis 
                 
                   
                   
                   
                 NO: 37 
               
               
                 
                   Neocallimastix 
                 
                   Neocallimastix  sp. 
                 99% 
                 100%  
                 
                   Neocallimastix 
                 
                 99% 
                 100%  
                 Ascusf_45 
                 SEQ ID 
                 0.86185 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 38 
               
               
                 
                   Orpinomyces 
                 
                   Orpinomyces  sp. 
                 99% 
                 100%  
                 
                   Orpinomyces 
                 
                 96% 
                 96% 
                 Ascusf_60 
                 SEQ ID 
                 0.72985 
               
               
                 (Genus) 
                   
                   
                   
                 
                   joyonii 
                 
                   
                   
                   
                 NO: 39 
               
               
                 
                   Orpinomyces 
                 
                 
                   Neocallimastix 
                 
                 86% 
                 78% 
                 
                   Neocallimastix 
                 
                 86% 
                 78% 
                 Ascusf_73 
                 SEQ ID 
                 0.76064 
               
               
                 (Genus) 
                 
                   frontalis 
                 
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 40 
               
               
                 
                   Neocallimastix 
                 
                   Neocallimastix  sp. 
                 98% 
                 100%  
                 
                   Neocallimastix 
                 
                 93% 
                 100%  
                 Ascusf_77 
                 SEQ ID 
                 0.83475 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 41 
               
               
                 
                   Neocallimastix 
                 
                 
                   Neocallimastix 
                 
                 97% 
                 100%  
                 
                   Neocallimastix 
                 
                 97% 
                 100%  
                 Ascusf_94 
                 SEQ ID 
                 0.77644 
               
               
                 (Genus) 
                 
                   frontalis 
                 
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 42 
               
               
                 
                   Ascomycota 
                 
                   Basidiomycota  sp. 
                 85% 
                 98% 
                 
                   Sugiyamaella 
                 
                 97% 
                 26% 
                 Ascusf_95 
                 SEQ ID 
                 0.7089 
               
               
                 (Genus) 
                   
                   
                   
                 
                   lignohabitans 
                 
                   
                   
                   
                 NO: 43 
               
               
                 
                   Piromyces 
                 
                   Caecomyces  sp. 
                 94% 
                 100%  
                 
                   Cyllamyces 
                 
                 86% 
                 89% 
                 Ascusf_108 
                 SEQ ID 
                 0.68405 
               
               
                 (Genus) 
                   
                   
                   
                 
                   aberensis 
                 
                   
                   
                   
                 NO: 44 
               
               
                 
                   Orpinomyces 
                 
                   Orpinomyces  sp. 
                 95% 
                 100%  
                 
                   Orpinomyces 
                 
                 87% 
                 96% 
                 Ascusf_119 
                 SEQ ID 
                 0.80055 
               
               
                 (Genus) 
                   
                   
                   
                 
                   joyonii 
                 
                   
                   
                   
                 NO: 45 
               
               
                 
                   Cyllamyces 
                 
                   Caecomyces  sp. 
                 90% 
                 100%  
                 
                   Caecomyces 
                 
                 90% 
                 83% 
                 Ascusf_127 
                 SEQ ID 
                 0.66812 
               
               
                 (Genus) 
                   
                   
                   
                 
                   communis 
                 
                   
                   
                   
                 NO: 46 
               
               
                 
                   Piromyces 
                 
                   Caecomyces  sp. 
                 91% 
                 100%  
                 
                   Caecomyces 
                 
                 92% 
                 83% 
                 Ascusf_136 
                 SEQ ID 
                 0.73201 
               
               
                 (Genus) 
                   
                   
                   
                 
                   communis 
                 
                   
                   
                   
                 NO: 47 
               
               
                 
                   Cyllamyces 
                 
                   Cyllamyces  sp. 
                 97% 
                 100%  
                 
                   Cyllamyces 
                 
                 94% 
                 89% 
                 Ascusf_193 
                 SEQ ID 
                 0.7586 
               
               
                 (Genus) 
                   
                   
                   
                 
                   aberensis 
                 
                   
                   
                   
                 NO: 48 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 92% 
                 100%  
                 
                   Neocallimastix 
                 
                 84% 
                 100%  
                 Ascusf_228 
                 SEQ ID 
                 0.83403 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 49 
               
               
                 
                   Piromyces 
                 
                   Caecomyces  sp. 
                 94% 
                 100%  
                 
                   Cyllamyces 
                 
                 86% 
                 89% 
                 Ascusf_249 
                 SEQ ID 
                 0.78679 
               
               
                 (Genus) 
                   
                   
                   
                 
                   aberensis 
                 
                   
                   
                   
                 NO: 50 
               
               
                 
                   Neocallimastix 
                 
                   Neocallimastix  sp. 
                 98% 
                 100%  
                 
                   Neocallimastix 
                 
                 92% 
                 100%  
                 Ascusf_307 
                 SEQ ID 
                 0.77859 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 51 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 94% 
                 100%  
                 
                   Neocallimastix 
                 
                 83% 
                 100%  
                 Ascusf_315 
                 SEQ ID 
                 0.81028 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 52 
               
               
                 
                   Neocallimastix 
                 
                   Neocallimastix  sp. 
                 100%  
                 98% 
                 
                   Neocallimastix 
                 
                 100%  
                 90% 
                 Ascusf_334 
                 SEQ ID 
                 0.76456 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 53 
               
               
                 Saccharomycetales 
                 
                   Candida ethanolica 
                 
                 100%  
                 100%  
                 
                   Candida ethanolica 
                 
                 100%  
                 100%  
                 Ascusf_353 
                 SEQ ID 
                 0.82628 
               
               
                 (Order) 
                   
                   
                   
                   
                   
                   
                   
                 NO: 54 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 91% 
                 100%  
                 
                   Neocallimastix 
                 
                 83% 
                 100%  
                 Ascusf_448 
                 SEQ ID 
                 0.70021 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 55 
               
               
                 
                   Orpinomyces 
                 
                   Neocallimastix  sp. 
                 88% 
                 91% 
                 
                   Neocallimastix 
                 
                 96% 
                 88% 
                 Ascusf_786 
                 SEQ ID 
                 0.63201 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 56 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 91% 
                 100%  
                 
                   Neocallimastix 
                 
                 83% 
                 100%  
                 Ascusf_836 
                 SEQ ID 
                 0.65492 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 57 
               
               
                 
                   Phyllosticta 
                 
                   Tremellales  sp. 
                 96% 
                 74% 
                 
                   Tremella giraffa 
                 
                 83% 
                 96% 
                 Ascusf_923 
                 SEQ ID 
                 0.76115 
               
               
                 
                   capitalensis 
                 
                   
                   
                   
                   
                   
                   
                   
                 NO: 58 
               
               
                 (Genus + Species) 
               
               
                 
                   Orpinomyces 
                 
                 
                   Neocallimastix 
                 
                 87% 
                 77% 
                 
                   Neocallimastix 
                 
                 87% 
                 77% 
                 Ascusf_1020 
                 SEQ ID 
                 0.68043 
               
               
                 (Genus) 
                 
                   frontalis 
                 
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 59 
               
               
                 
                   Orpinomyces 
                 
                 
                   Neocallimastix 
                 
                 85% 
                 80% 
                 
                   Neocallimastix 
                 
                 85% 
                 80% 
                 Ascusf_1103 
                 SEQ ID 
                 0.73004 
               
               
                 (Genus) 
                 
                   frontalis 
                 
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 60 
               
               
                 
                   Orpinomyces 
                 
                 Fungal sp. 
                 99% 
                 100%  
                 
                   Orpinomyces 
                 
                 94% 
                 96% 
                 Ascusf_81 
                 SEQ ID 
                 0.44471 
               
               
                 (Genus) 
                 Tianzhu-Yak6 
                   
                   
                 
                   joyonii 
                 
                   
                   
                   
                 NO: 2104 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 99% 
                 100%  
                 
                   Neocallimastix 
                 
                 84% 
                 100%  
                 Ascusf_206 
                 SEQ ID 
                 0.49752 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 2105 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 96% 
                 100%  
                 
                   Neocallimastix 
                 
                 82% 
                 100%  
                 Ascusf_208 
                 SEQ ID 
                 0.4176 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 2106 
               
               
                 
                   Piromyces 
                 
                   Piromyces  sp. 
                 99% 
                 100%  
                 
                   Neocallimastix 
                 
                 82% 
                 100%  
                 Ascusf_1012 
                 SEQ ID 
                 0.55922 
               
               
                 (Genus) 
                   
                   
                   
                 
                   frontalis 
                 
                   
                   
                   
                 NO: 2107 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Microbial Deposits Corresponding to the Microbes of Table 1 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Predicted Taxa 
                   
                   
                   
                 Predicted Taxa 
                   
                   
                   
               
               
                 of Isolated 
                 Strain 
                 Sequence 
                   
                 of Isolated 
                 Strain 
                 Sequence 
               
               
                 Microbes 
                 Designation 
                 Identifier 
                 Deposit No. 
                 Microbes 
                 Designation 
                 Identifier 
                 Deposit No. 
               
               
                   
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Streptococcus 
                 
                 Ascusb_1786 
                 SEQ ID 
                 PATENT201612011, 
               
               
                   bovis  sp. nov. 
                 (consortia) 
                 NO: 1 
                 PATENT201612007, 
                 (Genus) 
                   
                 NO: 2077 
                 PATENT201612012, 
               
               
                 (Species - Not 
                   
                   
                 PATENT201612009, 
                   
                   
                   
                 PATENT201612013 
               
               
                 predicted, rather a 
                   
                   
                 PATENT201612010, 
               
               
                 new species) 
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5 
                 SEQ ID 
                 PTA-125917 1   
                   Clostridium _XlVa 
                 Ascusb_1812 
                 SEQ ID 
                 PATENT201612011, 
               
               
                   bovis  sp. nov. 
                 (pure 
                 NO: 2108 
                 TSD-225 2   
                 (Cluster) 
                   
                 NO: 2078 
                 PATENT201612012 
               
               
                 (Species - Not 
                 culture) 
                   
                 NARRL B-67764 3   
               
               
                 predicted, rather a 
                   
                   
                 NCTC 14479 4   
               
               
                 new species) 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_7 
                 SEQ ID 
                 PATENT201612005, 
                   Clostridium _XlVa 
                 Ascusb_1850 
                 SEQ ID 
                 PATENT201612013 
               
               
                 (Genus) 
                   
                 NO: 2 
                 PATENT201612007, 
                 (Cluster) 
                   
                 NO: 2079 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                 PATENT201612013 
               
               
                   Clostridium  IV 
                 Ascusb_26 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Roseburia 
                 
                 Ascusb_1879 
                 SEQ ID 
               
               
                 (Cluster) 
                   
                 NO: 3 
                 PATENT201612009, 
                 (Genus) 
                   
                 NO: 2080 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Roseburia 
                 
                 Ascusb_27 
                 SEQ ID 
                 PATENT201612009 
                   Clostridium _IV 
                 Ascusb_2090 
                 SEQ ID 
                 PATENT201612007, 
               
               
                 (Genus) 
                   
                 NO: 4 
                   
                 (Cluster) 
                   
                 NO: 2081 
                 PATENT201612009 
               
               
                   Hydrogenoanaero - 
                 Ascusb_32 
                 SEQ ID 
                 PATENT201612006, 
                   Clostridium _XICa 
                 Ascusb_2124 
                 SEQ ID 
                 PATENT201612012 
               
               
                   bacterium  (Genus) 
                   
                 NO: 5 
                 PATENT201612009, 
                 (Cluster) 
                   
                 NO: 2082 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                   Clostridium  XIVa 
                 Ascusb_79 
                 SEQ ID 
                 PATENT201612011, 
                 Lachnospiracea 
                 Ascusb_2198 
                 SEQ ID 
                 PATENT201612012 
               
               
                 (Cluster) 
                   
                 NO: 6 
                 PATENT201612012 
                 incertae sedis 
                   
                 NO: 2083 
               
               
                   
                   
                   
                   
                 (Family) 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_82 
                 SEQ ID 
                 PATENT201612005, 
                 Erysipelotrichaceae 
                 Ascusb_2511 
                 SEQ ID 
                 PATENT201612001, 
               
               
                 (Genus) 
                   
                 NO: 7 
                 PATENT201612006, 
                 incertae sedis 
                   
                 NO: 2084 
                 PATENT201612007, 
               
               
                   
                   
                   
                 PATENT201612007, 
                 (Family) 
                   
                   
                 PATENT201612009 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_102 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Solobacterium 
                 
                 Ascusb_2530 
                 SEQ ID 
                 PATENT201612011, 
               
               
                 (Genus) 
                   
                 NO: 8 
                 PATENT201612007, 
                 (Genus) 
                   
                 NO: 2085 
                 PATENT201612012 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_89 
                 SEQ ID 
                 PATENT201612011, 
                 Lachnospiraceae 
                 Ascusb_2597 
                 SEQ ID 
                 PATENT201612013 
               
               
                 (Genus) 
                   
                 NO: 9 
                 PATENT201612012 
                 incertae sedis 
                   
                 NO: 2086 
               
               
                   
                   
                   
                   
                 (Genus) 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_111 
                 SEQ ID 
                 PATENT201612005, 
                   Clostridium _XlVa 
                 Ascusb_2624 
                 SEQ ID 
                 PATENT201612009, 
               
               
                 (Genus) 
                   
                 NO: 10 
                 PATENT201612007, 
                 (Cluster) 
                   
                 NO: 2087 
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_119 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Ralstonia 
                 
                 Ascusb_2667 
                 SEQ ID 
                 PATENT201612013 
               
               
                 (Genus) 
                   
                 NO: 11 
                 PATENT201612012 
                 (Genus) 
                   
                 NO: 2088 
               
               
                   Hydrogenoanaero - 
                 Ascusb_145 
                 SEQ ID 
                 PATENT201612011, 
                   Clostridium _XlVa 
                 Ascusb_2836 
                 SEQ ID 
                 PATENT201612013 
               
               
                   bacterium  (Genus) 
                   
                 NO: 12 
                 PATENT201612012 
                 (Cluster) 
                   
                 NO: 2089 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_205 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Eubacterium 
                 
                 Ascusb_3003 
                 SEQ ID 
                 PATENT201612009 
               
               
                 (Genus) 
                   
                 NO: 13 
                 PATENT201612006, 
                 (Genus) 
                   
                 NO: 2090 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_232 
                 SEQ ID 
                 PATENT201612010, 
                 
                   Lachnobacterium 
                 
                 Ascusb_3504 
                 SEQ ID 
                 PATENT201612011, 
               
               
                 (Genus) 
                   
                 NO: 14 
                 PATENT201612011, 
                 (Genus) 
                   
                 NO: 2091 
                 PATENT201612012 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 Lachnospiraceae 
                 Ascusb_252 
                 SEQ ID 
                   
                 
                   Acholeplasma 
                 
                 Ascusb_3881 
                 SEQ ID 
                 PATENT201612007 
               
               
                 incertae sedis 
                   
                 NO: 15 
                   
                 (Genus) 
                   
                 NO: 2092 
               
               
                 (Family) 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_268 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Selenomonas 
                 
                 Ascusb_4728 
                 SEQ ID 
               
               
                 
                   sensu stricto 
                 
                   
                 NO: 16 
                 PATENT201612011, 
                 (Genus) 
                   
                 NO: 2093 
               
               
                 (Genus) 
                   
                   
                 PATENT201612012 
               
               
                 Lachnospiraceae 
                 Ascusb_374 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Prevotella 
                 
                 Ascusb_4934 
                 SEQ ID 
               
               
                 incertae sedis 
                   
                 NO: 17 
                 PATENT201612009, 
                 (Genus) 
                   
                 NO: 2094 
               
               
                 (Family) 
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_411 
                 SEQ ID 
                 PATENT201612007, 
                   Clostridium _XlVa 
                 Ascusb_4959 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 18 
                 PATENT201612011, 
                 (Cluster) 
                   
                 NO: 2095 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Clostridium sensu 
                 
                 Ascusb_546 
                 SEQ ID 
                 PATENT201612013 
                 
                   Succinivibrio 
                 
                 Ascusb_5525 
                 SEQ ID 
               
               
                   stricto  (Genus) 
                   
                 NO: 19 
                   
                 (Genus) 
                   
                 NO: 2096 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_672 
                 SEQ ID 
                   
                 
                   Ruminobacter 
                 
                 Ascusb_12103 
                 SEQ ID 
                 PATENT201612001 
               
               
                 (Genus) 
                   
                 NO: 20 
                   
                 (Genus) 
                   
                 NO: 2097 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_765 
                 SEQ ID 
                 PATENT201612013 
                 
                   Sharpea 
                 
                 Ascusb_14245 
                 SEQ ID 
                 PATENT201612001, 
               
               
                 (Genus) 
                   
                 NO: 21 
                   
                 (Genus) 
                   
                 NO: 2098 
                 PATENT201612008, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PATENT201612013 
               
               
                 
                   Rikenella 
                 
                 Ascusb_812 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Prevotella 
                 
                 Ascusb_14945 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 22 
                 PATENT201612006, 
                 (Genus) 
                   
                 NO: 2099 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Tannerella 
                 
                 Ascusb_1295 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Prevotella 
                 
                 Ascusb_17461 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 23 
                 PATENT201612009, 
                 (Genus) 
                   
                 NO: 2100 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Howardella 
                 
                 Ascusb_1763 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Prevotella 
                 
                 Ascusb_20083 
                 SEQ ID 
                 PATENT201612006 
               
               
                 (Genus) 
                   
                 NO: 24 
                 PATENT201612012 
                 (Genus) 
                   
                 NO: 2101 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1780 
                 SEQ ID 
                 PATENT201612013 
                 
                   Prevotella 
                 
                 Ascusb_20187 
                 SEQ ID 
                 PATENT201612009, 
               
               
                 (Genus) 
                   
                 NO: 25 
                   
                 (Genus) 
                   
                 NO: 2102 
                 PATENT201612011, 
               
               
                   
                   
                   
                   
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_1801 
                 SEQ ID 
                 PATENT201612005 
                 
                   Prevotella 
                 
                 Ascusb_20539 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 26 
                   
                 (Genus) 
                   
                 NO: 2103 
               
               
                 
                   Clostridium sensu 
                 
                 Ascusb_1833 
                 SEQ ID 
                 PATENT201612006, 
                 
                   Piromyces 
                 
                 Ascusf_11 
                 SEQ ID 
               
               
                 
                   stricto 
                 
                   
                 NO: 27 
                 PATENT201612007, 
                 (Genus) 
                   
                 NO: 31 
               
               
                 (Genus) 
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Clostridium sensu 
                 
                 Ascusb_3138 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Candida xylopsoc 
                 
                 Ascusf_15 
                 SEQ ID 
                 NRRL Y-67249, 
               
               
                 
                   stricto 
                 
                   
                 NO: 28 
                 PATENT201612006, 
                 (Genus + Species) 
                   
                 NO: 32 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                   
                 PATENT201612008, 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                 PATENT201612013, 
               
               
                   
                   
                   
                 NRRL B-67248 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_6589 
                 SEQ ID 
                 PATENT201612005 
                 
                   Orpinomyces 
                 
                 Ascusf_22 
                 SEQ ID 
                 PATENT201612002, 
               
               
                 (Genus) 
                   
                 NO: 29 
                   
                 (Genus) 
                   
                 NO: 33 
                 PATENT201612004 
               
               
                 Lachnospiraceae 
                 Ascusb_7921 
                 SEQ ID 
                   
                 
                   Orpinomycs 
                 
                 Ascusf_23 
                 SEQ ID 
                 PATENT201612014 
               
               
                 incertae sedis 
                   
                 NO: 30 
                   
                 (Genus) 
                   
                 NO: 34 
               
               
                 (Family) 
               
               
                 
                   Succinivibrio 
                 
                 Ascusb_11 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Orpinomyces 
                 
                 Ascusf_24 
                 SEQ ID 
                 PATENT201612002, 
               
               
                 (Genus) 
                   
                 NO: 2045 
                 PATENT201612008, 
                 (Genus) 
                   
                 NO: 35 
                 PATENT201612004 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Prevotella 
                 
                 Ascusb_36 
                 SEQ ID 
                 PATENT201612013 
                 
                   Candida apicol 
                 
                 Ascusf_25 
                 SEQ ID 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                 NO: 2046 
                   
                 (Genus + Species) 
                   
                 NO: 36 
               
               
                 
                   Prevotella 
                 
                 Ascusb_67 
                 SEQ ID 
                   
                 
                   Candida rugosa 
                 
                 Ascusf_38 
                 SEQ ID 
                 PATENT201612004 
               
               
                 (Genus) 
                   
                 NO: 2047 
                   
                 (Genus + Species) 
                   
                 NO: 37 
               
               
                 
                   Prevotella 
                 
                 Ascusb_87 
                 SEQ ID 
                   
                 
                   Neocallimastix 
                 
                 Ascusf_45 
                 SEQ ID 
                 PATENT201612002, 
               
               
                 (Genus) 
                   
                 NO: 2048 
                   
                 (Genus) 
                   
                 NO: 38 
                 PATENT201612014 
               
               
                 
                   Ruminobacter 
                 
                 Ascusb_101 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Orpinomyces 
                 
                 Ascusf_60 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2049 
                 PATENT201612005, 
                 (Genus) 
                   
                 NO: 39 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_104 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Orpinomyces 
                 
                 Ascusf_73 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2050 
                 PATENT201612006 
                 (Genus) 
                   
                 NO: 40 
               
               
                 
                   Succinivibrio 
                 
                 Ascusb_125 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Neocallimastix 
                 
                 Ascusf_77 
                 SEQ ID 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                 NO: 2051 
                 PATENT201612005, 
                 (Genus) 
                   
                 NO: 41 
               
               
                   
                   
                   
                 PATENT201612006, 
               
               
                   
                   
                   
                 PATENT201612008, 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 Ascusb_149 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Neocallimastix 
                 
                 Ascusf_94 
                 SEQ ID 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                 NO: 2052 
                 PATENT201612008, 
                 (Genus) 
                   
                 NO: 42 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                 PATENT201612013 
               
               
                 
                   Prevotella 
                 
                 Ascusb_159 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Ascomycota 
                 
                 Ascusf_95 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2053 
                 PATENT201612006, 
                 (Genus) 
                   
                 NO: 43 
               
               
                   
                   
                   
                 PATENT201612007, 
               
               
                   
                   
                   
                 PATENT201612008, 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Prevotella 
                 
                 Ascusb_183 
                 SEQ ID 
                 PATENT201612008, 
                 
                   Piromyces 
                 
                 Ascusf_108 
                 SEQ ID 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                 NO: 2054 
                 PATENT201612009 
                 (Genus) 
                   
                 NO: 44 
               
               
                 
                   Prevotella 
                 
                 Ascusb_187 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Orpinomyces 
                 
                 Ascusf_119 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2055 
                 PATENT201612008, 
                 (Genus) 
                   
                 NO: 45 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Prevotella 
                 
                 Ascusb_190 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Cyllamyces 
                 
                 Ascusf_127 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2056 
                 PATENT201612006, 
                 (Genus) 
                   
                 NO: 46 
               
               
                   
                   
                   
                 PATENT201612007, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 Lachnospiraceae 
                 Ascusb_199 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Piromyces 
                 
                 Ascusf_136 
                 SEQ ID 
               
               
                 incertae sedis 
                   
                 NO: 2057 
                 PATENT201612012 
                 (Genus) 
                   
                 NO: 47 
               
               
                 (Family) 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_278 
                 SEQ ID 
                 PATENT201612008 
                 
                   Cyllamyces 
                 
                 Ascusf_193 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2058 
                   
                 (Genus) 
                   
                 NO: 48 
               
               
                 
                   Ruminobacter 
                 
                 Ascusb_329 
                 SEQ ID 
                 PATENT201612010 
                 
                   Piromyces 
                 
                 Ascusf_228 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2059 
                   
                 (Genus) 
                   
                 NO: 49 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_368 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Piromyces 
                 
                 Ascusf_249 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2060 
                 PATENT201612012 
                 (Genus) 
                   
                 NO: 50 
               
               
                   Clostridium _XlVa 
                 Ascusb_469 
                 SEQ ID 
                   
                 
                   Neocallimastix 
                 
                 Ascusf_307 
                 SEQ ID 
                 PATENT201612002, 
               
               
                 (Cluster) 
                   
                 NO: 2061 
                   
                 (Genus) 
                   
                 NO: 51 
                 PATENT201612014 
               
               
                 
                   Prevotella 
                 
                 Ascusb_530 
                 SEQ ID 
                   
                 
                   Piromyces 
                 
                 Ascusf_315 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2062 
                   
                 (Genus) 
                   
                 NO: 52 
               
               
                 
                   Prevotella 
                 
                 Ascusb_728 
                 SEQ ID 
                 PATENT201612008, 
                 
                   Neocallimastix 
                 
                 Ascusf_334 
                 SEQ ID 
                 PATENT201612014 
               
               
                 (Genus) 
                   
                 NO: 2063 
                 PATENT201612009, 
                 (Genus) 
                   
                 NO: 53 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                 PATENT201612013 
               
               
                 Lachnospiraceae 
                 Ascusb_756 
                 SEQ ID 
                   
                 Saccharomycetales 
                 Ascusf_353 
                 SEQ ID 
                 PATENT201612014 
               
               
                 incertae sedis 
                   
                 NO: 2064 
                   
                 (Order) 
                   
                 NO: 54 
               
               
                 (Family) 
               
               
                 
                   Roseburia 
                 
                 Ascusb_810 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Piromyces 
                 
                 Ascusf_448 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2065 
                 PATENT201612012 
                 (Genus) 
                   
                 NO: 55 
               
               
                 Lachnospiraceae 
                 Ascusb_817 
                 SEQ ID 
                 PATENT201612001, 
                 
                   Orpinomyces 
                 
                 Ascusf_786 
                 SEQ ID 
               
               
                 incertae sedis 
                   
                 NO: 2066 
                 PATENT201612006, 
                 (Genus) 
                   
                 NO: 56 
               
               
                 (Family) 
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612012, 
               
               
                   
                   
                   
                 PATENT201612013, 
               
               
                   
                   
                   
                 NRRL B-67349 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_826 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Piromyces 
                 
                 Ascusf_836 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2067 
                 PATENT201612012, 
                 (Genus) 
                   
                 NO: 57 
               
               
                   
                   
                   
                 PATENT201612013, 
               
               
                   
                   
                   
                 NRRL B-67347 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 Ascusb_880 
                 SEQ ID 
                 PATENT201612008, 
                 
                   Phyllosticta 
                 
                 Ascusf_923 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2068 
                 PATENT201612009 
                 
                   capitalensis 
                 
                   
                 NO: 58 
               
               
                   
                   
                   
                   
                 (Genus + Species) 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_913 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Orpinomyces 
                 
                 Ascusf_1020 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2069 
                 PATENT201612008, 
                 (Genus) 
                   
                 NO: 59 
               
               
                   
                   
                   
                 PATENT201612009, 
               
               
                   
                   
                   
                 PATENT201612010, 
               
               
                   
                   
                   
                 PATENT201612011, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 Lachnospiraceae 
                 Ascusb_974 
                 SEQ ID 
                 PATENT201612013 
                 
                   Orpinomyces 
                 
                 Ascusf_1103 
                 SEQ ID 
               
               
                 incertae sedis 
                   
                 NO: 2070 
                   
                 (Genus) 
                   
                 NO: 60 
               
               
                 (Family) 
               
               
                 
                   Pseudobutyrivibrio 
                 
                 Ascusb_1069 
                 SEQ ID 
                 PATENT201612011, 
                 
                   Orpinomyces 
                 
                 Ascusf_81 
                 SEQ ID 
               
               
                 (Genus) 
                   
                 NO: 2071 
                 PATENT201612012, 
                 (Genus) 
                   
                 NO: 2104 
               
               
                   
                   
                   
                 NRRL B-67348 
               
               
                 
                   Anaerolinea 
                 
                 Ascusb_1074 
                 SEQ ID 
                 PATENT201612005, 
                 
                   Piromyces 
                 
                 Ascusf_206 
                 SEQ ID 
                 PATENT201612003 
               
               
                 (Genus) 
                   
                 NO: 2072 
                 PATENT201612007, 
                 (Genus) 
                   
                 NO: 2105 
               
               
                   
                   
                   
                 PATENT201612008, 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1293 
                 SEQ ID 
                   
                 
                   Piromyces 
                 
                 Ascusf_208 
                 SEQ ID 
                 PATENT201612003 
               
               
                 (Genus) 
                   
                 NO: 2073 
                   
                 (Genus) 
                   
                 NO: 2106 
               
               
                 
                   Propionibacterium 
                 
                 Ascusb_1367 
                 SEQ ID 
                 PATENT201612007, 
                 
                   Piromyces 
                 
                 Ascusf_1012 
                 SEQ ID 
                 PATENT201612003 
               
               
                 (Genus) 
                   
                 NO: 2074 
                 PATENT201612009, 
                 (Genus) 
                   
                 NO: 2107 
               
               
                   
                   
                   
                 PATENT201612012 
               
               
                   Clostridium _XIVa 
                 Ascusb_1632 
                 SEQ ID 
                 PATENT201612011, 
               
               
                 (Cluster) 
                   
                 NO: 2075 
                 PATENT201612012 
               
               
                 
                   Olsenella 
                 
                 Ascusb_1674 
                 SEQ ID 
                 PATENT201612001, 
               
               
                 (Genus) 
                   
                 NO: 2076 
                 PATENT201612009 
               
               
                   
               
               
                   1 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   2 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   3 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   4 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Bacteria of the present disclosure. 
               
            
           
           
               
               
               
            
               
                 Predicted Closest 
                   
                   
               
               
                 Taxa of Isolated 
                 Strain 
                 Sequence 
               
               
                 Microbes 
                 Designation 
                 Identifier 
               
               
                   
               
            
           
           
               
               
               
            
               
                 
                   Corynebacterium 
                 
                 Ascusb_3 
                 61 
               
               
                 
                   Prevotella 
                 
                 Ascusb_50 
                 62 
               
               
                 
                   Comamonas 
                 
                 Ascusb_90 
                 63 
               
               
                   Clostridium _XlVa 
                 Ascusb_117 
                 64 
               
               
                 
                   Hippea 
                 
                 Ascusb_171 
                 65 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_177 
                 66 
               
               
                   Clostridium _XlVa 
                 Ascusb_179 
                 67 
               
               
                 
                   Rummeliibacillus 
                 
                 Ascusb_224 
                 68 
               
               
                   Clostridium _XlVa 
                 Ascusb_234 
                 69 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_274 
                 70 
               
               
                 
                   Prevotella 
                 
                 Ascusb_276 
                 71 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_293 
                 72 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_327 
                 73 
               
               
                 
                   Prevotella 
                 
                 Ascusb_337 
                 74 
               
               
                   Clostridium _XlVa 
                 Ascusb_357 
                 75 
               
               
                   Clostridium _XlVa 
                 Ascusb_357 
                 76 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_361 
                 77 
               
               
                 
                   Pyramidobacter 
                 
                 Ascusb_388 
                 78 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_425 
                 79 
               
               
                 
                   Prevotella 
                 
                 Ascusb_444 
                 80 
               
               
                   Clostridium _XlVa 
                 Ascusb_456 
                 81 
               
               
                 
                   Prevotella 
                 
                 Ascusb_492 
                 82 
               
               
                 
                   Roseburia 
                 
                 Ascusb_523 
                 83 
               
               
                   Clostridium _XlVa 
                 Ascusb_526 
                 84 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_570 
                 85 
               
               
                   Clostridium _XlVa 
                 Ascusb_584 
                 86 
               
               
                 
                   Acidothermus 
                 
                 Ascusb_605 
                 87 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_606 
                 88 
               
               
                 
                   Prevotella 
                 
                 Ascusb_617 
                 89 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_635 
                 90 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_642 
                 91 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_647 
                 92 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_656 
                 93 
               
               
                 
                   Prevotella 
                 
                 Ascusb_669 
                 94 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_681 
                 95 
               
               
                   Clostridium _III 
                 Ascusb_704 
                 96 
               
               
                 
                   Prevotella 
                 
                 Ascusb_706 
                 97 
               
               
                 
                   Acinetobacter 
                 
                 Ascusb_717 
                 98 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_752 
                 99 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_790 
                 100 
               
               
                   Clostridium _XlVa 
                 Ascusb_797 
                 101 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_802 
                 102 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_805 
                 103 
               
               
                 
                   Prevotella 
                 
                 Ascusb_828 
                 104 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_890 
                 105 
               
               
                 
                   Prevotella 
                 
                 Ascusb_909 
                 106 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_924 
                 107 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_955 
                 108 
               
               
                 
                   Prevotella 
                 
                 Ascusb_958 
                 109 
               
               
                   Clostridium _XlVa 
                 Ascusb_980 
                 110 
               
               
                 
                   Prevotella 
                 
                 Ascusb_982 
                 111 
               
               
                 
                   Catonella 
                 
                 Ascusb_990 
                 112 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_993 
                 113 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_1013 
                 114 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1021 
                 115 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1033 
                 116 
               
               
                   Clostridium _XlVa 
                 Ascusb_1090 
                 117 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1108 
                 118 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1113 
                 119 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_1114 
                 120 
               
               
                 
                   Asteroleplasma 
                 
                 Ascusb_1116 
                 121 
               
               
                   Clostridium _XlVa 
                 Ascusb_1118 
                 122 
               
               
                 
                   Caulobacter 
                 
                 Ascusb_1123 
                 123 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1128 
                 124 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1152 
                 125 
               
               
                   Clostridium _XlVa 
                 Ascusb_1166 
                 126 
               
               
                 
                   Acinetobacter 
                 
                 Ascusb_1170 
                 127 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1176 
                 128 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_1182 
                 129 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1199 
                 130 
               
               
                   Clostridium _XlVa 
                 Ascusb_1201 
                 131 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1218 
                 132 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1239 
                 133 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_1269 
                 134 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_1296 
                 135 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_1296 
                 136 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1298 
                 137 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1304 
                 138 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1320 
                 139 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1330 
                 140 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_955 
                 108 
               
               
                 
                   Prevotella 
                 
                 Ascusb_958 
                 109 
               
               
                   Clostridium _XlVa 
                 Ascusb_980 
                 110 
               
               
                 
                   Prevotella 
                 
                 Ascusb_982 
                 111 
               
               
                 
                   Catonella 
                 
                 Ascusb_990 
                 112 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_993 
                 113 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_1013 
                 114 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1021 
                 115 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1033 
                 116 
               
               
                   Clostridium _XlVa 
                 Ascusb_1090 
                 117 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1108 
                 118 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1113 
                 119 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_1114 
                 120 
               
               
                 
                   Asteroleplasma 
                 
                 Ascusb_1116 
                 121 
               
               
                   Clostridium _XlVa 
                 Ascusb_1118 
                 122 
               
               
                 
                   Caulobacter 
                 
                 Ascusb_1123 
                 123 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1128 
                 124 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1152 
                 125 
               
               
                   Clostridium _XlVa 
                 Ascusb_1166 
                 126 
               
               
                 
                   Acinetobacter 
                 
                 Ascusb_1170 
                 127 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1176 
                 128 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_1182 
                 129 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1199 
                 130 
               
               
                   Clostridium _XlVa 
                 Ascusb_1201 
                 131 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1218 
                 132 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_1239 
                 133 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_1269 
                 134 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_1296 
                 135 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_1296 
                 136 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1298 
                 137 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_1304 
                 138 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1320 
                 139 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1330 
                 140 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_1336 
                 141 
               
               
                 
                   Atopobium 
                 
                 Ascusb_1341 
                 142 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_1347 
                 143 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_1355 
                 144 
               
               
                 
                   Neisseria 
                 
                 Ascusb_1357 
                 145 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_1362 
                 146 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1364 
                 147 
               
               
                 
                   Slackia 
                 
                 Ascusb_1389 
                 148 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1400 
                 149 
               
               
                   Clostridium _XlVa 
                 Ascusb_1410 
                 150 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1417 
                 151 
               
               
                 
                   Anaerorhabdus 
                 
                 Ascusb_1426 
                 152 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1433 
                 153 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1439 
                 154 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_1440 
                 155 
               
               
                 
                   Atopobium 
                 
                 Ascusb_1468 
                 156 
               
               
                 
                   Streptophyta 
                 
                 Ascusb_1473 
                 157 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1485 
                 158 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1490 
                 159 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1492 
                 160 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1528 
                 161 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_1538 
                 162 
               
               
                 
                   Rhodocista 
                 
                 Ascusb_1543 
                 163 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1546 
                 164 
               
               
                   Clostridium _XlVa 
                 Ascusb_1553 
                 165 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1554 
                 166 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1571 
                 167 
               
               
                 
                   Streptophyta 
                 
                 Ascusb_1578 
                 168 
               
               
                 
                   Ochrobactrum 
                 
                 Ascusb_1580 
                 169 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_1591 
                 170 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_1600 
                 171 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1609 
                 172 
               
               
                 
                   Riemerella 
                 
                 Ascusb_1627 
                 173 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1640 
                 174 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1645 
                 175 
               
               
                 
                   Slackia 
                 
                 Ascusb_1647 
                 176 
               
               
                   Clostridium _IV 
                 Ascusb_1656 
                 177 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_1659 
                 178 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1667 
                 179 
               
               
                 
                   Treponema 
                 
                 Ascusb_1689 
                 180 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1708 
                 181 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_1723 
                 182 
               
               
                 
                   Prevotella 
                 
                 Ascusb_1727 
                 183 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_1739 
                 184 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_1773 
                 185 
               
               
                   Clostridium _XlVa 
                 Ascusb_1793 
                 186 
               
               
                 
                   Alkaliphilus 
                 
                 Ascusb_1795 
                 187 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_1797 
                 188 
               
               
                   Clostridium _XlVa 
                 Ascusb_1806 
                 189 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_1819 
                 190 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_1835 
                 191 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1886 
                 192 
               
               
                 
                   Lentisphaera 
                 
                 Ascusb_1901 
                 193 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_1905 
                 194 
               
               
                 
                   Roseburia 
                 
                 Ascusb_1918 
                 195 
               
               
                   Clostridium _IV 
                 Ascusb_1922 
                 196 
               
               
                 
                   Hahella 
                 
                 Ascusb_1947 
                 197 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_1969 
                 198 
               
               
                   Clostridium _IV 
                 Ascusb_2016 
                 199 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2024 
                 200 
               
               
                   Clostridium _IV 
                 Ascusb_2058 
                 201 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_2081 
                 202 
               
               
                 
                   Sphingobacterium 
                 
                 Ascusb_2101 
                 203 
               
               
                 
                   Roseburia 
                 
                 Ascusb_2105 
                 204 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_2131 
                 205 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_2141 
                 206 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2156 
                 207 
               
               
                 
                   Asteroleplasma 
                 
                 Ascusb_2168 
                 208 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_2182 
                 209 
               
               
                 
                   Victivallis 
                 
                 Ascusb_2199 
                 210 
               
               
                 
                   Lachnobacterium 
                 
                 Ascusb_2210 
                 211 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_2211 
                 212 
               
               
                   Clostridium _IV 
                 Ascusb_2218 
                 213 
               
               
                 
                   Anaerorhabdus 
                 
                 Ascusb_2221 
                 214 
               
               
                 
                   Altererythrobacter 
                 
                 Ascusb_2236 
                 215 
               
               
                   Clostridium _XlVa 
                 Ascusb_2246 
                 216 
               
               
                   Clostridium _XlVa 
                 Ascusb_2263 
                 217 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_2264 
                 218 
               
               
                 
                   Bifidobacterium 
                 
                 Ascusb_2308 
                 219 
               
               
                   Clostridium _XlVa 
                 Ascusb_2322 
                 220 
               
               
                   Clostridium _XlVa 
                 Ascusb_2323 
                 221 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_2332 
                 222 
               
               
                   Clostridium _XlVa 
                 Ascusb_2353 
                 223 
               
               
                 
                   Nitrobacter 
                 
                 Ascusb_2375 
                 224 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_2414 
                 225 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_2429 
                 226 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_2435 
                 227 
               
               
                 
                   Nautilia 
                 
                 Ascusb_2437 
                 228 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_2447 
                 229 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_2452 
                 230 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_2461 
                 231 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_2462 
                 232 
               
               
                 
                   Rikenella 
                 
                 Ascusb_2470 
                 233 
               
               
                   Clostridium _XlVa 
                 Ascusb_2482 
                 234 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_2487 
                 235 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_2492 
                 236 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2503 
                 237 
               
               
                 
                   Haematobacter 
                 
                 Ascusb_2504 
                 238 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2523 
                 239 
               
               
                   Clostridium _XlVa 
                 Ascusb_2537 
                 240 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_2538 
                 241 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_2565 
                 242 
               
               
                 
                   Blautia 
                 
                 Ascusb_2591 
                 243 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_2592 
                 244 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_2607 
                 245 
               
               
                   Clostridium _XlVa 
                 Ascusb_2608 
                 246 
               
               
                 
                   Atopobium 
                 
                 Ascusb_2613 
                 247 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_2626 
                 248 
               
               
                   Clostridium _XlVa 
                 Ascusb_2629 
                 249 
               
               
                 Candidate Phylum OD1 
                 Ascusb_2643 
                 250 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_2645 
                 251 
               
               
                   Clostridium _XlVa 
                 Ascusb_2647 
                 252 
               
               
                   Clostridium _IV 
                 Ascusb_2649 
                 253 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_2653 
                 254 
               
               
                 
                   Roseburia 
                 
                 Ascusb_2663 
                 255 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_2671 
                 256 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_2696 
                 257 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_2712 
                 258 
               
               
                   Clostridium _XlVa 
                 Ascusb_2713 
                 259 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_2730 
                 260 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_2746 
                 261 
               
               
                 
                   Wautersiella 
                 
                 Ascusb_2757 
                 262 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_2762 
                 263 
               
               
                 
                   Planctomyces 
                 
                 Ascusb_2764 
                 264 
               
               
                 
                   Treponema 
                 
                 Ascusb_2800 
                 265 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_2806 
                 266 
               
               
                 
                   Paracoccus 
                 
                 Ascusb_2809 
                 267 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_2811 
                 268 
               
               
                 
                   Atopobium 
                 
                 Ascusb_2814 
                 269 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2825 
                 270 
               
               
                   Clostridium _IV 
                 Ascusb_2832 
                 271 
               
               
                   Clostridium _XlVa 
                 Ascusb_2838 
                 272 
               
               
                   Clostridium _XlVa 
                 Ascusb_2843 
                 273 
               
               
                   Clostridium _XlVa 
                 Ascusb_2853 
                 274 
               
               
                 
                   Prevotella 
                 
                 Ascusb_2857 
                 275 
               
               
                 
                   Dethiosulfovibrio 
                 
                 Ascusb_2872 
                 276 
               
               
                   Clostridium _XI 
                 Ascusb_2885 
                 277 
               
               
                   Clostridium _IV 
                 Ascusb_2907 
                 278 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_2909 
                 279 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_2912 
                 280 
               
               
                 
                   Roseburia 
                 
                 Ascusb_2914 
                 281 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_2930 
                 282 
               
               
                 Candidate phylum SR1 
                 Ascusb_2946 
                 283 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_2948 
                 284 
               
               
                 
                   Victivallis 
                 
                 Ascusb_2966 
                 285 
               
               
                   Clostridium _IV 
                 Ascusb_2983 
                 286 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_2988 
                 287 
               
               
                   Clostridium _XlVa 
                 Ascusb_2990 
                 288 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_3005 
                 289 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_3008 
                 290 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_3010 
                 291 
               
               
                   Clostridium _XlVa 
                 Ascusb_3022 
                 292 
               
               
                   Clostridium _XlVb 
                 Ascusb_3029 
                 293 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_3053 
                 294 
               
               
                 
                   Bartonella 
                 
                 Ascusb_3056 
                 295 
               
               
                   Clostridium _IV 
                 Ascusb_3058 
                 296 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_3061 
                 297 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_3066 
                 298 
               
               
                   Clostridium _IV 
                 Ascusb_3073 
                 299 
               
               
                 
                   Blautia 
                 
                 Ascusb_3074 
                 300 
               
               
                 
                   Prevotella 
                 
                 Ascusb_3079 
                 301 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_3087 
                 302 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_3120 
                 303 
               
               
                 
                   Treponema 
                 
                 Ascusb_3142 
                 304 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_3147 
                 305 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_3161 
                 306 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_3163 
                 307 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_3165 
                 308 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_3188 
                 309 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_3197 
                 310 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_3213 
                 311 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_3225 
                 312 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_3229 
                 313 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_3240 
                 314 
               
               
                   Clostridium _XlVa 
                 Ascusb_3242 
                 315 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_3248 
                 316 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_3263 
                 317 
               
               
                 
                   Agaricicola 
                 
                 Ascusb_3275 
                 318 
               
               
                 
                   Denitrobacterium 
                 
                 Ascusb_3285 
                 319 
               
               
                 
                   Armatimonadetes 
                 
                 Ascusb_3299 
                 320 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_3304 
                 321 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_3322 
                 322 
               
               
                 
                   Prevotella 
                 
                 Ascusb_3333 
                 323 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_3339 
                 324 
               
               
                   Clostridium _IV 
                 Ascusb_3351 
                 325 
               
               
                 
                   Streptococcus 
                 
                 Ascusb_3376 
                 326 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_3393 
                 327 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_3405 
                 328 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_3408 
                 329 
               
               
                 
                   Treponema 
                 
                 Ascusb_3415 
                 330 
               
               
                 
                   Roseburia 
                 
                 Ascusb_3417 
                 331 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3422 
                 332 
               
               
                 
                   Prevotella 
                 
                 Ascusb_3424 
                 333 
               
               
                 
                   Roseburia 
                 
                 Ascusb_3446 
                 334 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_3451 
                 335 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_3456 
                 336 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_3467 
                 337 
               
               
                 
                   Prevotella 
                 
                 Ascusb_3479 
                 338 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_3480 
                 339 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3481 
                 340 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_3482 
                 341 
               
               
                 
                   Treponema 
                 
                 Ascusb_3483 
                 342 
               
               
                 
                   Stenotrophomonas 
                 
                 Ascusb_3484 
                 343 
               
               
                   
                 Ascusb_3492 
                 344 
               
               
                   Clostridium _XlVa 
                 Ascusb_3494 
                 345 
               
               
                 
                   Sphingobium 
                 
                 Ascusb_3495 
                 346 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_3512 
                 347 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_3518 
                 348 
               
               
                 
                   Methylobacterium 
                 
                 Ascusb_3523 
                 349 
               
               
                 
                   Zhangella 
                 
                 Ascusb_3530 
                 350 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_3545 
                 351 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_3546 
                 352 
               
               
                   Clostridium _III 
                 Ascusb_3548 
                 353 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_3563 
                 354 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_3575 
                 355 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_3578 
                 356 
               
               
                   Clostridium _XlVa 
                 Ascusb_3587 
                 357 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_3592 
                 358 
               
               
                   Clostridium _IV 
                 Ascusb_3600 
                 359 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_3602 
                 360 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3638 
                 361 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_3642 
                 362 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_3647 
                 363 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_3674 
                 364 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_3687 
                 365 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_3700 
                 366 
               
               
                 
                   Acinetobacter 
                 
                 Ascusb_3717 
                 367 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3724 
                 368 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3725 
                 369 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_3728 
                 370 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_3746 
                 371 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_3748 
                 372 
               
               
                 
                   Dethiosulfovibrio 
                 
                 Ascusb_3750 
                 373 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_3751 
                 374 
               
               
                   Clostridium _IV 
                 Ascusb_3762 
                 375 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_3763 
                 376 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_3768 
                 377 
               
               
                 
                   Herbiconiux 
                 
                 Ascusb_3775 
                 378 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_3779 
                 379 
               
               
                 
                   Armatimonadetes 
                 
                 Ascusb_3789 
                 380 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_3796 
                 381 
               
               
                   Clostridium _IV 
                 Ascusb_3811 
                 382 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_3825 
                 383 
               
               
                   Clostridium _IV 
                 Ascusb_3838 
                 384 
               
               
                 
                   Roseburia 
                 
                 Ascusb_3849 
                 385 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_3866 
                 386 
               
               
                   Clostridium _III 
                 Ascusb_3875 
                 387 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_3903 
                 388 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_3911 
                 389 
               
               
                 
                   Prevotella 
                 
                 Ascusb_3914 
                 390 
               
               
                   Clostridium _XlVa 
                 Ascusb_3919 
                 391 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_3950 
                 392 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_3952 
                 393 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_3970 
                 394 
               
               
                 
                   Victivallis 
                 
                 Ascusb_3982 
                 395 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_4008 
                 396 
               
               
                   Clostridium _XlVb 
                 Ascusb_4019 
                 397 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4033 
                 398 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_4034 
                 399 
               
               
                 
                   Pelobacter 
                 
                 Ascusb_4040 
                 400 
               
               
                   Clostridium _XlVa 
                 Ascusb_4063 
                 401 
               
               
                   Clostridium _XlVa 
                 Ascusb_4067 
                 402 
               
               
                   Clostridium _XlVb 
                 Ascusb_4083 
                 403 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_4085 
                 404 
               
               
                   Clostridium _IV 
                 Ascusb_4086 
                 405 
               
               
                   Clostridium _IV 
                 Ascusb_4095 
                 406 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_4114 
                 407 
               
               
                 
                   Victivallis 
                 
                 Ascusb_4115 
                 408 
               
               
                   Clostridium _III 
                 Ascusb_4118 
                 409 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_4120 
                 410 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4124 
                 411 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_4142 
                 412 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4143 
                 413 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_4149 
                 414 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_4155 
                 415 
               
               
                 
                   Acetanaerobacterium 
                 
                 Ascusb_4156 
                 416 
               
               
                   Clostridium _XlVa 
                 Ascusb_4159 
                 417 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_4161 
                 418 
               
               
                   Clostridium _XlVa 
                 Ascusb_4167 
                 419 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_4171 
                 420 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_4172 
                 421 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4176 
                 422 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_4179 
                 423 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_4188 
                 424 
               
               
                 
                   Alkaliphilus 
                 
                 Ascusb_4213 
                 425 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_4215 
                 426 
               
               
                 
                   Hippea 
                 
                 Ascusb_4217 
                 427 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4223 
                 428 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4237 
                 429 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_4241 
                 430 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_4265 
                 431 
               
               
                 
                   Paraeggerthella 
                 
                 Ascusb_4266 
                 432 
               
               
                   Clostridium _XlVa 
                 Ascusb_4277 
                 433 
               
               
                   Clostridium _XlVa 
                 Ascusb_4279 
                 434 
               
               
                   Clostridium _IV 
                 Ascusb_4281 
                 435 
               
               
                   Clostridium _XlVa 
                 Ascusb_4292 
                 436 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_4313 
                 437 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_4316 
                 438 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_4317 
                 439 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_4326 
                 440 
               
               
                   Clostridium _IV 
                 Ascusb_4332 
                 441 
               
               
                   Clostridium _IV 
                 Ascusb_4345 
                 442 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_4347 
                 443 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_4375 
                 444 
               
               
                 
                   Sharpea 
                 
                 Ascusb_4380 
                 445 
               
               
                   Clostridium _IV 
                 Ascusb_4394 
                 446 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4416 
                 447 
               
               
                 
                   Blautia 
                 
                 Ascusb_4421 
                 448 
               
               
                   Clostridium _XlVa 
                 Ascusb_4422 
                 449 
               
               
                   Clostridium _IV 
                 Ascusb_4432 
                 450 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4433 
                 451 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_4434 
                 452 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_4442 
                 453 
               
               
                 
                   Aquiflexum 
                 
                 Ascusb_4449 
                 454 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_4450 
                 455 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_4457 
                 456 
               
               
                 
                   Pelomonas 
                 
                 Ascusb_4468 
                 457 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_4469 
                 458 
               
               
                 
                   Paracoccus 
                 
                 Ascusb_4479 
                 459 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_4486 
                 460 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_4496 
                 461 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_4505 
                 462 
               
               
                   Clostridium _IV 
                 Ascusb_4517 
                 463 
               
               
                 
                   Bacillus 
                 
                 Ascusb_4522 
                 464 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_4537 
                 465 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_4545 
                 466 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4548 
                 467 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_4556 
                 468 
               
               
                 
                   Herbiconiux 
                 
                 Ascusb_4559 
                 469 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_4560 
                 470 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_4563 
                 471 
               
               
                 
                   Anaerorhabdus 
                 
                 Ascusb_4566 
                 472 
               
               
                 
                   Victivallis 
                 
                 Ascusb_4569 
                 473 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4573 
                 474 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4579 
                 475 
               
               
                 
                   Aquiflexum 
                 
                 Ascusb_4606 
                 476 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_4618 
                 477 
               
               
                 
                   Altererythrobacter 
                 
                 Ascusb_4626 
                 478 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_4627 
                 479 
               
               
                   Clostridium _III 
                 Ascusb_4634 
                 480 
               
               
                   Clostridium _XlVb 
                 Ascusb_4639 
                 481 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_4644 
                 482 
               
               
                 
                   Roseburia 
                 
                 Ascusb_4652 
                 483 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_4657 
                 484 
               
               
                 
                   Planctomyces 
                 
                 Ascusb_4676 
                 485 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_4679 
                 486 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_4695 
                 487 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_4696 
                 488 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_4700 
                 489 
               
               
                 
                   Rummeliibacillus 
                 
                 Ascusb_4701 
                 490 
               
               
                   Clostridium _XlVa 
                 Ascusb_4716 
                 491 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_4731 
                 492 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_4737 
                 493 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_4738 
                 494 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_4758 
                 495 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_4763 
                 496 
               
               
                 
                   Paraeggerthella 
                 
                 Ascusb_4795 
                 497 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_4800 
                 498 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_4805 
                 499 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4820 
                 500 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_4828 
                 501 
               
               
                 
                   Streptococcus 
                 
                 Ascusb_4852 
                 502 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_4859 
                 503 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4861 
                 504 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4867 
                 505 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4873 
                 506 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_4882 
                 507 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4886 
                 508 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_4893 
                 509 
               
               
                   Clostridium _XlVa 
                 Ascusb_4897 
                 510 
               
               
                 
                   Atopobium 
                 
                 Ascusb_4945 
                 511 
               
               
                 
                   Prevotella 
                 
                 Ascusb_4969 
                 512 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_4972 
                 513 
               
               
                   Clostridium _XlVa 
                 Ascusb_4976 
                 514 
               
               
                   Clostridium _XlVa 
                 Ascusb_4997 
                 515 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_4999 
                 516 
               
               
                 
                   Blautia 
                 
                 Ascusb_5000 
                 517 
               
               
                 
                   Vampirovibrio 
                 
                 Ascusb_5006 
                 518 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_5040 
                 519 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_5058 
                 520 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5060 
                 521 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_5065 
                 522 
               
               
                 
                   Acidobacteria 
                 
                 Ascusb_5069 
                 523 
               
               
                   Clostridium _XlVa 
                 Ascusb_5081 
                 524 
               
               
                   Clostridium _XlVa 
                 Ascusb_5089 
                 525 
               
               
                   Clostridium _XlVa 
                 Ascusb_5095 
                 526 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_5103 
                 527 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5113 
                 528 
               
               
                 
                   Syntrophomonas 
                 
                 Ascusb_5137 
                 529 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_5144 
                 530 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_5165 
                 531 
               
               
                   Clostridium _III 
                 Ascusb_5171 
                 532 
               
               
                 
                   Flavobacterium 
                 
                 Ascusb_5181 
                 533 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_5191 
                 534 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5194 
                 535 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_5197 
                 536 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5198 
                 537 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5206 
                 538 
               
               
                   Clostridium _XlVa 
                 Ascusb_5223 
                 539 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_5225 
                 540 
               
               
                 
                   Blautia 
                 
                 Ascusb_5235 
                 541 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_5247 
                 542 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_5252 
                 543 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5253 
                 544 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_5255 
                 545 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5267 
                 546 
               
               
                 
                   Treponema 
                 
                 Ascusb_5280 
                 547 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_5281 
                 548 
               
               
                   Clostridium _XlVa 
                 Ascusb_5289 
                 549 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_5292 
                 550 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_5294 
                 551 
               
               
                   Clostridium _XlVa 
                 Ascusb_5295 
                 552 
               
               
                   Clostridium _III 
                 Ascusb_5301 
                 553 
               
               
                   Clostridium _IV 
                 Ascusb_5313 
                 554 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5324 
                 555 
               
               
                   Clostridium _XlVa 
                 Ascusb_5326 
                 556 
               
               
                   Clostridium _XI 
                 Ascusb_5335 
                 557 
               
               
                   Clostridium _XlVa 
                 Ascusb_5336 
                 558 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_5338 
                 559 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5342 
                 560 
               
               
                   Clostridium _IV 
                 Ascusb_5352 
                 561 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5353 
                 562 
               
               
                   Clostridium _IV 
                 Ascusb_5354 
                 563 
               
               
                 
                   Faecalibacterium 
                 
                 Ascusb_5360 
                 564 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_5368 
                 565 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_5397 
                 566 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_5411 
                 567 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_5422 
                 568 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5429 
                 569 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5440 
                 570 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_5441 
                 571 
               
               
                   Clostridium _IV 
                 Ascusb_5443 
                 572 
               
               
                 
                   Victivallis 
                 
                 Ascusb_5451 
                 573 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_5456 
                 574 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_5463 
                 575 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_5481 
                 576 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5485 
                 577 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_5495 
                 578 
               
               
                   Clostridium _IV 
                 Ascusb_5509 
                 579 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5510 
                 580 
               
               
                 
                   Victivallis 
                 
                 Ascusb_5512 
                 581 
               
               
                   Clostridium _XlVa 
                 Ascusb_5515 
                 582 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_5517 
                 583 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5530 
                 584 
               
               
                   Clostridium _XlVa 
                 Ascusb_5536 
                 585 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_5554 
                 586 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_5584 
                 587 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_5592 
                 588 
               
               
                 
                   Armatimonadetes 
                 
                 Ascusb_5609 
                 589 
               
               
                   Clostridium _XlVa 
                 Ascusb_5612 
                 590 
               
               
                 
                   Victivallis 
                 
                 Ascusb_5623 
                 591 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_5628 
                 592 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_5647 
                 593 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5650 
                 594 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5652 
                 595 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_5660 
                 596 
               
               
                   Clostridium _III 
                 Ascusb_5686 
                 597 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_5689 
                 598 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_5691 
                 599 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_5694 
                 600 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_5716 
                 601 
               
               
                 
                   Roseburia 
                 
                 Ascusb_5725 
                 602 
               
               
                   Clostridium _XlVa 
                 Ascusb_5738 
                 603 
               
               
                 
                   Anaerofustis 
                 
                 Ascusb_5746 
                 604 
               
               
                 
                   Succiniclasticum 
                 
                 Ascusb_5765 
                 605 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_5770 
                 606 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_5777 
                 607 
               
               
                   Escherichia / Shigella   
                 Ascusb_5789 
                 608 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5812 
                 609 
               
               
                   Clostridium _XlVa 
                 Ascusb_5830 
                 610 
               
               
                   Clostridium _XlVa 
                 Ascusb_5838 
                 611 
               
               
                   Clostridium _IV 
                 Ascusb_5841 
                 612 
               
               
                   Clostridium _III 
                 Ascusb_5845 
                 613 
               
               
                 
                   Prevotella 
                 
                 Ascusb_5847 
                 614 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_5849 
                 615 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_5858 
                 616 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_5862 
                 617 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5868 
                 618 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_5869 
                 619 
               
               
                 
                   Solobacterium 
                 
                 Ascusb_5870 
                 620 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5874 
                 621 
               
               
                   Clostridium _III 
                 Ascusb_5877 
                 622 
               
               
                 
                   Victivallis 
                 
                 Ascusb_5879 
                 623 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_5884 
                 624 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_5889 
                 625 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_5894 
                 626 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_5895 
                 627 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_5913 
                 628 
               
               
                   Clostridium _III 
                 Ascusb_5926 
                 629 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_5934 
                 630 
               
               
                 
                   Treponema 
                 
                 Ascusb_5939 
                 631 
               
               
                   Clostridium _XlVa 
                 Ascusb_5940 
                 632 
               
               
                   Clostridium _III 
                 Ascusb_5950 
                 633 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_5953 
                 634 
               
               
                 
                   Bacillus 
                 
                 Ascusb_5969 
                 635 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_5972 
                 636 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_5973 
                 637 
               
               
                 
                   Agarivorans 
                 
                 Ascusb_5975 
                 638 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_5979 
                 639 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_5984 
                 640 
               
               
                   Clostridium _XlVa 
                 Ascusb_5991 
                 641 
               
               
                   Clostridium _III 
                 Ascusb_5996 
                 642 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_5997 
                 643 
               
               
                   Clostridium _XlVa 
                 Ascusb_5998 
                 644 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_6003 
                 645 
               
               
                   Clostridium _XlVa 
                 Ascusb_6005 
                 646 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_6006 
                 647 
               
               
                 
                   Nitrobacter 
                 
                 Ascusb_6022 
                 648 
               
               
                   Clostridium _XlVa 
                 Ascusb_6026 
                 649 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_6035 
                 650 
               
               
                 
                   Limibacter 
                 
                 Ascusb_6037 
                 651 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_6053 
                 652 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_6067 
                 653 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_6070 
                 654 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_6074 
                 655 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_6079 
                 656 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_6081 
                 657 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_6106 
                 658 
               
               
                   Clostridium _III 
                 Ascusb_6115 
                 659 
               
               
                 
                   Victivallis 
                 
                 Ascusb_6151 
                 660 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_6168 
                 661 
               
               
                   Clostridium _IV 
                 Ascusb_6169 
                 662 
               
               
                 
                   Erysipelothrix 
                 
                 Ascusb_6172 
                 663 
               
               
                   Clostridium _III 
                 Ascusb_6200 
                 664 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_6207 
                 665 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_6212 
                 666 
               
               
                 
                   Roseburia 
                 
                 Ascusb_6219 
                 667 
               
               
                 
                   Neisseria 
                 
                 Ascusb_6270 
                 668 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6273 
                 669 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_6275 
                 670 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_6282 
                 671 
               
               
                 Candidate phylum TM7 
                 Ascusb_6313 
                 672 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6326 
                 673 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_6330 
                 674 
               
               
                 Erysipelotrichaceae_incertae_sedis 
                 Ascusb_6337 
                 675 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_6342 
                 676 
               
               
                   Clostridium _XlVa 
                 Ascusb_6372 
                 677 
               
               
                   Clostridium _XlVb 
                 Ascusb_6376 
                 678 
               
               
                   Clostridium _XlVa 
                 Ascusb_6387 
                 679 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_6389 
                 680 
               
               
                   Clostridium _XlVa 
                 Ascusb_6394 
                 681 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_6400 
                 682 
               
               
                   Clostridium _IV 
                 Ascusb_6403 
                 683 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_6406 
                 684 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6409 
                 685 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_6420 
                 686 
               
               
                 
                   Treponema 
                 
                 Ascusb_6433 
                 687 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6448 
                 688 
               
               
                   Clostridium _III 
                 Ascusb_6450 
                 689 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_6463 
                 690 
               
               
                   Clostridium _IV 
                 Ascusb_6468 
                 691 
               
               
                 
                   Sharpea 
                 
                 Ascusb_6473 
                 692 
               
               
                 
                   Dongia 
                 
                 Ascusb_6499 
                 693 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_6505 
                 694 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6507 
                 695 
               
               
                   Clostridium _IV 
                 Ascusb_6519 
                 696 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_6525 
                 697 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_6535 
                 698 
               
               
                   Clostridium _XlVa 
                 Ascusb_6540 
                 699 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_6541 
                 700 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_6558 
                 701 
               
               
                 
                   Victivallis 
                 
                 Ascusb_6561 
                 702 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_6563 
                 703 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_6564 
                 704 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_6570 
                 705 
               
               
                   Clostridium _XlVa 
                 Ascusb_6578 
                 706 
               
               
                   Clostridium _XlVa 
                 Ascusb_6581 
                 707 
               
               
                   Clostridium _IV 
                 Ascusb_6586 
                 708 
               
               
                 
                   Roseburia 
                 
                 Ascusb_6593 
                 709 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_6612 
                 710 
               
               
                   Clostridium _III 
                 Ascusb_6614 
                 711 
               
               
                   Clostridium _XlVa 
                 Ascusb_6621 
                 712 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_6630 
                 713 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_6633 
                 714 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_6635 
                 715 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_6645 
                 716 
               
               
                   Clostridium _IV 
                 Ascusb_6670 
                 717 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6672 
                 718 
               
               
                 
                   Helicobacter 
                 
                 Ascusb_6676 
                 719 
               
               
                   Clostridium _IV 
                 Ascusb_6683 
                 720 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_6684 
                 721 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_6701 
                 722 
               
               
                   Clostridium _XlVa 
                 Ascusb_6704 
                 723 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6706 
                 724 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_6708 
                 725 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_6709 
                 726 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_6715 
                 727 
               
               
                 
                   Sphingomonas 
                 
                 Ascusb_6718 
                 728 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6730 
                 729 
               
               
                   Clostridium _IV 
                 Ascusb_6734 
                 730 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_6735 
                 731 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_6746 
                 732 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_6756 
                 733 
               
               
                   Clostridium _III 
                 Ascusb_6757 
                 734 
               
               
                   Clostridium _III 
                 Ascusb_6774 
                 735 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_6792 
                 736 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6796 
                 737 
               
               
                   Clostridium _XlVa 
                 Ascusb_6803 
                 738 
               
               
                 
                   Fusibacter 
                 
                 Ascusb_6813 
                 739 
               
               
                   Clostridium _XlVa 
                 Ascusb_6824 
                 740 
               
               
                   Clostridium _IV 
                 Ascusb_6833 
                 741 
               
               
                 
                   Rummeliibacillus 
                 
                 Ascusb_6848 
                 742 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_6852 
                 743 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_6864 
                 744 
               
               
                 
                   Pelospora 
                 
                 Ascusb_6875 
                 745 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_6880 
                 746 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_6887 
                 747 
               
               
                 
                   Blautia 
                 
                 Ascusb_6889 
                 748 
               
               
                   Clostridium _XlVb 
                 Ascusb_6901 
                 749 
               
               
                 
                   Ehrlichia 
                 
                 Ascusb_6907 
                 750 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_6930 
                 751 
               
               
                 
                   Prevotella 
                 
                 Ascusb_6943 
                 752 
               
               
                   Clostridium _XlVa 
                 Ascusb_6952 
                 753 
               
               
                 
                   Treponema 
                 
                 Ascusb_6954 
                 754 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_6957 
                 755 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_6964 
                 756 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_6966 
                 757 
               
               
                   Clostridium _IV 
                 Ascusb_6971 
                 758 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_6976 
                 759 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_6979 
                 760 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_6997 
                 761 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_7001 
                 762 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_7017 
                 763 
               
               
                   Clostridium _XlVa 
                 Ascusb_7025 
                 764 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_7031 
                 765 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_7039 
                 766 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_7040 
                 767 
               
               
                   Clostridium _IV 
                 Ascusb_7043 
                 768 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_7046 
                 769 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_7048 
                 770 
               
               
                   Clostridium _XlVa 
                 Ascusb_7054 
                 771 
               
               
                 
                   Rhodocista 
                 
                 Ascusb_7078 
                 772 
               
               
                   Clostridium _XlVa 
                 Ascusb_7087 
                 773 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_7091 
                 774 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_7101 
                 775 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_7102 
                 776 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7113 
                 777 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_7114 
                 778 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_7123 
                 779 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7128 
                 780 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_7131 
                 781 
               
               
                   Clostridium _XlVb 
                 Ascusb_7141 
                 782 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_7148 
                 783 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_7149 
                 784 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_7151 
                 785 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_7153 
                 786 
               
               
                   Clostridium _III 
                 Ascusb_7159 
                 787 
               
               
                 
                   Acetanaerobacterium 
                 
                 Ascusb_7164 
                 788 
               
               
                 
                   Treponema 
                 
                 Ascusb_7168 
                 789 
               
               
                   Clostridium _XlVa 
                 Ascusb_7176 
                 790 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_7180 
                 791 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7188 
                 792 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_7199 
                 793 
               
               
                 
                   Aminobacter 
                 
                 Ascusb_7213 
                 794 
               
               
                   Clostridium _IV 
                 Ascusb_7224 
                 795 
               
               
                 
                   Rikenella 
                 
                 Ascusb_7225 
                 796 
               
               
                 
                   Gordonibacter 
                 
                 Ascusb_7240 
                 797 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_7245 
                 798 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_7246 
                 799 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_7256 
                 800 
               
               
                 
                   Hahella 
                 
                 Ascusb_7257 
                 801 
               
               
                 
                   Vampirovibrio 
                 
                 Ascusb_7264 
                 802 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_7275 
                 803 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_7299 
                 804 
               
               
                   Clostridium _III 
                 Ascusb_7300 
                 805 
               
               
                   Clostridium _XlVa 
                 Ascusb_7304 
                 806 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_7325 
                 807 
               
               
                 
                   Helicobacter 
                 
                 Ascusb_7373 
                 808 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_7380 
                 809 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7384 
                 810 
               
               
                   Clostridium _IV 
                 Ascusb_7385 
                 811 
               
               
                 
                   Paludibacter 
                 
                 Ascusb_7395 
                 812 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7401 
                 813 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7412 
                 814 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_7419 
                 815 
               
               
                   Clostridium _IV 
                 Ascusb_7420 
                 816 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_7424 
                 817 
               
               
                 
                   Idiomarina 
                 
                 Ascusb_7435 
                 818 
               
               
                   Clostridium _IV 
                 Ascusb_7437 
                 819 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_7440 
                 820 
               
               
                 
                   Acetanaerobacterium 
                 
                 Ascusb_7444 
                 821 
               
               
                 
                   Bifidobacterium 
                 
                 Ascusb_7446 
                 822 
               
               
                   Clostridium _XlVb 
                 Ascusb_7449 
                 823 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_7450 
                 824 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_7452 
                 825 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_7455 
                 826 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_7456 
                 827 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_7467 
                 828 
               
               
                   Clostridium _III 
                 Ascusb_7470 
                 829 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_7472 
                 830 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_7476 
                 831 
               
               
                 
                   Sphingomonas 
                 
                 Ascusb_7487 
                 832 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_7525 
                 833 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_7533 
                 834 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_7534 
                 835 
               
               
                 
                   Paraeggerthella 
                 
                 Ascusb_7539 
                 836 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7542 
                 837 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_7543 
                 838 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_7549 
                 839 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7553 
                 840 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_7555 
                 841 
               
               
                   Clostridium _XlVa 
                 Ascusb_7563 
                 842 
               
               
                   Clostridium _XlVa 
                 Ascusb_7568 
                 843 
               
               
                 
                   Roseburia 
                 
                 Ascusb_7572 
                 844 
               
               
                   Clostridium _XlVa 
                 Ascusb_7581 
                 845 
               
               
                   Clostridium _III 
                 Ascusb_7591 
                 846 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_7599 
                 847 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_7614 
                 848 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_7615 
                 849 
               
               
                   Clostridium _XlVa 
                 Ascusb_7622 
                 850 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_7626 
                 851 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_7638 
                 852 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_7645 
                 853 
               
               
                   Clostridium _XlVa 
                 Ascusb_7647 
                 854 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_7648 
                 855 
               
               
                   Clostridium _XlVb 
                 Ascusb_7650 
                 856 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_7662 
                 857 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_7663 
                 858 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_7669 
                 859 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_7677 
                 860 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_7680 
                 861 
               
               
                 
                   Streptomyces 
                 
                 Ascusb_7690 
                 862 
               
               
                 
                   Arcobacter 
                 
                 Ascusb_7694 
                 863 
               
               
                   Clostridium _XlVa 
                 Ascusb_7699 
                 864 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_7706 
                 865 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_7723 
                 866 
               
               
                 
                   Flavobacterium 
                 
                 Ascusb_7728 
                 867 
               
               
                 
                   Victivallis 
                 
                 Ascusb_7733 
                 868 
               
               
                   Clostridium _XlVa 
                 Ascusb_7735 
                 869 
               
               
                 
                   Ureaplasma 
                 
                 Ascusb_7748 
                 870 
               
               
                 
                   Acetanaerobacterium 
                 
                 Ascusb_7752 
                 871 
               
               
                 
                   Slackia 
                 
                 Ascusb_7753 
                 872 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7761 
                 873 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_7763 
                 874 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7765 
                 875 
               
               
                 
                   Proteiniphilum 
                 
                 Ascusb_7767 
                 876 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_7784 
                 877 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_7788 
                 878 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7792 
                 879 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_7796 
                 880 
               
               
                 
                   Devosia 
                 
                 Ascusb_7817 
                 881 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_7828 
                 882 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_7829 
                 883 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_7831 
                 884 
               
               
                 
                   Atopobium 
                 
                 Ascusb_7837 
                 885 
               
               
                   Clostridium _XlVa 
                 Ascusb_7838 
                 886 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_7839 
                 887 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_7849 
                 888 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_7853 
                 889 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_7855 
                 890 
               
               
                 
                   Enhydrobacter 
                 
                 Ascusb_7871 
                 891 
               
               
                 
                   Treponema 
                 
                 Ascusb_7872 
                 892 
               
               
                   Clostridium _XlVa 
                 Ascusb_7873 
                 893 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_7874 
                 894 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7890 
                 895 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_7896 
                 896 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_7898 
                 897 
               
               
                   Clostridium _IV 
                 Ascusb_7901 
                 898 
               
               
                 
                   Demequina 
                 
                 Ascusb_7902 
                 899 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_7904 
                 900 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_7924 
                 901 
               
               
                 
                   Sphaerisporangium 
                 
                 Ascusb_7925 
                 902 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_7939 
                 903 
               
               
                 
                   Geobacillus 
                 
                 Ascusb_7958 
                 904 
               
               
                 
                   Prevotella 
                 
                 Ascusb_7959 
                 905 
               
               
                   Clostridium _XlVa 
                 Ascusb_7967 
                 906 
               
               
                 
                   Victivallis 
                 
                 Ascusb_7973 
                 907 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_7989 
                 908 
               
               
                 
                   Demequina 
                 
                 Ascusb_7990 
                 909 
               
               
                 
                   Paraeggerthella 
                 
                 Ascusb_7994 
                 910 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_7996 
                 911 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_8013 
                 912 
               
               
                 
                   Roseburia 
                 
                 Ascusb_8018 
                 913 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_8038 
                 914 
               
               
                   Clostridium _IV 
                 Ascusb_8069 
                 915 
               
               
                 
                   Rhizobium 
                 
                 Ascusb_8076 
                 916 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_8081 
                 917 
               
               
                   Clostridium _XlVa 
                 Ascusb_8084 
                 918 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8091 
                 919 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8105 
                 920 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_8107 
                 921 
               
               
                 
                   Fusibacter 
                 
                 Ascusb_8113 
                 922 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_8120 
                 923 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_8123 
                 924 
               
               
                   Clostridium _XlVa 
                 Ascusb_8149 
                 925 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_8167 
                 926 
               
               
                 
                   Catenibacterium 
                 
                 Ascusb_8169 
                 927 
               
               
                   Clostridium _IV 
                 Ascusb_8172 
                 928 
               
               
                   Clostridium _IV 
                 Ascusb_8173 
                 929 
               
               
                   Clostridium _IV 
                 Ascusb_8179 
                 930 
               
               
                 
                   Nitrobacter 
                 
                 Ascusb_8182 
                 931 
               
               
                 
                   Victivallis 
                 
                 Ascusb_8189 
                 932 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_8196 
                 933 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_8200 
                 934 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_8202 
                 935 
               
               
                 
                   Roseburia 
                 
                 Ascusb_8206 
                 936 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8211 
                 937 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_8222 
                 938 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8230 
                 939 
               
               
                   Clostridium _XlVa 
                 Ascusb_8238 
                 940 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_8245 
                 941 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_8254 
                 942 
               
               
                   Clostridium _XlVa 
                 Ascusb_8260 
                 943 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8266 
                 944 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_8268 
                 945 
               
               
                 
                   Asteroleplasma 
                 
                 Ascusb_8280 
                 946 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_8283 
                 947 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_8311 
                 948 
               
               
                 
                   Bilophila 
                 
                 Ascusb_8317 
                 949 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_8318 
                 950 
               
               
                   Clostridium _IV 
                 Ascusb_8320 
                 951 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8321 
                 952 
               
               
                 
                   Geosporobacter 
                 
                 Ascusb_8329 
                 953 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_8363 
                 954 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_8366 
                 955 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_8367 
                 956 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_8370 
                 957 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8374 
                 958 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_8379 
                 959 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_8384 
                 960 
               
               
                 
                   Pelotomaculum 
                 
                 Ascusb_8394 
                 961 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_8396 
                 962 
               
               
                   Clostridium _IV 
                 Ascusb_8402 
                 963 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_8410 
                 964 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_8413 
                 965 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8439 
                 966 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8440 
                 967 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_8447 
                 968 
               
               
                   Clostridium _XlVa 
                 Ascusb_8470 
                 969 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8480 
                 970 
               
               
                   Clostridium _IV 
                 Ascusb_8484 
                 971 
               
               
                 
                   Howardella 
                 
                 Ascusb_8487 
                 972 
               
               
                 
                   Slackia 
                 
                 Ascusb_8498 
                 973 
               
               
                 
                   Methylobacter 
                 
                 Ascusb_8500 
                 974 
               
               
                 
                   Treponema 
                 
                 Ascusb_8508 
                 975 
               
               
                   Clostridium _XlVa 
                 Ascusb_8514 
                 976 
               
               
                 
                   Devosia 
                 
                 Ascusb_8518 
                 977 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_8537 
                 978 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_8569 
                 979 
               
               
                   Clostridium _III 
                 Ascusb_8580 
                 980 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_8595 
                 981 
               
               
                 
                   Paraprevotella 
                 
                 Ascusb_8600 
                 982 
               
               
                 
                   Desulfobulbus 
                 
                 Ascusb_8627 
                 983 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_8639 
                 984 
               
               
                   Clostridium _XlVa 
                 Ascusb_8657 
                 985 
               
               
                 
                   Dialister 
                 
                 Ascusb_8669 
                 986 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_8681 
                 987 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_8696 
                 988 
               
               
                   Clostridium _IV 
                 Ascusb_8712 
                 989 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_8713 
                 990 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8714 
                 991 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_8715 
                 992 
               
               
                   Clostridium _III 
                 Ascusb_8728 
                 993 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_8733 
                 994 
               
               
                 
                   Faecalibacterium 
                 
                 Ascusb_8746 
                 995 
               
               
                   Clostridium _XlVb 
                 Ascusb_8753 
                 996 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_8758 
                 997 
               
               
                   Clostridium _III 
                 Ascusb_8762 
                 998 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8769 
                 999 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_8771 
                 1000 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_8782 
                 1001 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_8786 
                 1002 
               
               
                   Clostridium _XlVa 
                 Ascusb_8787 
                 1003 
               
               
                 
                   Roseburia 
                 
                 Ascusb_8799 
                 1004 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_8804 
                 1005 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_8807 
                 1006 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_8815 
                 1007 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8822 
                 1008 
               
               
                 
                   Victivallis 
                 
                 Ascusb_8835 
                 1009 
               
               
                 
                   Roseburia 
                 
                 Ascusb_8840 
                 1010 
               
               
                 
                   Treponema 
                 
                 Ascusb_8857 
                 1011 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8860 
                 1012 
               
               
                 
                   Prevotella 
                 
                 Ascusb_8870 
                 1013 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_8873 
                 1014 
               
               
                   Clostridium _XlVa 
                 Ascusb_8883 
                 1015 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8884 
                 1016 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_8886 
                 1017 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_8888 
                 1018 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_8892 
                 1019 
               
               
                 
                   Dethiosulfovibrio 
                 
                 Ascusb_8916 
                 1020 
               
               
                 
                   Lutispora 
                 
                 Ascusb_8934 
                 1021 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_8942 
                 1022 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_8953 
                 1023 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_8956 
                 1024 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_8972 
                 1025 
               
               
                 
                   Bulleidia 
                 
                 Ascusb_9004 
                 1026 
               
               
                 
                   Aquiflexum 
                 
                 Ascusb_9015 
                 1027 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_9026 
                 1028 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_9073 
                 1029 
               
               
                   Clostridium _III 
                 Ascusb_9075 
                 1030 
               
               
                 
                   Roseburia 
                 
                 Ascusb_9081 
                 1031 
               
               
                 
                   Glaciecola 
                 
                 Ascusb_9086 
                 1032 
               
               
                   Clostridium _XlVa 
                 Ascusb_9090 
                 1033 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_9095 
                 1034 
               
               
                   Clostridium _IV 
                 Ascusb_9097 
                 1035 
               
               
                 
                   Sphaerobacter 
                 
                 Ascusb_9098 
                 1036 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_9105 
                 1037 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9109 
                 1038 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_9112 
                 1039 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_9122 
                 1040 
               
               
                   Clostridium _IV 
                 Ascusb_9131 
                 1041 
               
               
                   Clostridium _XlVa 
                 Ascusb_9145 
                 1042 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_9151 
                 1043 
               
               
                   Clostridium _XlVb 
                 Ascusb_9154 
                 1044 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_9160 
                 1045 
               
               
                 
                   Fibrobacter 
                 
                 Ascusb_9169 
                 1046 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_9176 
                 1047 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_9178 
                 1048 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_9184 
                 1049 
               
               
                 
                   Algoriphagus 
                 
                 Ascusb_9189 
                 1050 
               
               
                   Clostridium _XlVa 
                 Ascusb_9196 
                 1051 
               
               
                 
                   Howardella 
                 
                 Ascusb_9200 
                 1052 
               
               
                   Clostridium _XlVa 
                 Ascusb_9201 
                 1053 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_9211 
                 1054 
               
               
                   Clostridium _IV 
                 Ascusb_9234 
                 1055 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9238 
                 1056 
               
               
                   Clostridium _XlVa 
                 Ascusb_9251 
                 1057 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_9261 
                 1058 
               
               
                 
                   Blautia 
                 
                 Ascusb_9264 
                 1059 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9274 
                 1060 
               
               
                   Clostridium _XlVa 
                 Ascusb_9277 
                 1061 
               
               
                 
                   Blautia 
                 
                 Ascusb_9282 
                 1062 
               
               
                   Clostridium _IV 
                 Ascusb_9291 
                 1063 
               
               
                 
                   Flavobacterium 
                 
                 Ascusb_9292 
                 1064 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9300 
                 1065 
               
               
                   Clostridium _XlVa 
                 Ascusb_9301 
                 1066 
               
               
                   Clostridium _XlVa 
                 Ascusb_9302 
                 1067 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_9313 
                 1068 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_9340 
                 1069 
               
               
                 
                   Fluviicola 
                 
                 Ascusb_9343 
                 1070 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_9354 
                 1071 
               
               
                 
                   Blautia 
                 
                 Ascusb_9355 
                 1072 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_9367 
                 1073 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_9368 
                 1074 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_9369 
                 1075 
               
               
                   Clostridium _XI 
                 Ascusb_9372 
                 1076 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_9376 
                 1077 
               
               
                 
                   Roseburia 
                 
                 Ascusb_9381 
                 1078 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_9388 
                 1079 
               
               
                   Clostridium _XI 
                 Ascusb_9389 
                 1080 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_9401 
                 1081 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9402 
                 1082 
               
               
                   Clostridium _III 
                 Ascusb_9411 
                 1083 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_9415 
                 1084 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_9427 
                 1085 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_9432 
                 1086 
               
               
                   Clostridium _III 
                 Ascusb_9453 
                 1087 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_9454 
                 1088 
               
               
                   Clostridium _IV 
                 Ascusb_9455 
                 1089 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9465 
                 1090 
               
               
                 
                   Bifidobacterium 
                 
                 Ascusb_9497 
                 1091 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_9507 
                 1092 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_9518 
                 1093 
               
               
                 
                   Acetivibrio 
                 
                 Ascusb_9521 
                 1094 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_9532 
                 1095 
               
               
                 
                   Flammeovirga 
                 
                 Ascusb_9535 
                 1096 
               
               
                 
                   Dethiosulfovibrio 
                 
                 Ascusb_9543 
                 1097 
               
               
                 
                   Hippea 
                 
                 Ascusb_9545 
                 1098 
               
               
                 
                   Faecalibacterium 
                 
                 Ascusb_9558 
                 1099 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_9559 
                 1100 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_9563 
                 1101 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_9564 
                 1102 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_9580 
                 1103 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_9587 
                 1104 
               
               
                   Clostridium _IV 
                 Ascusb_9591 
                 1105 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_9605 
                 1106 
               
               
                   Clostridium _IV 
                 Ascusb_9617 
                 1107 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_9619 
                 1108 
               
               
                   Clostridium _XlVa 
                 Ascusb_9628 
                 1109 
               
               
                 
                   Faecalibacterium 
                 
                 Ascusb_9640 
                 1110 
               
               
                 
                   Altererythrobacter 
                 
                 Ascusb_9644 
                 1111 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_9656 
                 1112 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9662 
                 1113 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_9663 
                 1114 
               
               
                 
                   Riemerella 
                 
                 Ascusb_9664 
                 1115 
               
               
                 
                   Sphingobacterium 
                 
                 Ascusb_9666 
                 1116 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_9668 
                 1117 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_9669 
                 1118 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_9678 
                 1119 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_9679 
                 1120 
               
               
                   Clostridium _IV 
                 Ascusb_9680 
                 1121 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_9684 
                 1122 
               
               
                 
                   Marvinbryantia 
                 
                 Ascusb_9688 
                 1123 
               
               
                 
                   Brevibacillus 
                 
                 Ascusb_9701 
                 1124 
               
               
                   Clostridium _IV 
                 Ascusb_9715 
                 1125 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9719 
                 1126 
               
               
                   Clostridium _IV 
                 Ascusb_9734 
                 1127 
               
               
                 
                   Aminobacter 
                 
                 Ascusb_9759 
                 1128 
               
               
                 
                   Sporotomaculum 
                 
                 Ascusb_9764 
                 1129 
               
               
                   Clostridium _IV 
                 Ascusb_9779 
                 1130 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_9780 
                 1131 
               
               
                 
                   Victivallis 
                 
                 Ascusb_9782 
                 1132 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_9792 
                 1133 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9824 
                 1134 
               
               
                 
                   Wautersiella 
                 
                 Ascusb_9839 
                 1135 
               
               
                 
                   Slackia 
                 
                 Ascusb_9846 
                 1136 
               
               
                 
                   Pyramidobacter 
                 
                 Ascusb_9851 
                 1137 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_9862 
                 1138 
               
               
                   Clostridium _XlVa 
                 Ascusb_9869 
                 1139 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9876 
                 1140 
               
               
                 
                   Lentisphaera 
                 
                 Ascusb_9886 
                 1141 
               
               
                 
                   Desulfoluna 
                 
                 Ascusb_9895 
                 1142 
               
               
                   Clostridium _III 
                 Ascusb_9897 
                 1143 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_9925 
                 1144 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9929 
                 1145 
               
               
                   Clostridium _III 
                 Ascusb_9934 
                 1146 
               
               
                   Clostridium _IV 
                 Ascusb_9949 
                 1147 
               
               
                 
                   Prevotella 
                 
                 Ascusb_9951 
                 1148 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_9954 
                 1149 
               
               
                 
                   Helicobacter 
                 
                 Ascusb_9958 
                 1150 
               
               
                   Clostridium _XlVa 
                 Ascusb_9977 
                 1151 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_9982 
                 1152 
               
               
                 
                   Bradyrhizobium 
                 
                 Ascusb_9993 
                 1153 
               
               
                   Clostridium _IV 
                 Ascusb_9996 
                 1154 
               
               
                 
                   Sphingobacterium 
                 
                 Ascusb_10002 
                 1155 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_10023 
                 1156 
               
               
                 
                   Vasilyevaea 
                 
                 Ascusb_10029 
                 1157 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_10030 
                 1158 
               
               
                   Clostridium _XlVa 
                 Ascusb_10034 
                 1159 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_10044 
                 1160 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_10045 
                 1161 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10050 
                 1162 
               
               
                 
                   Treponema 
                 
                 Ascusb_10057 
                 1163 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_10058 
                 1164 
               
               
                 Erysipelotrichaceae_incertae_sedis 
                 Ascusb_10059 
                 1165 
               
               
                 
                   Sulfurovum 
                 
                 Ascusb_10084 
                 1166 
               
               
                   Clostridium _IV 
                 Ascusb_10085 
                 1167 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_10087 
                 1168 
               
               
                 
                   Paracoccus 
                 
                 Ascusb_10094 
                 1169 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_10102 
                 1170 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_10121 
                 1171 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_10126 
                 1172 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_10127 
                 1173 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_10129 
                 1174 
               
               
                 
                   Telmatospirillum 
                 
                 Ascusb_10138 
                 1175 
               
               
                   Clostridium _XlVa 
                 Ascusb_10144 
                 1176 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_10147 
                 1177 
               
               
                   Clostridium _IV 
                 Ascusb_10156 
                 1178 
               
               
                 
                   Vasilyevaea 
                 
                 Ascusb_10164 
                 1179 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_10177 
                 1180 
               
               
                 
                   Sporotomaculum 
                 
                 Ascusb_10193 
                 1181 
               
               
                   Clostridium _IV 
                 Ascusb_10194 
                 1182 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_10204 
                 1183 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_10208 
                 1184 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_10210 
                 1185 
               
               
                 
                   Rhodopirellula 
                 
                 Ascusb_10215 
                 1186 
               
               
                   Clostridium _XlVa 
                 Ascusb_10221 
                 1187 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_10243 
                 1188 
               
               
                 
                   Anaerofustis 
                 
                 Ascusb_10268 
                 1189 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_10269 
                 1190 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_10278 
                 1191 
               
               
                   Clostridium _XlVa 
                 Ascusb_10281 
                 1192 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_10284 
                 1193 
               
               
                   Clostridium _XlVa 
                 Ascusb_10299 
                 1194 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_10309 
                 1195 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_10313 
                 1196 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_10325 
                 1197 
               
               
                 
                   Treponema 
                 
                 Ascusb_10327 
                 1198 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_10344 
                 1199 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_10368 
                 1200 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10374 
                 1201 
               
               
                 
                   Pseudaminobacter 
                 
                 Ascusb_10380 
                 1202 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10392 
                 1203 
               
               
                 
                   Treponema 
                 
                 Ascusb_10450 
                 1204 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_10456 
                 1205 
               
               
                   Clostridium _IV 
                 Ascusb_10457 
                 1206 
               
               
                 
                   Tenacibaculum 
                 
                 Ascusb_10462 
                 1207 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_10466 
                 1208 
               
               
                 
                   Luteimonas 
                 
                 Ascusb_10469 
                 1209 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_10488 
                 1210 
               
               
                 
                   Roseburia 
                 
                 Ascusb_10495 
                 1211 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_10504 
                 1212 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_10529 
                 1213 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10547 
                 1214 
               
               
                   Clostridium _IV 
                 Ascusb_10548 
                 1215 
               
               
                 
                   Treponema 
                 
                 Ascusb_10557 
                 1216 
               
               
                   Clostridium _IV 
                 Ascusb_10561 
                 1217 
               
               
                 
                   Victivallis 
                 
                 Ascusb_10562 
                 1218 
               
               
                   Clostridium _XlVa 
                 Ascusb_10576 
                 1219 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_10586 
                 1220 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_10598 
                 1221 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_10604 
                 1222 
               
               
                 
                   Treponema 
                 
                 Ascusb_10607 
                 1223 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_10609 
                 1224 
               
               
                 
                   Coraliomargarita 
                 
                 Ascusb_10612 
                 1225 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_10613 
                 1226 
               
               
                 
                   Blautia 
                 
                 Ascusb_10615 
                 1227 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_10617 
                 1228 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10622 
                 1229 
               
               
                   Clostridium _IV 
                 Ascusb_10623 
                 1230 
               
               
                   Clostridium _IV 
                 Ascusb_10635 
                 1231 
               
               
                   Clostridium _III 
                 Ascusb_10655 
                 1232 
               
               
                 
                   Neptunomonas 
                 
                 Ascusb_10677 
                 1233 
               
               
                   Clostridium _IV 
                 Ascusb_10682 
                 1234 
               
               
                 
                   Howardella 
                 
                 Ascusb_10685 
                 1235 
               
               
                   Clostridium _IV 
                 Ascusb_10687 
                 1236 
               
               
                 
                   Roseburia 
                 
                 Ascusb_10711 
                 1237 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_10739 
                 1238 
               
               
                   Clostridium _XlVa 
                 Ascusb_10740 
                 1239 
               
               
                   Clostridium _IV 
                 Ascusb_10741 
                 1240 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_10749 
                 1241 
               
               
                   Clostridium _XlVa 
                 Ascusb_10769 
                 1242 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_10774 
                 1243 
               
               
                   Clostridium _XlVa 
                 Ascusb_10787 
                 1244 
               
               
                 
                   Filomicrobium 
                 
                 Ascusb_10788 
                 1245 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_10790 
                 1246 
               
               
                   Clostridium _XlVa 
                 Ascusb_10809 
                 1247 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_10812 
                 1248 
               
               
                   Clostridium _IV 
                 Ascusb_10817 
                 1249 
               
               
                 
                   Paracoccus 
                 
                 Ascusb_10818 
                 1250 
               
               
                 
                   Schlegelella 
                 
                 Ascusb_10837 
                 1251 
               
               
                   Clostridium _XI 
                 Ascusb_10844 
                 1252 
               
               
                 
                   Diaphorobacter 
                 
                 Ascusb_10847 
                 1253 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_10858 
                 1254 
               
               
                 
                   Saccharopolyspora 
                 
                 Ascusb_10863 
                 1255 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10871 
                 1256 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_10878 
                 1257 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_10888 
                 1258 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10899 
                 1259 
               
               
                 
                   Pseudomonas 
                 
                 Ascusb_10922 
                 1260 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10927 
                 1261 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10937 
                 1262 
               
               
                 
                   Prevotella 
                 
                 Ascusb_10940 
                 1263 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_10945 
                 1264 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_10982 
                 1265 
               
               
                   Clostridium _XlVa 
                 Ascusb_11015 
                 1266 
               
               
                 
                   Photobacterium 
                 
                 Ascusb_11027 
                 1267 
               
               
                   Clostridium _XlVa 
                 Ascusb_11031 
                 1268 
               
               
                   Clostridium _XlVb 
                 Ascusb_11032 
                 1269 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11037 
                 1270 
               
               
                   Clostridium _IV 
                 Ascusb_11046 
                 1271 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_11051 
                 1272 
               
               
                 
                   Caldilinea 
                 
                 Ascusb_11053 
                 1273 
               
               
                   Clostridium _XlVa 
                 Ascusb_11059 
                 1274 
               
               
                 
                   Victivallis 
                 
                 Ascusb_11061 
                 1275 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_11063 
                 1276 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11074 
                 1277 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11120 
                 1278 
               
               
                 
                   Slackia 
                 
                 Ascusb_11124 
                 1279 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_11125 
                 1280 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11129 
                 1281 
               
               
                 
                   Trueperella 
                 
                 Ascusb_11141 
                 1282 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_11170 
                 1283 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11185 
                 1284 
               
               
                 
                   Victivallis 
                 
                 Ascusb_11199 
                 1285 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_11200 
                 1286 
               
               
                 
                   Micrococcus 
                 
                 Ascusb_11207 
                 1287 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_11209 
                 1288 
               
               
                 
                   Anaerophaga 
                 
                 Ascusb_11211 
                 1289 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_11214 
                 1290 
               
               
                 
                   Megasphaera 
                 
                 Ascusb_11219 
                 1291 
               
               
                   Clostridium _XlVa 
                 Ascusb_11221 
                 1292 
               
               
                   Clostridium _XlVa 
                 Ascusb_11241 
                 1293 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_11245 
                 1294 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11253 
                 1295 
               
               
                   Clostridium _XlVa 
                 Ascusb_11287 
                 1296 
               
               
                 
                   Treponema 
                 
                 Ascusb_11288 
                 1297 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_11289 
                 1298 
               
               
                 
                   Xanthomonas 
                 
                 Ascusb_11301 
                 1299 
               
               
                 
                   Asteroleplasma 
                 
                 Ascusb_11302 
                 1300 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11315 
                 1301 
               
               
                 
                   Sporotomaculum 
                 
                 Ascusb_11321 
                 1302 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_11324 
                 1303 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_11330 
                 1304 
               
               
                   Clostridium _IV 
                 Ascusb_11343 
                 1305 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11348 
                 1306 
               
               
                   Clostridium _XlVa 
                 Ascusb_11362 
                 1307 
               
               
                 
                   Treponema 
                 
                 Ascusb_11365 
                 1308 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11384 
                 1309 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_11388 
                 1310 
               
               
                   Clostridium _IV 
                 Ascusb_11389 
                 1311 
               
               
                   Clostridium _IV 
                 Ascusb_11397 
                 1312 
               
               
                   Clostridium _IV 
                 Ascusb_11403 
                 1313 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_11410 
                 1314 
               
               
                 
                   Deinococcus 
                 
                 Ascusb_11423 
                 1315 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_11427 
                 1316 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_11435 
                 1317 
               
               
                   Clostridium _IV 
                 Ascusb_11442 
                 1318 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_11445 
                 1319 
               
               
                   Clostridium _IV 
                 Ascusb_11461 
                 1320 
               
               
                 
                   Rhodococcus 
                 
                 Ascusb_11463 
                 1321 
               
               
                 
                   Treponema 
                 
                 Ascusb_11464 
                 1322 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_11475 
                 1323 
               
               
                   Clostridium _XlVa 
                 Ascusb_11503 
                 1324 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_11510 
                 1325 
               
               
                   Clostridium _XlVa 
                 Ascusb_11519 
                 1326 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_11581 
                 1327 
               
               
                   Clostridium _XlVb 
                 Ascusb_11584 
                 1328 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_11600 
                 1329 
               
               
                 
                   Methanobrevibacter 
                 
                 Ascusb_11602 
                 1330 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_11612 
                 1331 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_11653 
                 1332 
               
               
                 Erysipelotrichaceae_incertae_sedis 
                 Ascusb_11656 
                 1333 
               
               
                 
                   Mesorhizobium 
                 
                 Ascusb_11681 
                 1334 
               
               
                   Clostridium _XI 
                 Ascusb_11695 
                 1335 
               
               
                 
                   Planctomyces 
                 
                 Ascusb_11698 
                 1336 
               
               
                 
                   Aerococcus 
                 
                 Ascusb_11713 
                 1337 
               
               
                 
                   Victivallis 
                 
                 Ascusb_11721 
                 1338 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11736 
                 1339 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_11752 
                 1340 
               
               
                   Clostridium _XI 
                 Ascusb_11753 
                 1341 
               
               
                   Clostridium _XlVa 
                 Ascusb_11757 
                 1342 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_11761 
                 1343 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_11780 
                 1344 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_11781 
                 1345 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_11783 
                 1346 
               
               
                 
                   Fibrobacter 
                 
                 Ascusb_11793 
                 1347 
               
               
                 
                   Kiloniella 
                 
                 Ascusb_11809 
                 1348 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_11819 
                 1349 
               
               
                   Clostridium _IV 
                 Ascusb_11821 
                 1350 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_11865 
                 1351 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11870 
                 1352 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_11881 
                 1353 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11884 
                 1354 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_11885 
                 1355 
               
               
                 
                   Prevotella 
                 
                 Ascusb_11892 
                 1356 
               
               
                 
                   Leifsonia 
                 
                 Ascusb_11896 
                 1357 
               
               
                   Clostridium _IV 
                 Ascusb_11901 
                 1358 
               
               
                 
                   Victivallis 
                 
                 Ascusb_11903 
                 1359 
               
               
                 
                   Treponema 
                 
                 Ascusb_11929 
                 1360 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_11952 
                 1361 
               
               
                 
                   Sporotomaculum 
                 
                 Ascusb_11954 
                 1362 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_11955 
                 1363 
               
               
                   Clostridium _III 
                 Ascusb_11960 
                 1364 
               
               
                   Clostridium _XlVa 
                 Ascusb_11962 
                 1365 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_11963 
                 1366 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_11964 
                 1367 
               
               
                 
                   Victivallis 
                 
                 Ascusb_11988 
                 1368 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_11993 
                 1369 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_11997 
                 1370 
               
               
                   Clostridium _XlVb 
                 Ascusb_12000 
                 1371 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_12004 
                 1372 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12013 
                 1373 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_12046 
                 1374 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_12054 
                 1375 
               
               
                   Clostridium _XlVa 
                 Ascusb_12061 
                 1376 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_12069 
                 1377 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12106 
                 1378 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_12110 
                 1379 
               
               
                 
                   Lentisphaera 
                 
                 Ascusb_12116 
                 1380 
               
               
                   Clostridium _XlVa 
                 Ascusb_12119 
                 1381 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_12127 
                 1382 
               
               
                 
                   Porphyrobacter 
                 
                 Ascusb_12128 
                 1383 
               
               
                 
                   Rhodobacter 
                 
                 Ascusb_12140 
                 1384 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_12153 
                 1385 
               
               
                 
                   Roseburia 
                 
                 Ascusb_12160 
                 1386 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12175 
                 1387 
               
               
                 
                   Aquiflexum 
                 
                 Ascusb_12177 
                 1388 
               
               
                 
                   Rhodopirellula 
                 
                 Ascusb_12187 
                 1389 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_12191 
                 1390 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_12216 
                 1391 
               
               
                   Clostridium _XlVa 
                 Ascusb_12221 
                 1392 
               
               
                   Clostridium _IV 
                 Ascusb_12227 
                 1393 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12243 
                 1394 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_12248 
                 1395 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12252 
                 1396 
               
               
                   Clostridium _XlVa 
                 Ascusb_12269 
                 1397 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12270 
                 1398 
               
               
                 
                   Capnocytophaga 
                 
                 Ascusb_12276 
                 1399 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_12282 
                 1400 
               
               
                   Clostridium _IV 
                 Ascusb_12310 
                 1401 
               
               
                 
                   Succinivibrio 
                 
                 Ascusb_12327 
                 1402 
               
               
                 
                   Pseudonocardia 
                 
                 Ascusb_12339 
                 1403 
               
               
                   Clostridium _XlVa 
                 Ascusb_12353 
                 1404 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_12354 
                 1405 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_12355 
                 1406 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12383 
                 1407 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_12399 
                 1408 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_12407 
                 1409 
               
               
                   Clostridium _XlVa 
                 Ascusb_12413 
                 1410 
               
               
                   Clostridium _XlVb 
                 Ascusb_12417 
                 1411 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_12428 
                 1412 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_12452 
                 1413 
               
               
                 
                   Riemerella 
                 
                 Ascusb_12461 
                 1414 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_12487 
                 1415 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_12489 
                 1416 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_12499 
                 1417 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_12511 
                 1418 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_12512 
                 1419 
               
               
                   Clostridium _IV 
                 Ascusb_12520 
                 1420 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_12534 
                 1421 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_12553 
                 1422 
               
               
                   Clostridium _XlVa 
                 Ascusb_12574 
                 1423 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_12577 
                 1424 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_12578 
                 1425 
               
               
                   Clostridium _IV 
                 Ascusb_12599 
                 1426 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_12600 
                 1427 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_12606 
                 1428 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_12618 
                 1429 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_12627 
                 1430 
               
               
                   Clostridium _XlVb 
                 Ascusb_12628 
                 1431 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_12661 
                 1432 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12662 
                 1433 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_12679 
                 1434 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_12703 
                 1435 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_12704 
                 1436 
               
               
                 
                   Thermoanaerobacter 
                 
                 Ascusb_12709 
                 1437 
               
               
                 
                   Armatimonadetes 
                 
                 Ascusb_12719 
                 1438 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_12723 
                 1439 
               
               
                 
                   Sphingobium 
                 
                 Ascusb_12731 
                 1440 
               
               
                   Clostridium _XlVa 
                 Ascusb_12737 
                 1441 
               
               
                 
                   Geosporobacter 
                 
                 Ascusb_12740 
                 1442 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_12746 
                 1443 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_12747 
                 1444 
               
               
                   Clostridium _XlVa 
                 Ascusb_12749 
                 1445 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_12750 
                 1446 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_12769 
                 1447 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_12775 
                 1448 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_12779 
                 1449 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12804 
                 1450 
               
               
                 
                   Roseburia 
                 
                 Ascusb_12819 
                 1451 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_12826 
                 1452 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_12835 
                 1453 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_12838 
                 1454 
               
               
                 
                   Prevotella 
                 
                 Ascusb_12853 
                 1455 
               
               
                 
                   Rikenella 
                 
                 Ascusb_12873 
                 1456 
               
               
                 
                   Anaerophaga 
                 
                 Ascusb_12894 
                 1457 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_12901 
                 1458 
               
               
                   Clostridium _IV 
                 Ascusb_12910 
                 1459 
               
               
                 
                   Weissella 
                 
                 Ascusb_12931 
                 1460 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_12946 
                 1461 
               
               
                 
                   Hahella 
                 
                 Ascusb_12953 
                 1462 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_12960 
                 1463 
               
               
                   Clostridium _XlVa 
                 Ascusb_12962 
                 1464 
               
               
                 
                   Cellulosilyticum 
                 
                 Ascusb_12987 
                 1465 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_12995 
                 1466 
               
               
                   Clostridium _XlVa 
                 Ascusb_13002 
                 1467 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_13028 
                 1468 
               
               
                 
                   Calditerricola 
                 
                 Ascusb_13035 
                 1469 
               
               
                   Clostridium _IV 
                 Ascusb_13039 
                 1470 
               
               
                   Clostridium _IV 
                 Ascusb_13050 
                 1471 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_13054 
                 1472 
               
               
                 
                   Bulleidia 
                 
                 Ascusb_13088 
                 1473 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_13089 
                 1474 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_13115 
                 1475 
               
               
                 
                   Victivallis 
                 
                 Ascusb_13128 
                 1476 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_13130 
                 1477 
               
               
                   Clostridium _XlVb 
                 Ascusb_13134 
                 1478 
               
               
                   Clostridium _XlVa 
                 Ascusb_13154 
                 1479 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13155 
                 1480 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_13163 
                 1481 
               
               
                 
                   Schwartzia 
                 
                 Ascusb_13165 
                 1482 
               
               
                 
                   Pyramidobacter 
                 
                 Ascusb_13226 
                 1483 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_13230 
                 1484 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_13244 
                 1485 
               
               
                   Clostridium _XlVa 
                 Ascusb_13249 
                 1486 
               
               
                 
                   Roseburia 
                 
                 Ascusb_13254 
                 1487 
               
               
                   Clostridium _XlVb 
                 Ascusb_13276 
                 1488 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_13284 
                 1489 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_13291 
                 1490 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_13296 
                 1491 
               
               
                   Clostridium _XlVa 
                 Ascusb_13328 
                 1492 
               
               
                   Clostridium _III 
                 Ascusb_13343 
                 1493 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_13349 
                 1494 
               
               
                   Clostridium _IV 
                 Ascusb_13353 
                 1495 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_13371 
                 1496 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13412 
                 1497 
               
               
                 
                   Faecalibacterium 
                 
                 Ascusb_13417 
                 1498 
               
               
                 
                   Microbacterium 
                 
                 Ascusb_13419 
                 1499 
               
               
                 
                   Leucobacter 
                 
                 Ascusb_13424 
                 1500 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13426 
                 1501 
               
               
                 
                   Sphingobacterium 
                 
                 Ascusb_13457 
                 1502 
               
               
                 
                   Fusibacter 
                 
                 Ascusb_13458 
                 1503 
               
               
                 
                   Howardella 
                 
                 Ascusb_13463 
                 1504 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_13488 
                 1505 
               
               
                 
                   Caldilinea 
                 
                 Ascusb_13504 
                 1506 
               
               
                 
                   Turicibacter 
                 
                 Ascusb_13513 
                 1507 
               
               
                   Clostridium _IV 
                 Ascusb_13516 
                 1508 
               
               
                 
                   Alistipes 
                 
                 Ascusb_13546 
                 1509 
               
               
                   Clostridium _XlVa 
                 Ascusb_13547 
                 1510 
               
               
                   Clostridium _XlVa 
                 Ascusb_13567 
                 1511 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13597 
                 1512 
               
               
                   Clostridium _XlVa 
                 Ascusb_13611 
                 1513 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_13648 
                 1514 
               
               
                 
                   Anaerovibrio 
                 
                 Ascusb_13663 
                 1515 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13675 
                 1516 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_13679 
                 1517 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_13763 
                 1518 
               
               
                 
                   Leucobacter 
                 
                 Ascusb_13780 
                 1519 
               
               
                 
                   Kerstersia 
                 
                 Ascusb_13819 
                 1520 
               
               
                 
                   Slackia 
                 
                 Ascusb_13835 
                 1521 
               
               
                 
                   Lactococcus 
                 
                 Ascusb_13839 
                 1522 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13840 
                 1523 
               
               
                   Clostridium _IV 
                 Ascusb_13845 
                 1524 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13848 
                 1525 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_13867 
                 1526 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_13881 
                 1527 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13892 
                 1528 
               
               
                   Clostridium _XlVa 
                 Ascusb_13895 
                 1529 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_13903 
                 1530 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_13904 
                 1531 
               
               
                   Clostridium _XlVa 
                 Ascusb_13921 
                 1532 
               
               
                 
                   Victivallis 
                 
                 Ascusb_13923 
                 1533 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_13940 
                 1534 
               
               
                 
                   Acidobacteria 
                 
                 Ascusb_13951 
                 1535 
               
               
                   Clostridium _XlVa 
                 Ascusb_13953 
                 1536 
               
               
                 
                   Prevotella 
                 
                 Ascusb_13954 
                 1537 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_13955 
                 1538 
               
               
                   Clostridium _XlVa 
                 Ascusb_13981 
                 1539 
               
               
                 
                   Treponema 
                 
                 Ascusb_13982 
                 1540 
               
               
                 
                   Pyramidobacter 
                 
                 Ascusb_13983 
                 1541 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_13992 
                 1542 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_13995 
                 1543 
               
               
                   Clostridium _XI 
                 Ascusb_13996 
                 1544 
               
               
                 
                   Bifidobacterium 
                 
                 Ascusb_14005 
                 1545 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_14013 
                 1546 
               
               
                 
                   Gordonibacter 
                 
                 Ascusb_14016 
                 1547 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_14055 
                 1548 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_14059 
                 1549 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_14074 
                 1550 
               
               
                 
                   Prevotella 
                 
                 Ascusb_14086 
                 1551 
               
               
                 
                   Tannerella 
                 
                 Ascusb_14141 
                 1552 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_14145 
                 1553 
               
               
                 
                   Prevotella 
                 
                 Ascusb_14151 
                 1554 
               
               
                   Clostridium _XlVb 
                 Ascusb_14163 
                 1555 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_14189 
                 1556 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_14213 
                 1557 
               
               
                 
                   Rhodoplanes 
                 
                 Ascusb_14224 
                 1558 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_14226 
                 1559 
               
               
                   Escherichia / Shigella   
                 Ascusb_14256 
                 1560 
               
               
                 
                   Rikenella 
                 
                 Ascusb_14278 
                 1561 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_14285 
                 1562 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_14290 
                 1563 
               
               
                 
                   Hyphomicrobium 
                 
                 Ascusb_14304 
                 1564 
               
               
                 Erysipelotrichaceae_incertae_sedis 
                 Ascusb_14320 
                 1565 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_14324 
                 1566 
               
               
                 
                   Staphylococcus 
                 
                 Ascusb_14335 
                 1567 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_14358 
                 1568 
               
               
                 
                   Victivallis 
                 
                 Ascusb_14359 
                 1569 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_14423 
                 1570 
               
               
                 
                   Desulfobulbus 
                 
                 Ascusb_14425 
                 1571 
               
               
                   Clostridium _III 
                 Ascusb_14450 
                 1572 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_14451 
                 1573 
               
               
                 
                   Kordia 
                 
                 Ascusb_14514 
                 1574 
               
               
                 
                   Bosea 
                 
                 Ascusb_14521 
                 1575 
               
               
                 
                   Enterococcus 
                 
                 Ascusb_14525 
                 1576 
               
               
                   Clostridium _III 
                 Ascusb_14530 
                 1577 
               
               
                 
                   Xanthobacter 
                 
                 Ascusb_14538 
                 1578 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_14555 
                 1579 
               
               
                 
                   Prevotella 
                 
                 Ascusb_14583 
                 1580 
               
               
                 
                   Acidaminococcus 
                 
                 Ascusb_14595 
                 1581 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_14596 
                 1582 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_14611 
                 1583 
               
               
                   Clostridium _XlVa 
                 Ascusb_14613 
                 1584 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_14626 
                 1585 
               
               
                 
                   Devosia 
                 
                 Ascusb_14628 
                 1586 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_14667 
                 1587 
               
               
                   Clostridium _IV 
                 Ascusb_14747 
                 1588 
               
               
                   Clostridium _XlVa 
                 Ascusb_14785 
                 1589 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_14790 
                 1590 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_14792 
                 1591 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_14828 
                 1592 
               
               
                   Clostridium _XlVa 
                 Ascusb_14869 
                 1593 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_14888 
                 1594 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_14898 
                 1595 
               
               
                 
                   Slackia 
                 
                 Ascusb_14906 
                 1596 
               
               
                 
                   Limibacter 
                 
                 Ascusb_14951 
                 1597 
               
               
                 
                   Sphingobium 
                 
                 Ascusb_14952 
                 1598 
               
               
                   Clostridium _XlVa 
                 Ascusb_14987 
                 1599 
               
               
                 
                   Riemerella 
                 
                 Ascusb_14990 
                 1600 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_15032 
                 1601 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_15048 
                 1602 
               
               
                 
                   Prevotella 
                 
                 Ascusb_15076 
                 1603 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15097 
                 1604 
               
               
                 
                   Victivallis 
                 
                 Ascusb_15122 
                 1605 
               
               
                 
                   Howardella 
                 
                 Ascusb_15128 
                 1606 
               
               
                 
                   Pelospora 
                 
                 Ascusb_15132 
                 1607 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_15151 
                 1608 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15156 
                 1609 
               
               
                 
                   Fibrobacter 
                 
                 Ascusb_15181 
                 1610 
               
               
                   Clostridium _III 
                 Ascusb_15215 
                 1611 
               
               
                 
                   Sphingomonas 
                 
                 Ascusb_15220 
                 1612 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15226 
                 1613 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_15326 
                 1614 
               
               
                 
                   Treponema 
                 
                 Ascusb_15352 
                 1615 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_15357 
                 1616 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_15390 
                 1617 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15394 
                 1618 
               
               
                 
                   Methylomicrobium 
                 
                 Ascusb_15404 
                 1619 
               
               
                 
                   Leuconostoc 
                 
                 Ascusb_15413 
                 1620 
               
               
                 
                   Pyramidobacter 
                 
                 Ascusb_15427 
                 1621 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_15438 
                 1622 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_15454 
                 1623 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_15455 
                 1624 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_15461 
                 1625 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_15482 
                 1626 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_15488 
                 1627 
               
               
                 
                   Corynebacterium 
                 
                 Ascusb_15494 
                 1628 
               
               
                 
                   Proteiniborus 
                 
                 Ascusb_15526 
                 1629 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_15539 
                 1630 
               
               
                 
                   Acetitomaculum 
                 
                 Ascusb_15549 
                 1631 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15552 
                 1632 
               
               
                 
                   Altererythrobacter 
                 
                 Ascusb_15556 
                 1633 
               
               
                 
                   Atopobium 
                 
                 Ascusb_15587 
                 1634 
               
               
                   Clostridium _IV 
                 Ascusb_15615 
                 1635 
               
               
                   Clostridium _XlVa 
                 Ascusb_15624 
                 1636 
               
               
                   Clostridium _XlVa 
                 Ascusb_15695 
                 1637 
               
               
                   Clostridium _IV 
                 Ascusb_15703 
                 1638 
               
               
                   Clostridium _III 
                 Ascusb_15720 
                 1639 
               
               
                 Candidate phylum TM7 
                 Ascusb_15737 
                 1640 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_15741 
                 1641 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_15746 
                 1642 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_15750 
                 1643 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_15754 
                 1644 
               
               
                 
                   Microbacterium 
                 
                 Ascusb_15768 
                 1645 
               
               
                 
                   Treponema 
                 
                 Ascusb_15824 
                 1646 
               
               
                 
                   Dethiosulfovibrio 
                 
                 Ascusb_15830 
                 1647 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_15832 
                 1648 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_15846 
                 1649 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_15864 
                 1650 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_15877 
                 1651 
               
               
                 
                   Treponema 
                 
                 Ascusb_15915 
                 1652 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_15951 
                 1653 
               
               
                 
                   Roseburia 
                 
                 Ascusb_15963 
                 1654 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_15992 
                 1655 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_16010 
                 1656 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_16051 
                 1657 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_16066 
                 1658 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_16101 
                 1659 
               
               
                 
                   Methylococcus 
                 
                 Ascusb_16111 
                 1660 
               
               
                 
                   Enterorhabdus 
                 
                 Ascusb_16113 
                 1661 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_16124 
                 1662 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_16149 
                 1663 
               
               
                 
                   Sporobacter 
                 
                 Ascusb_16168 
                 1664 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_16185 
                 1665 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_16194 
                 1666 
               
               
                 
                   Syntrophococcus 
                 
                 Ascusb_16198 
                 1667 
               
               
                 
                   Slackia 
                 
                 Ascusb_16200 
                 1668 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_16215 
                 1669 
               
               
                 
                   Prevotella 
                 
                 Ascusb_16239 
                 1670 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_16244 
                 1671 
               
               
                 
                   Veillonella 
                 
                 Ascusb_16257 
                 1672 
               
               
                   Clostridium _XlVa 
                 Ascusb_16278 
                 1673 
               
               
                 
                   Bacillus 
                 
                 Ascusb_16299 
                 1674 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_16316 
                 1675 
               
               
                   Clostridium _IV 
                 Ascusb_16329 
                 1676 
               
               
                 
                   Fibrobacter 
                 
                 Ascusb_16330 
                 1677 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_16336 
                 1678 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_16345 
                 1679 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_16373 
                 1680 
               
               
                   Clostridium _XI 
                 Ascusb_16374 
                 1681 
               
               
                 
                   Helicobacter 
                 
                 Ascusb_16383 
                 1682 
               
               
                 
                   Prevotella 
                 
                 Ascusb_16420 
                 1683 
               
               
                   Clostridium _XlVa 
                 Ascusb_16423 
                 1684 
               
               
                 
                   Prevotella 
                 
                 Ascusb_16436 
                 1685 
               
               
                 
                   Herbiconiux 
                 
                 Ascusb_16453 
                 1686 
               
               
                   Clostridium _IV 
                 Ascusb_16461 
                 1687 
               
               
                 
                   Rikenella 
                 
                 Ascusb_16470 
                 1688 
               
               
                   Clostridium _XlVa 
                 Ascusb_16473 
                 1689 
               
               
                 
                   Hippea 
                 
                 Ascusb_16536 
                 1690 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_16537 
                 1691 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_16541 
                 1692 
               
               
                   Clostridium _IV 
                 Ascusb_16546 
                 1693 
               
               
                   Clostridium _III 
                 Ascusb_16560 
                 1694 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_16565 
                 1695 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_16574 
                 1696 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_16578 
                 1697 
               
               
                 
                   Prevotella 
                 
                 Ascusb_16618 
                 1698 
               
               
                 
                   Staphylococcus 
                 
                 Ascusb_16628 
                 1699 
               
               
                 
                   Tenacibaculum 
                 
                 Ascusb_16632 
                 1700 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_16655 
                 1701 
               
               
                   Clostridium _XlVa 
                 Ascusb_16668 
                 1702 
               
               
                   Clostridium _IV 
                 Ascusb_16671 
                 1703 
               
               
                   Clostridium _IV 
                 Ascusb_16674 
                 1704 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_16682 
                 1705 
               
               
                 
                   Helicobacter 
                 
                 Ascusb_16686 
                 1706 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_16691 
                 1707 
               
               
                 
                   Anaplasma 
                 
                 Ascusb_16711 
                 1708 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_16734 
                 1709 
               
               
                   Clostridium _IV 
                 Ascusb_16749 
                 1710 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_16803 
                 1711 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_16829 
                 1712 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_16884 
                 1713 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_16931 
                 1714 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_16933 
                 1715 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_16948 
                 1716 
               
               
                 
                   Weissella 
                 
                 Ascusb_16968 
                 1717 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_16992 
                 1718 
               
               
                   Clostridium _XI 
                 Ascusb_16995 
                 1719 
               
               
                 
                   Sphingomonas 
                 
                 Ascusb_16998 
                 1720 
               
               
                 
                   Treponema 
                 
                 Ascusb_17013 
                 1721 
               
               
                 
                   Geobacter 
                 
                 Ascusb_17017 
                 1722 
               
               
                   Clostridium _XlVa 
                 Ascusb_17018 
                 1723 
               
               
                 
                   Filomicrobium 
                 
                 Ascusb_17036 
                 1724 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17038 
                 1725 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_17057 
                 1726 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_17058 
                 1727 
               
               
                   Clostridium _XlVa 
                 Ascusb_17064 
                 1728 
               
               
                 
                   Bifidobacterium 
                 
                 Ascusb_17066 
                 1729 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_17092 
                 1730 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_17136 
                 1731 
               
               
                 
                   Flavobacterium 
                 
                 Ascusb_17138 
                 1732 
               
               
                 
                   Rhodopirellula 
                 
                 Ascusb_17161 
                 1733 
               
               
                 
                   Roseburia 
                 
                 Ascusb_17171 
                 1734 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17177 
                 1735 
               
               
                 
                   Limibacter 
                 
                 Ascusb_17182 
                 1736 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_17203 
                 1737 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_17206 
                 1738 
               
               
                   Clostridium _III 
                 Ascusb_17243 
                 1739 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17275 
                 1740 
               
               
                 
                   Pseudoxanthomonas 
                 
                 Ascusb_17283 
                 1741 
               
               
                 
                   Anaerorhabdus 
                 
                 Ascusb_17325 
                 1742 
               
               
                   Clostridium _III 
                 Ascusb_17360 
                 1743 
               
               
                 
                   Streptomyces 
                 
                 Ascusb_17372 
                 1744 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_17388 
                 1745 
               
               
                 
                   Cellulomonas 
                 
                 Ascusb_17414 
                 1746 
               
               
                   Clostridium _XlVa 
                 Ascusb_17416 
                 1747 
               
               
                 
                   Olivibacter 
                 
                 Ascusb_17425 
                 1748 
               
               
                 
                   Treponema 
                 
                 Ascusb_17433 
                 1749 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_17437 
                 1750 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_17439 
                 1751 
               
               
                   Clostridium _IV 
                 Ascusb_17446 
                 1752 
               
               
                 
                   Gemmatimonas 
                 
                 Ascusb_17450 
                 1753 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17459 
                 1754 
               
               
                 
                   Ethanoligenens 
                 
                 Ascusb_17477 
                 1755 
               
               
                 
                   Leucobacter 
                 
                 Ascusb_17494 
                 1756 
               
               
                   Clostridium _XlVa 
                 Ascusb_17502 
                 1757 
               
               
                   Clostridium _XlVa 
                 Ascusb_17507 
                 1758 
               
               
                 
                   Eggerthella 
                 
                 Ascusb_17540 
                 1759 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17553 
                 1760 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17569 
                 1761 
               
               
                 
                   Solobacterium 
                 
                 Ascusb_17571 
                 1762 
               
               
                 
                   Xanthobacter 
                 
                 Ascusb_17581 
                 1763 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_17649 
                 1764 
               
               
                 
                   Desulfovibrio 
                 
                 Ascusb_17670 
                 1765 
               
               
                 
                   Microbacterium 
                 
                 Ascusb_17717 
                 1766 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_17718 
                 1767 
               
               
                 
                   Blautia 
                 
                 Ascusb_17735 
                 1768 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_17736 
                 1769 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17759 
                 1770 
               
               
                 
                   Lentisphaera 
                 
                 Ascusb_17766 
                 1771 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_17767 
                 1772 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_17769 
                 1773 
               
               
                 
                   Catonella 
                 
                 Ascusb_17771 
                 1774 
               
               
                   Clostridium _XlVa 
                 Ascusb_17773 
                 1775 
               
               
                   Clostridium _IV 
                 Ascusb_17782 
                 1776 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_17802 
                 1777 
               
               
                   Clostridium _XI 
                 Ascusb_17804 
                 1778 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17810 
                 1779 
               
               
                 Candidate phylum TM7 
                 Ascusb_17824 
                 1780 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_17838 
                 1781 
               
               
                   Clostridium _XlVa 
                 Ascusb_17846 
                 1782 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_17857 
                 1783 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_17866 
                 1784 
               
               
                   Clostridium _IV 
                 Ascusb_17892 
                 1785 
               
               
                 
                   Rhodomicrobium 
                 
                 Ascusb_17896 
                 1786 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_17957 
                 1787 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_17975 
                 1788 
               
               
                 
                   Prevotella 
                 
                 Ascusb_17978 
                 1789 
               
               
                 
                   Mannheimia 
                 
                 Ascusb_17981 
                 1790 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_18078 
                 1791 
               
               
                   Clostridium _IV 
                 Ascusb_18081 
                 1792 
               
               
                   Clostridium _IV 
                 Ascusb_18091 
                 1793 
               
               
                 
                   Adlercreutzia 
                 
                 Ascusb_18107 
                 1794 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_18110 
                 1795 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_18123 
                 1796 
               
               
                   Clostridium _IV 
                 Ascusb_18140 
                 1797 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_18148 
                 1798 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_18161 
                 1799 
               
               
                 
                   Wandonia 
                 
                 Ascusb_18170 
                 1800 
               
               
                 
                   Puniceicoccus 
                 
                 Ascusb_18179 
                 1801 
               
               
                 
                   Lactonifactor 
                 
                 Ascusb_18183 
                 1802 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_18248 
                 1803 
               
               
                 
                   Brevundimonas 
                 
                 Ascusb_18262 
                 1804 
               
               
                 
                   Prevotella 
                 
                 Ascusb_18273 
                 1805 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_18283 
                 1806 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_18287 
                 1807 
               
               
                   Clostridium _XlVa 
                 Ascusb_18303 
                 1808 
               
               
                 
                   Coprococcus 
                 
                 Ascusb_18329 
                 1809 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_18335 
                 1810 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_18339 
                 1811 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_18351 
                 1812 
               
               
                   Clostridium _XlVa 
                 Ascusb_18354 
                 1813 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_18371 
                 1814 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_18389 
                 1815 
               
               
                 
                   Parasporobacterium 
                 
                 Ascusb_18444 
                 1816 
               
               
                 
                   Prevotella 
                 
                 Ascusb_18449 
                 1817 
               
               
                 
                   Parapedobacter 
                 
                 Ascusb_18475 
                 1818 
               
               
                 
                   Streptomyces 
                 
                 Ascusb_18495 
                 1819 
               
               
                 Candidate phylum TM7 
                 Ascusb_18503 
                 1820 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_18516 
                 1821 
               
               
                 
                   Alkaliflexus 
                 
                 Ascusb_18519 
                 1822 
               
               
                 
                   Oscillibacter 
                 
                 Ascusb_18557 
                 1823 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_18564 
                 1824 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_18566 
                 1825 
               
               
                   Clostridium _XI 
                 Ascusb_18567 
                 1826 
               
               
                 
                   Sporotomaculum 
                 
                 Ascusb_18585 
                 1827 
               
               
                 
                   Sporacetigenium 
                 
                 Ascusb_18592 
                 1828 
               
               
                 
                   Bulleidia 
                 
                 Ascusb_18608 
                 1829 
               
               
                   Clostridium _IV 
                 Ascusb_18636 
                 1830 
               
               
                 
                   Syntrophomonas 
                 
                 Ascusb_18648 
                 1831 
               
               
                 
                   Desulfatiferula 
                 
                 Ascusb_18678 
                 1832 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_18680 
                 1833 
               
               
                   Clostridium _XlVa 
                 Ascusb_18695 
                 1834 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_18731 
                 1835 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_18733 
                 1836 
               
               
                 
                   Prevotella 
                 
                 Ascusb_18735 
                 1837 
               
               
                 
                   Treponema 
                 
                 Ascusb_18738 
                 1838 
               
               
                 
                   Spiroplasma 
                 
                 Ascusb_18764 
                 1839 
               
               
                   Clostridium _XlVa 
                 Ascusb_18766 
                 1840 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_18795 
                 1841 
               
               
                 
                   Treponema 
                 
                 Ascusb_18814 
                 1842 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_18829 
                 1843 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_18846 
                 1844 
               
               
                 
                   Gelidibacter 
                 
                 Ascusb_18866 
                 1845 
               
               
                 
                   Acetitomaculum 
                 
                 Ascusb_18876 
                 1846 
               
               
                 
                   Proteiniclasticum 
                 
                 Ascusb_18907 
                 1847 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_18930 
                 1848 
               
               
                 
                   Prevotella 
                 
                 Ascusb_18949 
                 1849 
               
               
                 
                   Elusimicrobium 
                 
                 Ascusb_18970 
                 1850 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_18998 
                 1851 
               
               
                 
                   Devosia 
                 
                 Ascusb_19006 
                 1852 
               
               
                 
                   Roseburia 
                 
                 Ascusb_19052 
                 1853 
               
               
                 
                   Mucilaginibacter 
                 
                 Ascusb_19054 
                 1854 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_19056 
                 1855 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_19063 
                 1856 
               
               
                 
                   Paenibacillus 
                 
                 Ascusb_19092 
                 1857 
               
               
                 
                   Anaerotruncus 
                 
                 Ascusb_19101 
                 1858 
               
               
                 
                   Leucobacter 
                 
                 Ascusb_19114 
                 1859 
               
               
                   Clostridium _XlVa 
                 Ascusb_19148 
                 1860 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_19160 
                 1861 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_19170 
                 1862 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19200 
                 1863 
               
               
                   Clostridium _III 
                 Ascusb_19206 
                 1864 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_19219 
                 1865 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_19237 
                 1866 
               
               
                 
                   Butyrivibrio 
                 
                 Ascusb_19245 
                 1867 
               
               
                 
                   Acholeplasma 
                 
                 Ascusb_19267 
                 1868 
               
               
                 
                   Filomicrobium 
                 
                 Ascusb_19288 
                 1869 
               
               
                   Clostridium _III 
                 Ascusb_19335 
                 1870 
               
               
                 
                   Pseudoflavonifractor 
                 
                 Ascusb_19340 
                 1871 
               
               
                 
                   Anaerophaga 
                 
                 Ascusb_19341 
                 1872 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_19347 
                 1873 
               
               
                 
                   Asaccharobacter 
                 
                 Ascusb_19353 
                 1874 
               
               
                 
                   Kordia 
                 
                 Ascusb_19371 
                 1875 
               
               
                 
                   Ruminococcus 
                 
                 Ascusb_19376 
                 1876 
               
               
                   Clostridium _III 
                 Ascusb_19379 
                 1877 
               
               
                 
                   Ethanoligenens 
                 
                 Ascusb_19392 
                 1878 
               
               
                   Clostridium _XlVa 
                 Ascusb_19412 
                 1879 
               
               
                 
                   Barnesiella 
                 
                 Ascusb_19414 
                 1880 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_19444 
                 1881 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19457 
                 1882 
               
               
                 
                   Anaerophaga 
                 
                 Ascusb_19496 
                 1883 
               
               
                 
                   Acetitomaculum 
                 
                 Ascusb_19498 
                 1884 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19503 
                 1885 
               
               
                   Clostridium _III 
                 Ascusb_19507 
                 1886 
               
               
                 
                   Marinoscillum 
                 
                 Ascusb_19558 
                 1887 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_19568 
                 1888 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19579 
                 1889 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19613 
                 1890 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_19633 
                 1891 
               
               
                   Clostridium _XlVa 
                 Ascusb_19658 
                 1892 
               
               
                   Clostridium _IV 
                 Ascusb_19662 
                 1893 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_19681 
                 1894 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_19694 
                 1895 
               
               
                 
                   Lishizhenia 
                 
                 Ascusb_19698 
                 1896 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_19700 
                 1897 
               
               
                 
                   Howardella 
                 
                 Ascusb_19731 
                 1898 
               
               
                 
                   Roseburia 
                 
                 Ascusb_19745 
                 1899 
               
               
                   Clostridium _XlVa 
                 Ascusb_19754 
                 1900 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_19765 
                 1901 
               
               
                 
                   Lentisphaera 
                 
                 Ascusb_19772 
                 1902 
               
               
                 
                   Prevotella 
                 
                 Ascusb_19778 
                 1903 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_19779 
                 1904 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_19818 
                 1905 
               
               
                 
                   Proteiniphilum 
                 
                 Ascusb_19824 
                 1906 
               
               
                 
                   Schwartzia 
                 
                 Ascusb_19855 
                 1907 
               
               
                 
                   Anaerorhabdus 
                 
                 Ascusb_19884 
                 1908 
               
               
                 
                   Robinsoniella 
                 
                 Ascusb_19885 
                 1909 
               
               
                   Clostridium _IV 
                 Ascusb_19904 
                 1910 
               
               
                 Erysipelotrichaceae_incertae_sedis 
                 Ascusb_19936 
                 1911 
               
               
                 
                   Flavobacterium 
                 
                 Ascusb_19950 
                 1912 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_19955 
                 1913 
               
               
                   Clostridium _III 
                 Ascusb_19982 
                 1914 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_20001 
                 1915 
               
               
                 
                   Rhizobium 
                 
                 Ascusb_20027 
                 1916 
               
               
                 
                   Victivallis 
                 
                 Ascusb_20044 
                 1917 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_20062 
                 1918 
               
               
                 
                   Parabacteroides 
                 
                 Ascusb_20064 
                 1919 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_20067 
                 1920 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_20086 
                 1921 
               
               
                 
                   Acidobacteria 
                 
                 Ascusb_20100 
                 1922 
               
               
                 
                   Treponema 
                 
                 Ascusb_20104 
                 1923 
               
               
                   Clostridium _XlVa 
                 Ascusb_20108 
                 1924 
               
               
                   Clostridium _XlVa 
                 Ascusb_20135 
                 1925 
               
               
                 
                   Schwartzia 
                 
                 Ascusb_20143 
                 1926 
               
               
                 
                   Prevotella 
                 
                 Ascusb_20162 
                 1927 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_20172 
                 1928 
               
               
                 
                   Beijerinckia 
                 
                 Ascusb_20219 
                 1929 
               
               
                 
                   Eubacterium 
                 
                 Ascusb_20221 
                 1930 
               
               
                 
                   Adhaeribacter 
                 
                 Ascusb_20251 
                 1931 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_20264 
                 1932 
               
               
                 
                   Desulfobulbus 
                 
                 Ascusb_20275 
                 1933 
               
               
                 
                   Bacteroides 
                 
                 Ascusb_20278 
                 1934 
               
               
                 
                   Rummeliibacillus 
                 
                 Ascusb_20291 
                 1935 
               
               
                 
                   Agarivorans 
                 
                 Ascusb_20293 
                 1936 
               
               
                   Clostridium _XlVa 
                 Ascusb_20306 
                 1937 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_20312 
                 1938 
               
               
                 
                   Verrucomicrobia 
                 
                 Ascusb_20365 
                 1939 
               
               
                 
                   Prevotella 
                 
                 Ascusb_20368 
                 1940 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_20392 
                 1941 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_20405 
                 1942 
               
               
                 
                   Spiroplasma 
                 
                 Ascusb_20424 
                 1943 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_20440 
                 1944 
               
               
                   Clostridium _XlVa 
                 Ascusb_20449 
                 1945 
               
               
                 
                   Cyanobacteria 
                 
                 Ascusb_20456 
                 1946 
               
               
                 
                   Lactobacillus 
                 
                 Ascusb_20463 
                 1947 
               
               
                   Clostridium _XlVa 
                 Ascusb_20529 
                 1948 
               
               
                 
                   Prevotella 
                 
                 Ascusb_20534 
                 1949 
               
               
                 
                   Prevotella 
                 
                 Ascusb_20540 
                 1950 
               
               
                 
                   Marinobacter 
                 
                 Ascusb_20569 
                 1951 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_20576 
                 1952 
               
               
                 
                   Prevotella 
                 
                 Ascusb_20594 
                 1953 
               
               
                 
                   Dongia 
                 
                 Ascusb_20595 
                 1954 
               
               
                 
                   Anaerovorax 
                 
                 Ascusb_20639 
                 1955 
               
               
                 
                   Butyricimonas 
                 
                 Ascusb_20757 
                 1956 
               
               
                 
                   Cryptanaerobacter 
                 
                 Ascusb_20826 
                 1957 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_20904 
                 1958 
               
               
                 
                   Clostridium 
                   — 
                   sensu 
                   — 
                   stricto 
                 
                 Ascusb_20938 
                 1959 
               
               
                   Escherichia / Shigella   
                 Ascusb_20943 
                 1960 
               
               
                 
                   Butyricicoccus 
                 
                 Ascusb_20986 
                 1961 
               
               
                 
                   Prevotella 
                 
                 Ascusb_21013 
                 1962 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_21027 
                 1963 
               
               
                 
                   Thermotalea 
                 
                 Ascusb_21035 
                 1964 
               
               
                 
                   Cohaesibacter 
                 
                 Ascusb_21042 
                 1965 
               
               
                   Clostridium _XVIII 
                 Ascusb_21043 
                 1966 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_21085 
                 1967 
               
               
                 
                   Spirochaeta 
                 
                 Ascusb_21095 
                 1968 
               
               
                   Clostridium _XlVa 
                 Ascusb_21112 
                 1969 
               
               
                 
                   Hydrogenoanaerobacterium 
                 
                 Ascusb_21147 
                 1970 
               
               
                   Clostridium _IV 
                 Ascusb_21151 
                 1971 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_21160 
                 1972 
               
               
                 
                   Sporosarcina 
                 
                 Ascusb_21190 
                 1973 
               
               
                 
                   Selenomonas 
                 
                 Ascusb_21219 
                 1974 
               
               
                 
                   Papillibacter 
                 
                 Ascusb_21229 
                 1975 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_21244 
                 1976 
               
               
                   Clostridium _XlVa 
                 Ascusb_21271 
                 1977 
               
               
                 
                   Saccharofermentans 
                 
                 Ascusb_21297 
                 1978 
               
               
                   Clostridium _IV 
                 Ascusb_21309 
                 1979 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_21348 
                 1980 
               
               
                   Clostridium _IV 
                 Ascusb_21425 
                 1981 
               
               
                 Lachnospiracea_incertae_sedis 
                 Ascusb_21436 
                 1982 
               
               
                 
                   Desulfotomaculum 
                 
                 Ascusb_21466 
                 1983 
               
               
                 
                   Pedobacter 
                 
                 Ascusb_21484 
                 1984 
               
               
                 
                   Anaeroplasma 
                 
                 Ascusb_21546 
                 1985 
               
               
                   Clostridium _IV 
                 Ascusb_21585 
                 1986 
               
               
                 
                   Treponema 
                 
                 Ascusb_21595 
                 1987 
               
               
                 
                   Mogibacterium 
                 
                 Ascusb_21601 
                 1988 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Budapest Treaty Deposits of the Disclosure 
               
            
           
           
               
               
               
               
            
               
                   
                 Depository 
                 Accession Number 
                 Date of Deposit 
               
               
                   
                   
               
               
                   
                 NRRL 
                 NRRL Y-67249 
                 Apr. 27, 2016 
               
               
                   
                 NRRL 
                 NRRL B-67248 
                 Apr. 27, 2016 
               
               
                   
                 NRRL 
                 NRRL B-67347 
                 Dec. 15, 2016 
               
               
                   
                 NRRL 
                 NRRL B-67348 
                 Dec. 15, 2016 
               
               
                   
                 NRRL 
                 NRRL B-67349 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612001 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612002 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612003 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612004 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612005 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612006 
                 Dec. 12, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612007 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612008 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612009 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612010 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612011 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612012 
                 Dec. 15, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612013 
                 Dec. 19, 2016 
               
               
                   
                 Bigelow 
                 PATENT201612014 
                 Dec. 28, 2016 
               
               
                   
                 ATCC 
                 PTA-125917 5   
                 May 7, 2019 
               
               
                   
                 ATCC 
                 TSD-225 6   
                 Oct. 31, 2020 
               
               
                   
                 NRRL 
                 NRRL B-67764 7   
                 Apr. 11, 2019 
               
               
                   
                 NCTC 
                 NCTC 14479 8   
                 Jan. 21, 2021 
               
               
                   
                   
               
               
                   
                   5 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   
                   6 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   
                   7 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
               
                   
                   8 Deposit number applicable to Budapest treaty and/or type stain rules and procedures 
               
            
           
         
       
     
     DETAILED DESCRIPTION 
     Definitions 
     While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. 
     The term “a” or “an” may refer to one or more of that entity, i.e. can refer to plural referents. As such, the terms “a” or “an”, “one or more” and “at least one” are used interchangeably herein. In addition, reference to “an element” by the indefinite article “a” or “an” does not exclude the possibility that more than one of the elements is present, unless the context clearly requires that there is one and only one of the elements. 
     Reference throughout this specification to “one embodiment”, “an embodiment”, “one aspect”, or “an aspect” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present disclosure. Thus, the appearances of the phrases “in one embodiment” or “in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics can be combined in any suitable manner in one or more embodiments. 
     As used herein, in particular embodiments, the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 10%. 
     As used herein the terms “microorganism” or “microbe” should be taken broadly. These terms are used interchangeably and include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea, eukaryotic fungi and protists, as well as viruses. In some embodiments, the disclosure refers to the “microbes” of Table 1 or Table 3, or the “microbes” incorporated by reference. This characterization can refer to not only the predicted taxonomic microbial identifiers of the table, but also the identified strains of the microbes listed in the table. 
     The term “microbial consortia” or “microbial consortium” refers to a subset of a microbial community of individual microbial species, or strains of a species, which can be described as carrying out a common function, or can be described as participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g. increased milk production in a ruminant). The community may comprise two or more species, or strains of a species, of microbes. In some instances, the microbes coexist within the community symbiotically. 
     The term “microbial community” means a group of microbes comprising two or more species or strains. Unlike microbial consortia, a microbial community does not have to be carrying out a common function, or does not have to be participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g. increased milk production in a ruminant). 
     As used herein, “isolate,” “isolated,” “isolated microbe,” and like terms, are intended to mean that the one or more microorganisms has been separated from at least one of the materials with which it is associated in a particular environment (for example soil, water, animal tissue). 
     Microbes of the present disclosure may include spores and/or vegetative cells. In some embodiments, microbes of the present disclosure include microbes in a viable but non-culturable (VBNC) state. See Liao and Zhao (US Publication US2015267163A1). In some embodiments, microbes of the present disclosure include microbes in a biofilm. See Merritt et al. (U.S. Pat. No. 7,427,408). 
     Thus, an “isolated microbe” does not exist in its naturally occurring environment; rather, it is through the various techniques described herein that the microbe has been removed from its natural setting and placed into a non-naturally occurring state of existence. Thus, the isolated strain or isolated microbe may exist as, for example, a biologically pure culture, or as spores (or other forms of the strain) in association with an acceptable carrier. 
     As used herein, “spore” or “spores” refer to structures produced by bacteria and fungi that are adapted for survival and dispersal. Spores are generally characterized as dormant structures, however spores are capable of differentiation through the process of germination. Germination is the differentiation of spores into vegetative cells that are capable of metabolic activity, growth, and reproduction. The germination of a single spore results in a single fungal or bacterial vegetative cell. Fungal spores are units of asexual reproduction, and in some cases are necessary structures in fungal life cycles. Bacterial spores are structures for surviving conditions that may ordinarily be nonconductive to the survival or growth of vegetative cells. 
     As used herein, “microbial composition” refers to a composition comprising one or more microbes of the present disclosure, wherein a microbial composition, in some embodiments, is administered to animals of the present disclosure. 
     As used herein, “carrier”, “acceptable carrier”, or “pharmaceutical carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin; such as peanut oil, soybean oil, mineral oil, sesame oil, and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, in some embodiments as injectable solutions. Alternatively, the carrier can be a solid dosage form carrier, including but not limited to one or more of a binder (for compressed pills), a glidant, an encapsulating agent, a flavorant, and a colorant. The choice of carrier can be selected with regard to the intended route of administration and standard pharmaceutical practice. See Hardee and Baggo (1998. Development and Formulation of Veterinary Dosage Forms. 2 nd  Ed. CRC Press. 504 pg.); E.W. Martin (1970. Remington&#39;s Pharmaceutical Sciences. 17 th  Ed. Mack Pub. Co.); and Blaser et al. (US Publication US20110280840A1). 
     In certain aspects of the disclosure, the isolated microbes exist as isolated and biologically pure cultures. It will be appreciated by one of skill in the art, that an isolated and biologically pure culture of a particular microbe, denotes that said culture is substantially free (within scientific reason) of other living organisms and contains only the individual microbe in question. The culture can contain varying concentrations of said microbe. The present disclosure notes that isolated and biologically pure microbes often “necessarily differ from less pure or impure materials.” See, e.g. In re Bergstrom, 427 F.2d 1394, (CCPA 1970) (discussing purified prostaglandins), see also, In re Bergy, 596 F.2d 952 (CCPA 1979) (discussing purified microbes), see also, Parke-Davis &amp; Co. v. H.K. Mulford &amp; Co., 189 F. 95 (S.D.N.Y. 1911) (Learned Hand discussing purified adrenaline), aff&#39;d in part, rev&#39;d in part, 196 F. 496 (2d Cir. 1912), each of which are incorporated herein by reference. Furthermore, in some aspects, the disclosure provides for certain quantitative measures of the concentration, or purity limitations, that must be found within an isolated and biologically pure microbial culture. The presence of these purity values, in certain embodiments, is a further attribute that distinguishes the presently disclosed microbes from those microbes existing in a natural state. See, e.g., Merck &amp; Co. v. Olin Aathieson Chemical Corp., 253 F.2d 156 (4th Cir. 1958) (discussing purity limitations for vitamin B12 produced by microbes), incorporated herein by reference. 
     As used herein, “individual isolates” should be taken to mean a composition, or culture, comprising a predominance of a single genera, species, or strain, of microorganism, following separation from one or more other microorganisms. The phrase should not be taken to indicate the extent to which the microorganism has been isolated or purified. However, “individual isolates” can comprise substantially only one genus, species, or strain, of microorganism. 
     As used herein, “microbiome” refers to the collection of microorganisms that inhabit the digestive tract or gastrointestinal tract of an animal (including the rumen if said animal is a ruminant) and the microorgansims&#39; physical environment (i.e. the microbiome has a biotic and physical component). The microbiome is fluid and may be modulated by numerous naturally occurring and artificial conditions (e.g., change in diet, disease, antimicrobial agents, influx of additional microorganisms, etc.). The modulation of the microbiome of a rumen that can be achieved via administration of the compositions of the disclosure, can take the form of: (a) increasing or decreasing a particular Family, Genus, Species, or functional grouping of microbe (i.e. alteration of the biotic component of the rumen microbiome) and/or (b) increasing or decreasing volatile fatty acids in the rumen, increasing or decreasing rumen pH, increasing or decreasing any other physical parameter important for rumen health (i.e. alteration of the abiotic component of the rumen microbiome). 
     As used herein, “probiotic” refers to a substantially pure microbe (i.e., a single isolate) or a mixture of desired microbes, and may also include any additional components that can be administered to a mammal for restoring microbiota. Probiotics or microbial inoculant compositions of the invention may be administered with an agent to allow the microbes to survive the environment of the gastrointestinal tract, i.e., to resist low pH and to grow in the gastrointestinal environment. In some embodiments, the present compositions (e.g., microbial compositions) are probiotics in some aspects. 
     As used herein, “prebiotic” refers to an agent that increases the number and/or activity of one or more desired microbes. Non-limiting examples of prebiotics that may be useful in the methods of the present disclosure include fructooligosaccharides (e.g., oligofructose, inulin, inulin-type fructans), galactooligosaccharides, amino acids, alcohols, and mixtures thereof. See Ramirez-Farias et al. (2008 . Br. J. Nutr.  4:1-10) and Pool-Zobel and Sauer (2007 . J. Nutr.  137:2580-2584 and supplemental). 
     The term “growth medium” as used herein, is any medium which is suitable to support growth of a microbe. By way of example, the media may be natural or artificial including gastrin supplemental agar, LB media, blood serum, and tissue culture gels. It should be appreciated that the media may be used alone or in combination with one or more other media. It may also be used with or without the addition of exogenous nutrients. 
     The medium may be amended or enriched with additional compounds or components, for example, a component which may assist in the interaction and/or selection of specific groups of microorganisms. For example, antibiotics (such as penicillin) or sterilants (for example, quaternary ammonium salts and oxidizing agents) could be present and/or the physical conditions (such as salinity, nutrients (for example organic and inorganic minerals (such as phosphorus, nitrogenous salts, ammonia, potassium and micronutrients such as cobalt and magnesium), pH, and/or temperature) could be amended. 
     As used herein, the term “ruminant” includes mammals that are capable of acquiring nutrients from plant-based food by fermenting it in a specialized stomach (rumen) prior to digestion, principally through microbial actions. Ruminants included cattle, goats, sheep, giraffes, yaks, deer, antelope, and others. 
     As used herein, the term “bovid” includes any member of family Bovidae, which include hoofed mammals such as antelope, sheep, goats, and cattle, among others. 
     As used herein, “energy-corrected milk” or “ECM” represents the amount of energy in milk based upon milk volume, milk fat, and milk protein. ECM adjusts the milk components to 3.5% fat and 3.2% protein, thus equalizing animal performance and allowing for comparison of production at the individual animal and herd levels over time. An equation used to calculate ECM, as related to the present disclosure, is: 
       ECM=(0.327×milk pounds)+(12.95×fat pounds)+(7.2×protein pounds)
 
     As used herein, “improved” should be taken broadly to encompass improvement of a characteristic of interest, as compared to a control group, or as compared to a known average quantity associated with the characteristic in question. For example, “improved” milk production associated with application of a beneficial microbe, or consortia, of the disclosure can be demonstrated by comparing the milk produced by an ungulate treated by the microbes taught herein to the milk of an ungulate not treated. In the present disclosure, “improved” does not necessarily demand that the data be statistically significant (i.e. p&lt;0.05); rather, any quantifiable difference demonstrating that one value (e.g. the average treatment value) is different from another (e.g. the average control value) can rise to the level of “improved.” 
     As used herein, “inhibiting and suppressing” and like terms should not be construed to require complete inhibition or suppression, although this may be desired in some embodiments. 
     The term “marker” or “unique marker” as used herein is an indicator of unique microorganism type, microorganism strain or activity of a microorganism strain. A marker can be measured in biological samples and includes without limitation, a nucleic acid-based marker such as a ribosomal RNA gene, a peptide- or protein-based marker, and/or a metabolite or other small molecule marker. 
     The term “metabolite” as used herein is an intermediate or product of metabolism. A metabolite in one embodiment is a small molecule. Metabolites have various functions, including in fuel, structural, signaling, stimulatory and inhibitory effects on enzymes, as a cofactor to an enzyme, in defense, and in interactions with other organisms (such as pigments, odorants and pheromones). A primary metabolite is directly involved in normal growth, development and reproduction. A secondary metabolite is not directly involved in these processes but usually has an important ecological function. Examples of metabolites include but are not limited to antibiotics and pigments such as resins and terpenes, etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, tryptophan. Metabolites, as used herein, include small, hydrophilic carbohydrates; large, hydrophobic lipids and complex natural compounds. 
     As used herein, the term “genotype” refers to the genetic makeup of an individual cell, cell culture, tissue, organism, or group of organisms. 
     As used herein, the term “allele(s)” means any of one or more alternative forms of a gene, all of which alleles relate to at least one trait or characteristic. In a diploid cell, the two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes. Since the present disclosure, in embodiments, relates to QTLs, i.e. genomic regions that may comprise one or more genes or regulatory sequences, it is in some instances more accurate to refer to “haplotype” (i.e. an allele of a chromosomal segment) instead of “allele”, however, in those instances, the term “allele” should be understood to comprise the term “haplotype”. Alleles are considered identical when they express a similar phenotype. Differences in sequence are possible but not important as long as they do not influence phenotype. 
     As used herein, the term “locus” (loci plural) means a specific place or places or a site on a chromosome where for example a gene or genetic marker is found. 
     As used herein, the term “genetically linked” refers to two or more traits that are co-inherited at a high rate during breeding such that they are difficult to separate through crossing. 
     A “recombination” or “recombination event” as used herein refers to a chromosomal crossing over or independent assortment. The term “recombinant” refers to an organism having a new genetic makeup arising as a result of a recombination event. 
     As used herein, the term “molecular marker” or “genetic marker” refers to an indicator that is used in methods for visualizing differences in characteristics of nucleic acid sequences. Examples of such indicators are restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPs), insertion mutations, microsatellite markers (SSRs), sequence-characterized amplified regions (SCARs), cleaved amplified polymorphic sequence (CAPS) markers or isozyme markers or combinations of the markers described herein which defines a specific genetic and chromosomal location. Markers further include polynucleotide sequences encoding 16S or 18S rRNA, and internal transcribed spacer (ITS) sequences, which are sequences found between small-subunit and large-subunit rRNA genes that have proven to be especially useful in elucidating relationships or distinctions among when compared against one another. Mapping of molecular markers in the vicinity of an allele is a procedure which can be performed by the average person skilled in molecular-biological techniques. 
     The primary structure of major rRNA subunit 16S comprise a particular combination of conserved, variable, and hypervariable regions that evolve at different rates and enable the resolution of both very ancient lineages such as domains, and more modern lineages such as genera. The secondary structure of the 16S subunit include approximately 50 helices which result in base pairing of about 67% of the residues. These highly conserved secondary structural features are of great functional importance and can be used to ensure positional homology in multiple sequence alignments and phylogenetic analysis. Over the previous few decades, the 16S rRNA gene has become the most sequenced taxonomic marker and is the cornerstone for the current systematic classification of bacteria and archaea (Yarza et al. 2014 . Nature Rev. Micro.  12:635-45). 
     A sequence identity of 94.5% or lower for two 16S rRNA genes is strong evidence for distinct genera, 86.5% or lower is strong evidence for distinct families, 82% or lower is strong evidence for distinct orders, 78.5% is strong evidence for distinct classes, and 75% or lower is strong evidence for distinct phyla. The comparative analysis of 16S rRNA gene sequences enables the establishment of taxonomic thresholds that are useful not only for the classification of cultured microorganisms but also for the classification of the many environmental sequences. Yarza et al. 2014 . Nature Rev. Micro.  12:635-45). 
     As used herein, the term “trait” refers to a characteristic or phenotype. For example, in the context of some embodiments of the present disclosure, quantity of milk fat produced relates to the amount of triglycerides, triacylglycerides, diacylglycerides, monoacylglycerides, phospholipids, cholesterol, glycolipids, and fatty acids present in milk. Desirable traits may also include other milk characteristics, including but not limited to: predominance of short chain fatty acids, medium chain fatty acids, and long chain fatty acids; quantity of carbohydrates such as lactose, glucose, galactose, and other oligosaccharides; quantity of proteins such as caseins and whey; quantity of vitamins, minerals, milk yield/volume; reductions in methane emissions or manure; improved efficiency of nitrogen utilization; improved dry matter intake; improved feed efficiency and digestibility; increased degradation of cellulose, lignin, and hemicellulose; increased rumen concentrations of fatty acids such as acetic acid, propionic acid, and butyric acid; etc. 
     A trait may be inherited in a dominant or recessive manner, or in a partial or incomplete-dominant manner. A trait may be monogenic (i.e. determined by a single locus) or polygenic (i.e. determined by more than one locus) or may also result from the interaction of one or more genes with the environment. 
     In the context of this disclosure, traits may also result from the interaction of one or more mammalian genes and one or more microorganism genes. 
     As used herein, the term “homozygous” means a genetic condition existing when two identical alleles reside at a specific locus, but are positioned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism. Conversely, as used herein, the term “heterozygous” means a genetic condition existing when two different alleles reside at a specific locus, but are positioned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism. 
     As used herein, the term “phenotype” refers to the observable characteristics of an individual cell, cell culture, organism (e.g., a ruminant), or group of organisms which results from the interaction between that individual&#39;s genetic makeup (i.e., genotype) and the environment. 
     As used herein, the term “chimeric” or “recombinant” when describing a nucleic acid sequence or a protein sequence refers to a nucleic acid, or a protein sequence, that links at least two heterologous polynucleotides, or two heterologous polypeptides, into a single macromolecule, or that re-arranges one or more elements of at least one natural nucleic acid or protein sequence. For example, the term “recombinant” can refer to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques. 
     As used herein, a “synthetic nucleotide sequence” or “synthetic polynucleotide sequence” is a nucleotide sequence that is not known to occur in nature or that is not naturally occurring. Generally, such a synthetic nucleotide sequence will comprise at least one nucleotide difference when compared to any other naturally occurring nucleotide sequence. 
     As used herein, the term “nucleic acid” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides, or analogs thereof. This term refers to the primary structure of the molecule, and thus includes double- and single-stranded DNA, as well as double- and single-stranded RNA. It also includes modified nucleic acids such as methylated and/or capped nucleic acids, nucleic acids containing modified bases, backbone modifications, and the like. The terms “nucleic acid” and “nucleotide sequence” are used interchangeably. 
     As used herein, the term “gene” refers to any segment of DNA associated with a biological function. Thus, genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression. Genes can also include non-expressed DNA segments that, for example, form recognition sequences for other proteins. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters. 
     As used herein, the term “homologous” or “homologue” or “ortholog” is known in the art and refers to related sequences that share a common ancestor or family member and are determined based on the degree of sequence identity. The terms “homology,” “homologous,” “substantially similar” and “corresponding substantially” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant disclosure such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the disclosure encompasses more than the specific exemplary sequences. These terms describe the relationship between a gene found in one species, subspecies, variety, cultivar or strain and the corresponding or equivalent gene in another species, subspecies, variety, cultivar or strain. For purposes of this disclosure homologous sequences are compared. “Homologous sequences” or “homologues” or “orthologs” are thought, believed, or known to be functionally related. A functional relationship may be indicated in any one of a number of ways, including, but not limited to: (a) degree of sequence identity and/or (b) the same or similar biological function. Preferably, both (a) and (b) are indicated. Homology can be determined using software programs readily available in the art, such as those discussed in Current Protocols in Molecular Biology (F. M. Ausubel el al., eds., 1987) Supplement 30, section 7.718, Table 7.71. Some alignment programs are MacVector (Oxford Molecular Ltd, Oxford, U.K.), ALIGN Plus (Scientific and Educational Software, Pennsylvania) and AlignX (Vector NTi, Invitrogen, Carlsbad, Calif.). Another alignment program is Sequencher (Gene Codes, Ann Arbor, Mich.), using default parameters. 
     As used herein, the term “nucleotide change” refers to, e.g., nucleotide substitution, deletion, and/or insertion, as is well understood in the art. For example, mutations contain alterations that produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded protein or how the proteins are made. 
     As used herein, the term “protein modification” refers to, e.g., amino acid substitution, amino acid modification, deletion, and/or insertion, as is well understood in the art. 
     As used herein, the term “at least a portion” or “fragment” of a nucleic acid or polypeptide means a portion having the minimal size characteristics of such sequences, or any larger fragment of the full length molecule, up to and including the full length molecule. A fragment of a polynucleotide of the disclosure may encode a biologically active portion of a genetic regulatory element. A biologically active portion of a genetic regulatory element can be prepared by isolating a portion of one of the polynucleotides of the disclosure that comprises the genetic regulatory element and assessing activity as described herein. Similarly, a portion of a polypeptide may be 4 amino acids, 5 amino acids, 6 amino acids, 7 amino acids, and so on, going up to the full length polypeptide. The length of the portion to be used will depend on the particular application. A portion of a nucleic acid useful as a hybridization probe may be as short as 12 nucleotides; in some embodiments, it is 20 nucleotides. A portion of a polypeptide useful as an epitope may be as short as 4 amino acids. A portion of a polypeptide that performs the function of the full-length polypeptide would generally be longer than 4 amino acids. 
     Variant polynucleotides also encompass sequences derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) PNAS 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zbang et al. (1997) PNAS 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458. For PCR amplifications of the polynucleotides disclosed herein, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like. 
     The term “primer” as used herein refers to an oligonucleotide which is capable of annealing to the amplification target allowing a DNA polymerase to attach, thereby serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of primer extension product is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH. The (amplification) primer is preferably single stranded for maximum efficiency in amplification. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agent for polymerization. The exact lengths of the primers will depend on many factors, including temperature and composition (A/T vs. G/C content) of primer. A pair of bi-directional primers consists of one forward and one reverse primer as commonly used in the art of DNA amplification such as in PCR amplification. 
     The terms “stringency” or “stringent hybridization conditions” refer to hybridization conditions that affect the stability of hybrids, e.g., temperature, salt concentration, pH, formamide concentration and the like. These conditions are empirically optimized to maximize specific binding and minimize non-specific binding of primer or probe to its target nucleic acid sequence. The terms as used include reference to conditions under which a probe or primer will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g. at least 2-fold over background). Stringent conditions are sequence dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe or primer. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M Na+ ion, typically about 0.01 to 1.0 M Na+ ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes or primers (e.g. 10 to 50 nucleotides) and at least about 60° C. for long probes or primers (e.g. greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringent conditions or “conditions of reduced stringency” include hybridization with a buffer solution of 30% formamide, 1 M NaCl, 1% SDS at 37° C. and a wash in 2×SSC at 40° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60° C. Hybridization procedures are well known in the art and are described by e.g. Ausubel et al., 1998 and Sambrook et al., 2001. In some embodiments, stringent conditions are hybridization in 0.25 M Na2HPO4 buffer (pH 7.2) containing 1 mM Na2EDTA, 0.5-20% sodium dodecyl sulfate at 45° C., such as 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19% or 20%, followed by a wash in 5-SSC, containing 0.1% (w/v) sodium dodecyl sulfate, at 55° C. to 65° C. 
     As used herein, “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence that can stimulate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of some variation may have identical promoter activity. 
     As used herein, a “constitutive promoter” is a promoter which is active under most conditions and/or during most development stages. There are several advantages to using constitutive promoters in expression vectors used in biotechnology, such as: high level of production of proteins used to select transgenic cells or organisms; high level of expression of reporter proteins or scorable markers, allowing easy detection and quantification; high level of production of a transcription factor that is part of a regulatory transcription system; production of compounds that requires ubiquitous activity in the organism; and production of compounds that are required during all stages of development. Non-limiting exemplary constitutive promoters include, CaMV 35S promoter, opine promoters, ubiquitin promoter, alcohol dehydrogenase promoter, etc. 
     As used herein, a “non-constitutive promoter” is a promoter which is active under certain conditions, in certain types of cells, and/or during certain development stages. For example, tissue specific, tissue preferred, cell type specific, cell type preferred, inducible promoters, and promoters under development control are non-constitutive promoters. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues. 
     As used herein, “inducible” or “repressible” promoter is a promoter which is under chemical or environmental factors control. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, certain chemicals, the presence of light, acidic or basic conditions, etc. 
     As used herein, a “tissue specific” promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive expression of genes, tissue-specific expression is the result of several interacting levels of gene regulation. As such, in the art sometimes it is preferable to use promoters from homologous or closely related species to achieve efficient and reliable expression of transgenes in particular tissues. This is one of the main reasons for the large amount of tissue-specific promoters isolated from particular tissues found in both scientific and patent literature. 
     As used herein, the term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is regulated by the other. For example, a promoter is operably linked with a coding sequence when it is capable of regulating the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in a sense or antisense orientation. In another example, the complementary RNA regions of the disclosure can be operably linked, either directly or indirectly, 5′ to the target mRNA, or 3′ to the target mRNA, or within the target mRNA, or a first complementary region is 5′ and its complement is 3′ to the target mRNA. 
     As used herein, the phrases “recombinant construct”, “expression construct”, “chimeric construct”, “construct”, and “recombinant DNA construct” are used interchangeably herein. A recombinant construct comprises an artificial combination of nucleic acid fragments, e.g., regulatory and coding sequences that are not found together in nature. For example, a chimeric construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such construct may be used by itself or may be used in conjunction with a vector. If a vector is used then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid fragments of the disclosure. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) EMBO J. 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, immunoblotting analysis of protein expression, or phenotypic analysis, among others. Vectors can be plasmids, viruses, bacteriophages, pro-viruses, phagemids, transposons, artificial chromosomes, and the like, that replicate autonomously or can integrate into a chromosome of a host cell. A vector can also be a naked RNA polynucleotide, a naked DNA polynucleotide, a polynucleotide composed of both DNA and RNA within the same strand, a poly-lysine-conjugated DNA or RNA, a peptide-conjugated DNA or RNA, a liposome-conjugated DNA, or the like, that is not autonomously replicating. As used herein, the term “expression” refers to the production of a functional end-product e.g., an mRNA or a protein (precursor or mature). 
     In some embodiments, the cell or organism has at least one heterologous trait. As used herein, the term “heterologous trait” refers to a phenotype imparted to a transformed host cell or transgenic organism by an exogenous DNA segment, heterologous polynucleotide or heterologous nucleic acid. Various changes in phenotype are of interest to the present disclosure, including but not limited to modifying the fatty acid composition in milk, altering the carbohydrate content of milk, increasing an ungulate&#39;s yield of an economically important trait (e.g., milk, milk fat, milk proteins, etc.) and the like. These results can be achieved by providing expression of heterologous products or increased expression of endogenous products in organisms using the methods and compositions of the present disclosure. 
     As used herein, the term “MIC” means maximal information coefficient. MIC is a type of nonparamentric network analysis that identifies a score (MIC score) between active microbial strains of the present disclosure and at least one measured metadata (e.g., milk fat). Further, U.S. application Ser. No. 15/217,575, filed on Jul. 22, 2016 (issued as U.S. Pat. No. 9,540,676 on Jan. 10, 2017) is hereby incorporated by reference in its entirety. 
     The maximal information coefficient (MIC) is then calculated between strains and metadata 3021a, and between strains 3021b; as seen in  FIG.  3   . Results are pooled to create a list of all relationships and their corresponding MIC scores 3022. If the relationship scores below a given threshold 3023, the relationship is deemed/identified as irrelevant 3023b. If the relationship is above a given threshold 3023, the relationship deemed/identified as relevant 2023a, and is further subject to network analysis 3024. The following code fragment shows an exemplary methodology for such analysis, according to one embodiment: 
     
       
         
           
               
               
             
               
                   
                   
               
             
            
               
                   
                 Read total list of relationships file as links 
               
               
                   
                 threshold = 0.8 
               
               
                   
                 for i in range(len(links)): 
               
               
                   
                  if links &gt;= threshold 
               
               
                   
                   multiplier[i] = 1 
               
               
                   
                  else 
               
               
                   
                   multiplier[i] = 0 
               
               
                   
                  end if 
               
               
                   
                  links_temp = multiplier*links 
               
               
                   
                  final_links = links_temp[links_temp != 0] 
               
               
                   
                  savetxt(output_file,final_links) 
               
               
                   
                  output_file.close( ) 
               
               
                   
                   
               
            
           
         
       
     
     Based on the output of the network analysis, active strains are selected 3025 for preparing products (e.g., ensembles, aggregates, and/or other synthetic groupings) containing the selected strains. The output of the network analysis can also be used to inform the selection of strains for further product composition testing. 
     The use of thresholds is discussed above for analyses and determinations. Thresholds can be, depending on the implementation and application: (1) empirically determined (e.g., based on distribution levels, setting a cutoff at a number that removes a specified or significant portion of low level reads); (2) any non-zero value; (3) percentage/percentile based; (4) only strains whose normalized second marker (i.e., activity) reads is greater than normalized first marker (cell count) reads; (5) log 2 fold change between activity and quantity or cell count; (6) normalized second marker (activity) reads is greater than mean second marker (activity) reads for entire sample (and/or sample set); and/or any magnitude threshold described above in addition to a statistical threshold (i.e., significance testing). The following example provides thresholding detail for distributions of RNA-based second marker measurements with respect to DNA-based first marker measurements, according to one embodiment. 
     As used herein “shelf-stable” refers to a functional attribute and new utility acquired by the microbes formulated according to the disclosure, which enable said microbes to exist in a useful/active state outside of their natural environment in the rumen (i.e. a markedly different characteristic). Thus, shelf-stable is a functional attribute created by the formulations/compositions of the disclosure and denoting that the microbe formulated into a shelf-stable composition can exist outside the rumen and under ambient conditions for a period of time that can be determined depending upon the particular formulation utilized, but in general means that the microbes can be formulated to exist in a composition that is stable under ambient conditions for at least a few days and generally at least one week. Accordingly, a “shelf-stable ruminant supplement” is a composition comprising one or more microbes of the disclosure, said microbes formulated in a composition, such that the composition is stable under ambient conditions for at least one week, meaning that the microbes comprised in the composition (e.g. whole cell, spore, or lysed cell) are able to impart one or more beneficial phenotypic properties to a ruminant when administered (e.g. increased milk yield, improved milk compositional characteristics, improved rumen health, and/or modulation of the rumen microbiome). 
     Isolated Microbes 
     In some aspects, the present disclosure provides isolated microbes, including novel strains of microbes, presented in Table 1 and Table 3. 
     In other aspects, the present disclosure provides isolated whole microbial cultures of the microbes identified in Table 1 and Table 3. These cultures may comprise microbes at various concentrations. 
     In some aspects, the disclosure provides for utilizing one or more microbes selected from Table 1 and Table 3 to increase a phenotypic trait of interest in a ruminant. 
     In some embodiments, the disclosure provides isolated microbial species belonging to taxonomic families of Clostridiaceae, Ruminococcaceae, Lachnospiraceae, Acidaminococcaceae, Peptococcaceae, Porphyromonadaceae, Prevotellaceae, Neocallimastigaceae, Saccharomycetaceae, Phaeosphaeriaceae, Erysipelotrichia, Anaerolinaeceae, Atopobiaceae, Botryosphaeriaceae, Eubacteriaceae, Acholeplasmataceae, Succinivibrionaceae, Lactobacillaceae, Selenomonadaceae, Burkholderiaceae, and Streptococcaceae. 
     In further embodiments, isolated microbial species may be selected from genera of family Clostridiaceae, including  Acetanaerobacterium, Acetivibrio, Acidaminobacter, Alkaliphilus, Anaerobacter, Anaerostipes, Anaerotruncus, Anoxynatronum, Bryantella, Butyricicoccus, Caldanaerocella, Caloramator, Caloranaerobacter, Caminicella, Candidatus Arthromitus, Clostridium, Coprobacillus, Dorea, Ethanologenbacterium, Faecalibacterium, Garciella, Guggenheimella, Hespellia, Linmingia, Natronincola, Oxobacter, Parasporobacterium, Sarcina, Soehngenia, Sporobacter, Subdoligranulum, Tepidibacter, Tepidimicrobium, Thermobrachium, Thermohalobacter , and  Tindallia.    
     In further embodiments, isolated microbial species may be selected from genera of family Ruminococcaceae, including  Ruminococcus, Acetivibrio, Sporobacter, Anaerofilium, Papillibacter, Oscillospira, Gemmiger, Faecalibacterium, Fastidiosipila, Anaerotruncus, Ethanolingenens, Acetanaerobacterium, Subdoligranulum, Hydrogenoanaerobacterium , and  Candidadus Soleaferrea.    
     In further embodiments, isolated microbial species may be selected from genera of family Lachnospiraceae, including  Butyrivibrio, Roseburia, Lachnospira, Acetitomaculum, Coprococcus, Johnsonella, Catonella, Pseudobutyrivibrio, Syntrophococcus, Sporobacterium, Parasporobacterium, Lachnobacterium, Shuttleworthia, Dorea, Anaerostipes, Hespellia, Marvinbryantia, Oribacterium, Moryella, Blautia, Robinsoniella, Cellulosilyticum, Lachnoanaerobaculum, Stomatobaculum, Fusicatenibacter, Acetatifactor , and  Eisenbergiella.    
     In further embodiments, isolated microbial species may be selected from genera of family Acidaminococcaceae, including  Acidaminococcus, Phascolarctobacterium, Succiniclasticum , and  Succinispira.    
     In further embodiments, isolated microbial species may be selected from genera of family Peptococcaceae, including  Desulfotomaculum, Peptococcus, Desulfitobacterium, Syntrophobotulus, Dehalobacter, Sporotomaculum, Desulfosporosinus, Desulfonispora, Pelotomaculum, Thermincola, Cryptanaerobacter, Desulfitibacter, Candidatus Desulforudis, Desulfurispora , and  Desulfitospora.    
     In further embodiments, isolated microbial species may be selected from genera of family Porphyromonadaceae, including  Porphyromonas, Dysgonomonas, Tannerella, Odoribacter, Proteiniphilum, Petrimonas, Paludibacter, Parabacteroides, Barnesiella, Candidatus Vestibaculum, Butyricimonas, Macellibacteroides , and  Coprobacter.    
     In further embodiments, isolated microbial species may be selected from genera of family Anaerolinaeceae including  Anaerolinea, Bellilinea, Leptolinea, Levilinea, Longilinea, Ornatilinea , and  Pelolinea.    
     In further embodiments, isolated microbial species may be selected from genera of family Atopobiaceae including Atopbium and Olsenella. 
     In further embodiments, isolated microbial species may be selected from genera of family Eubacteriaceae including Acetobacterium,  Alkalibacter, Alkalibaculum, Aminicella, Anaerofustis. Eubacterium, Garciella , and  Pseudoramibacter.    
     In further embodiments, isolated microbial species may be selected from genera of family Acholeplasmataceae including  Acholeplasma.    
     In further embodiments, isolated microbial species may be selected from genera of family Succinivibrionaceae including  Anaerobiospirillun, Ruminobacter, Succinatimonas, Succininonas , and  Succinivibrio.    
     In further embodiments, isolated microbial species may be selected from genera of family Lactobacillaceae including  Lactobacillus, Paralactobacillus, Pediococcus , and  Sharpea.    
     In further embodiments, isolated microbial species may be selected from genera of family Selenomonadaceae including  Anaerovibrio, Centipeda, Megamonas, Mitsuokella, Pectinatus, Propionispira, Schwartzia, Selenomonas , and  Zymophilus.    
     In further embodiments, isolated microbial species may be selected from genera of family Burkholderiaceae including  Burkholderia, Chitinimonas, Cupriavidus, Lautropia, Limnobacter, Pandoraea, Paraburkholderia, Paucimonas, Polynucleobacter, Ralstonia, Thermothrix , and  Wautersia.    
     In further embodiments, isolated microbial species may be selected from genera of family Streptococcaceae including  Lactococcus, Lactovum , and  Streptococcus.    
     In further embodiments, isolated microbial species may be selected from genera of family Anaerolinaeceae including  Aestuariimicrobium, Arachnia, Auraticoccus, Brooklawnia, Friedmanniella, Granulicoccus, Luteococcus, Mariniluteicoccus, Microlunatus, Micropruina, Naumannella, Propionibacterium, Propionicicella, Propioniciclava, Propioniferax, Propionimicrobium , and  Tessaracoccus.    
     In further embodiments, isolated microbial species may be selected from genera of family Prevotellaceae, including  Paraprevotella, Prevotella, hallella, Xylanibacter , and  Alloprevotella.    
     In further embodiments, isolated microbial species may be selected from genera of family Neocallimastigaceae, including  Anaeromyces, Caecomyces, Cyllamyces, Neocallimastix, Orpinomyces , and  Piromyces.    
     In further embodiments, isolated microbial species may be selected from genera of family Saccharomycetaceae, including  Brettanomyces, Candida, Citeromyces, CyWiclomyces, Debaryonyces, Issatchenkia, Kazachstania  (syn.  Arxiozyma ),  Kluyveromyces, Komagataella, Kuraishia, Lachancea, Lodderomyces, Nakaseomyces, Pachysolen, Pichia, Saccharomyces, Spathaspora, Tetrapisispora, Vanderwaltoryma, Torulaspora, Williopsis, Zygosaccharomyces, and Zygotorulaspora.    
     In further embodiments, isolated microbial species may be selected from genera of family Erysipelotrichaceae, including  Erysipelothrix, Solobacterium, Turicibacter, Faecalibaculum, Faecalicoccus, Faecalitalea, Holdemanella, Holdemania, Dielma, Eggerthia, Erysipelatoclostridium, Allobacterium, Breznakia, Bulleidia, Catenibacterium, Catenisphaera , and  Coprobacillus.    
     In further embodiments, isolated microbial species may be selected from genera of family Phaeosphaeriaceae, including  Barria, Bricookea, Carinispora, Chaetoplea, Eudarluca, Hadrospora, lsthmosporella, Katumotoa, Lautitia, Metameris, Mixtura, Neophaeosphaeria, Nodulosphaeria, Ophiosphaerella, Phaeosphaeris, Phaeosphaeriopsis, Setomelanomma, Stagonospora, Teratosphaeria , and  Wilmia.    
     In further embodiments, isolated microbial species may be selected from genera of family Botryosphaeriaceae, including  Amarenomyces, Aplosporella, Auerswaldiella, Botryosphaeria, Dichomera, Diplodia, Discochora, Dothidothia, Dothiorella, Fusicoccum, Granulodiplodia, Guignardia, Lasiodiplodia, Leptodothiorella, Leptodothiorella, Leptoguignardia, Macrophoma, Macrophomina, Nattrassia, Neodeightonia, Neofusicocum, Neoscytalidium, Otthia, Phaeobotryosphaeria, Phomatosphaeropsis, Phyllosticta, Pseudofusicoccum, Saccharata, Sivanesania , and  Thyrostroma.    
     In some embodiments, the disclosure provides isolated microbial species belonging to genera of:  Clostridium, Ruminococcus, Roseburia, Hydrogenoanaerobacterium, Saccharofermentans, Papillibacter, Pelotomaculum, Butyricicoccus, Tannerella, Prevotella, Butyricimonas, Piromyces, Candida, Vrystaatia, Orpinomyces, Neocallimastix , and  Phyllosticta . In further embodiments, the disclosure provides isolated microbial species belonging to the family of Lachnospiraceae, and the order of Saccharomycetales. In further embodiments, the disclosure provides isolated microbial species of  Candida xylopsoci, Vrystaatia aloeicola , and  Phyllosticta capitalensis.    
     In some embodiments, a microbe from the taxa disclosed herein are utilized to impart one or more beneficial properties or improved traits to milk in ruminants. 
     In some embodiments, the disclosure provides isolated microbial species, selected from the group consisting of:  Clostridium, Ruminococcus, Roseburia, Hydrogenoanaerobacterium, Saccharofermentans, Papillibacter, Pelotomaculum, Butyricicoccus, Tannerella, Prevotella, Butyricimonas, Piromyces, Pichia, Candida, Vrystaatia, Orpinomyces, Neocallimastix , and  Phyllosticta.    
     In some embodiments, the disclosure provides novel isolated microbial strains of species, selected from the group consisting of:  Clostridium, Ruminococcus, Roseburia, Hydrogenoanaerobacterium, Saccharofermentans, Papillibacter, Pelotomaculum, Butyricicoccus, Mannerella, Prevotella, Butvricimonas, Piromyces, Pichia, Candida, Vrystaatia, Orpinomyces, Neocallinastix, Ruminococcus , and  Phyllosticta . Particular novel strains of these aforementioned taxonomic groups can be found in Table 1 and/or Table 3. 
     In some embodiments, the disclosure provides isolated microbial strains of  Ruminococcus bovis . In some embodiments, the isolated microbial strain of  Ruminococcus bovis  comprises the 16S nucleic acid sequence of SEQ ID NO: 2108. In some embodiments, the isolated microbial strain of  Ruminococcus bovis  comprises the deposit accession number PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479. In some embodiments, the isolated strain of  Ruminococcus bovis  comprises one or more mutations selected from the group consisting of: (a) a G→T substitution at position 297 of SEQ ID NO: 2109; (b) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111; (c) a T→G substitution at position 307 of SEQ ID NO: 2111; (d) a −A deletion at position 300 of SEQ ID NO: 2113; (e) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115; (f) a +T insertion between positions 105-106 of SEQ ID NO: 2117; (g) a C→T substitution at position 298 of SEQ ID NO: 2119; (h) a C→A substitution at position 298 of SEQ ID NO: 2121; and (i) a +AC insertion between positions 43-44 of SEQ ID NO: 2123. In some embodiments, the isolated strain of  Ruminococcus bovis  comprises a nucleic acid sequence selected from any one of SEQ ID NOs: 2110, 2112, 2114, 2116, 2118, 2120, 2122, or 2124. 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a)  Ruminococcus bovis  comprising one or more mutations selected from the group consisting of: (i) a G→T substitution at position 297 of SEQ ID NO: 2109; (ii) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111; (iii) a T→G substitution at position 307 of SEQ ID NO: 2111; (iv) a −A deletion at position 300 of SEQ ID NO: 2113; (v) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115; (vi) a +T insertion between positions 105-106 of SEQ ID NO: 2117; (vii) a C→T substitution at position 298 of SEQ ID NO: 2119; (viii) a C→A substitution at position 298 of SEQ ID NO: 2121; and (ix) a +AC insertion between positions 43-44 of SEQ ID NO: 2123; and (b) a carrier suitable for oral ruminant administration. 
     In some embodiments, the present disclosure provides an orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising: (a)  Ruminococcus bovis  comprising a nucleic acid sequence selected from any one of SEQ ID NOs: 2110, 2112, 2114, 2116, 2118, 2120, 2122, or 2124; and (b) a carrier suitable for oral ruminant administration. 
     Furthermore, the disclosure relates to microbes having characteristics substantially similar to that of a microbe identified in Table 1 or Table 3. 
     The isolated microbial species, and novel strains of said species, identified in the present disclosure, are able to impart beneficial properties or traits to ruminant milk production. For instance, the isolated microbes described in Table 1 and Table 3, or consortia of said microbes, are able to increase total milk fat in ruminant milk. The increase can be quantitatively measured, for example, by measuring the effect that said microbial application has upon the modulation of total milk fat. 
     In some embodiments, the isolated microbial strains are microbes of the present disclosure that have been genetically modified. In some embodiments, the genetically modified or recombinant microbes comprise polynucleotide sequences which do not naturally occur in said microbes. In some embodiments, the microbes may comprise heterologous polynucleotides. In further embodiments, the heterologous polynucleotides may be operably linked to one or more polynucleotides native to the microbes. 
     In some embodiments, the heterologous polynucleotides may be reporter genes or selectable markers. In some embodiments, reporter genes may be selected from any of the family of fluorescence proteins (e.g., GFP, RFP, YFP, and the like), β-galactosidase, luciferase. In some embodiments, selectable markers may be selected from neomycin phosphotransferase, hygromycin phosphotransferase, aminoglycoside adenyltransferase, dihydrofolate reductase, acetolactase synthase, bromoxynil nitrilase, β-glucuronidase, dihydrogolate reductase, and chloramphenicol acetyltransferase. In some embodiments, the heterologous polynucleotide may be operably linked to one or more promoter. 
     
       
         
           
               
             
               
                 TABLE 5 
               
               
                   
               
               
                 Taxa (largely Genera) of the present disclosure not 
               
               
                 known to have been utilized in animal agriculture. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 
                   Intestinimonas 
                 
                 
                   Anaerolinea 
                 
               
               
                   
                 
                   Pseudobutyrivibrio 
                 
                 
                   Olsenella 
                 
               
               
                   
                 
                   Eubacterium 
                 
                 
                   Catenisphaera 
                 
               
               
                   
                 
                   Faecalibacterium 
                 
                 
                   Solobacterium 
                 
               
               
                   
                 
                   Blautia 
                 
                 
                   Ralsonia 
                 
               
               
                   
                 
                   Coprococcus 
                 
                 
                   Casaltella 
                 
               
               
                   
                 
                   Anaeroplasma 
                 
                 
                   Acholeplasma 
                 
               
               
                   
                 
                   Aminiphilus 
                 
                 
                   Mitsuokella 
                 
               
               
                   
                 
                   Alistipes 
                 
                 
                   Sharpea 
                 
               
               
                   
                 
                   Oscillibacter 
                 
                 
                   Neocallimastix 
                 
               
               
                   
                 
                   Odoribacter 
                 
                 
                   Pichia 
                 
               
               
                   
                 
                   Tannerella 
                 
                 
                   Candida 
                 
               
               
                   
                 
                   Hydrogenoanaerobacterium 
                 
                 
                   Orpinomyces 
                 
               
               
                   
                 
                   Succinivibrio 
                 
                 
                   Sugiyamaella 
                 
               
               
                   
                 
                   Ruminobacter 
                 
                 
                   Cyllamyces 
                 
               
               
                   
                 
                   Lachnospira 
                 
                 
                   Caecomyces 
                 
               
               
                   
                 
                   Sinimarinibacterium 
                 
                 
                   Tremella 
                 
               
               
                   
                 
                   Hydrogenoanaerobacterium 
                 
                 
                   Turicibacter 
                 
               
               
                   
                   Clostridium  XlVa 
                 
                   Anaerolinea 
                 
               
               
                   
                 
                   Saccharofermentans 
                 
                 
                   Piromyces 
                 
               
               
                   
                 
                   Butyricicoccus 
                 
                 
                   Olsenella 
                 
               
               
                   
                 
                   Papillibacter 
                 
                   Clostridium  XICa 
               
               
                   
                 
                   Pelotomaculum 
                 
                 Erysipelotrichaceae 
               
               
                   
                 
                   Lachnospiracea 
                 
                 
                   Solobacterium 
                 
               
               
                   
                 
                   Anaeroplasma 
                 
                 
                   Ralstonia 
                 
               
               
                   
                 
                   Clostridium 
                 
                 
                   Eubacterium 
                 
               
               
                   
                 
                   Rikenella 
                 
                 
                   Lachnobacterium 
                 
               
               
                   
                 
                   Tannerella 
                 
                 
                   Acholeplasma 
                 
               
               
                   
                 
                   Howardella 
                 
                 
                   Selenomonas 
                 
               
               
                   
                 
                   Butyricimonas 
                 
                 
                   Sharpea 
                 
               
               
                   
                 
                   Succinivibrio 
                 
                 
                   Phyllosticta 
                 
               
               
                   
                 
                   Ruminobacter 
                 
                 
                   Candida xylopsoc 
                 
               
               
                   
                 
                   Syntrophococcus 
                 
                 
                   Candida apicol 
                 
               
               
                   
                 
                   Pseudobutyrivibrio 
                 
                 
                   Saccharomycetales 
                 
               
               
                   
                 
                   Ascomycota 
                 
                 
                   Candida rugos 
                 
               
               
                   
                   
               
            
           
         
       
     
     Microbial Consortia 
     In some aspects, the disclosure provides microbial consortia comprising a combination of at least any two microbes selected from amongst the microbes identified in Table 1 and/or Table 3. 
     In certain embodiments, the consortia of the present disclosure comprise two microbes, or three microbes, or four microbes, or five microbes, or six microbes, or seven microbes, or eight microbes, or nine microbes, or ten or more microbes. Said microbes of the consortia are different microbial species, or different strains of a microbial species. 
     In some embodiments, the disclosure provides consortia, comprising: at least two isolated microbial species belonging to genera of:  Clostridium, Ruminococcus, Roseburia, Hydrogenoanaerobacterium, Saccharofermentans, Papillibacter, Pelotomacuium, Butnricicoccus, Tannerella, Prevotella, Butyricimonas, Piromyces, Pichia, Candida, Vrystaatia, Orpinomyces, Neocallimastix , and  Phyllosticta . Particular novel strains of species of these aforementioned genera can be found in Table 1 and/or Table 3. 
     In some embodiments, the disclosure provides consortia, comprising: at least two isolated microbial species, selected from the group consisting of species of the family of Lachnospiraceae, and the order of Saccharomycetales. 
     In particular aspects, the disclosure provides microbial consortia, comprising species as grouped in Tables 6-12. With respect to Tables 6-12, the letters A through I represent a non-limiting selection of microbes of the present disclosure, defined as: 
     A=Strain designation Ascusb_5 (SEQ ID NO: 1) identified in Table 1; 
     B=Strain designation Ascusb_3138 (SEQ ID NO: 28) identified in Table 1: 
     C=Strain designation Ascusb_5 (SEQ ID NO: 2108) identified in Table 1; 
     D=Strain designation Ascusb_826 (SEQ ID NO: 2067) identified in Table; 
     E=Strain designation Ascusf_22 (SEQ ID NO: 33) identified in Table 1; 
     F=Strain designation Ascusf_23 (SEQ ID NO: 34) identified in Table 1; 
     G=Strain designation Ascusf_24 (SEQ ID NO. 35) identified in Table 1; 
     H=Strain designation Ascusf_45 (SEQ ID NO: 38) identified in Table 1; and 
     I=Strain designation Ascusf_15 (SEQ ID NO: 32) identified in Table 1. 
     
       
         
           
               
             
               
                 TABLE 6 
               
               
                   
               
               
                 Eight and Nine Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 A, B, C, D, E, F, G, H 
                 A, B, C, D, E, F, G, I 
                 A, B, C, D, E, F, H, I 
                 A, B, C, D, E, G, H, I 
                 A, B, C, D, F, G, H, I 
                 A, B, C, E, F, G, H, I 
               
               
                 A, B, D, E, F, G, H, I 
                 A, C, D, E, F, G, H, I 
                 B, C, D, E, F, G, H, I 
                 A, B, C, D, E, F, G, H, I 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
               
                   
               
               
                 Seven Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 A, B, C, D, E, F, G 
                 A, B, C, D, E, F, H 
                 A, B, C, D, E, F, I 
                 A, B, C, D, E, G, H 
                 A, B, C, D, E, G, I 
                 A, B, C, D, E, H, I 
               
               
                 A, B, C, D, F, G, H 
                 A, B, C, D, F, G, I 
                 A, B, C, D, F, H, I 
                 A, B, C, D, G, H, I 
                 A, B, C, E, F, G, H 
                 A, B, C, E, F, G, I 
               
               
                 A, B, C, E, F, H, I 
                 A, B, C, E, G, H, I 
                 A, B, C, F, G, H, I 
                 A, B, D, E, F, G, H 
                 A, B, D, E, F, G, I 
                 A, B, D, E, F, H, I 
               
               
                 A, B, D, E, G, H, I 
                 A, B, D, F, G, H, I 
                 A, B, E, F, G, H, I 
                 A, C, D, E, F, G, H 
                 A, C, D, E, F, G, I 
                 A, C, D, E, F, H, I 
               
               
                 A, C, D, E, G, H, I 
                 A, C, D, F, G, H, I 
                 A, C, E, F, G, H, I 
                 A, D, E, F, G, H, I 
                 B, C, D, E, F, G, H 
                 B, C, D, E, F, G, I 
               
               
                 B, C, D, E, F, H, I 
                 B, C, D, E, G, H, I 
                 B, C, D, F, G, H, I 
                 B, C, E, F, G, H, I 
                 B, D, E, F, G, H, I 
                 C, D, E, F, G, H, I 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
               
                   
               
               
                 Six Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 A, B, C, D, E, F 
                 A, B, C, D, E, G 
                 A, B, C, D, E, H 
                 A, B, C, D, E, I 
                 A, B, C, D, F, G 
                 A, B, C, D, F, H 
                 A, B, C, D, F, I 
               
               
                 A, B, C, D, G, H 
                 A, B, C, D, G, I 
                 A, B, C, D, H, I 
                 A, B, C, E, F, G 
                 A, B, C, E, F, H 
                 A, B, C, E, F, I 
                 A, B, C, E, G, H 
               
               
                 A, B, C, E, G, I 
                 A, B, C, E, H, I 
                 A, B, C, F, G, H 
                 A, B, C, F, G, I 
                 A, B, C, F, H, I 
                 A, B, C, G, H, I 
                 A, B, D, E, F, G 
               
               
                 A, B, D, E, F, H 
                 A, B, D, E, F, I 
                 A, B, D, E, G, H 
                 A, B, D, E, G, I 
                 A, B, D, E, H, I 
                 A, B, D, F, G, H 
                 A, B, D, F, G, I 
               
               
                 D, E, F, G, H, I 
                 C, E, F, G, H, I 
                 A, B, D, F, H, I 
                 A, B, D, G, H, I 
                 A, B, E, F, G, H 
                 A, B, E, F, G, I 
                 A, B, E, F, H, I 
               
               
                 A, B, E, G, H, I 
                 A, B, F, G, H, I 
                 A, C, D, E, F, G 
                 A, C, D, E, F, H 
                 A, C, D, E, F, I 
                 A, C, D, E, G, H 
                 A, C, D, E, G, I 
               
               
                 A, C, D, E, H, I 
                 A, C, D, F, G, H 
                 A, C, D, F, G, I 
                 A, C, D, F, H, I 
                 A, C, D, G, H, I 
                 A, C, E, F, G, H 
                 A, C, E, F, G, I 
               
               
                 A, C, E, F, H, I 
                 A, C, E, G, H, I 
                 A, C, F, G, H, I 
                 A, D, E, F, G, H 
                 A, D, E, F, G, I 
                 A, D, E, F, H, I 
                 A, D, E, G, H, I 
               
               
                 A, D, F, G, H, I 
                 A, E, F, G, H, I 
                 B, C, D, E, F, G 
                 B, C, D, E, F, H 
                 B, C, D, E, F, I 
                 B, C, D, E, G, H 
                 B, C, D, E, G, I 
               
               
                 B, C, D, E, H, I 
                 B, C, D, F, G, H 
                 B, C, D, F, G, I 
                 B, C, D, F, H, I 
                 B, C, D, G, H, I 
                 B, C, E, F, G, H 
                 B, C, E, F, G, I 
               
               
                 B, C, E, F, H, I 
                 B, C, E, G, H, I 
                 B, C, F, G, H, I 
                 B, D, E, F, G, H 
                 B, D, E, F, G, I 
                 B, D, E, F, H, I 
                 B, D, E, G, H, I 
               
               
                 B, D, F, G, H, I 
                 B, E, F, G, H, I 
                 C, D, E, F, G, H 
                 C, D, E, F, G, I 
                 C, D, E, F, H, I 
                 C, D, E, G, H, I 
                 C, D, F, G, H, I 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 9 
               
               
                   
               
               
                 Five Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 A, B, C, D, E 
                 A, B, C, D, F 
                 A, B, C, D, G 
                 A, B, C, D, H 
                 A, B, C, D, I 
                 A, B, C, E, F 
                 A, B, C, E, G 
                 A, B, C, E, H 
               
               
                 A, B, C, F, H 
                 A, B, C, F, G 
                 A, B, C, F, I 
                 A, B, C, G, H 
                 A, B, C, G, I 
                 A, B, C, H, I 
                 A, B, D, E, F 
                 A, B, D, E, G 
               
               
                 A, B, D, E, I 
                 A, B, D, F, G 
                 A, B, D, F, H 
                 A, B, D, F, I 
                 A, B, D, G, H 
                 A, B, D, G, I 
                 A, B, D, H, I 
                 A, B, E, F, G 
               
               
                 A, B, E, F, I 
                 A, B, E, G, H 
                 A, B, E, G, I 
                 A, B, E, H, I 
                 A, B, F, G, H 
                 A, B, F, G, I 
                 A, B, F, H, I 
                 A, B, G, H, I 
               
               
                 A, C, D, E, G 
                 A, C, D, E, H 
                 A, C, D, E, I 
                 A, C, D, F, G 
                 A, C, D, F, H 
                 A, C, D, F, I 
                 A, C, D, G, H 
                 A, C, D, G, I 
               
               
                 A, C, E, F, G 
                 A, C, E, F, H 
                 A, C, E, F, I 
                 A, C, E, G, H 
                 A, C, E, G, I 
                 A, C, E, H, I 
                 A, C, F, G, H 
                 A, C, F, G, I 
               
               
                 A, C, G, H, I 
                 A, D, E, F, G 
                 A, D, E, F, H 
                 A, D, E, F, I 
                 A, D, E, G, H 
                 A, D, E, G, I 
                 A, D, E, H, I 
                 A, D, F, G, H 
               
               
                 A, D, F, H, I 
                 A, D, G, H, I 
                 A, E, F, G, H 
                 A, E, F, G, I 
                 A, E, F, H, I 
                 A, E, G, H, I 
                 A, F, G, H, I 
                 B, C, D, E, F 
               
               
                 B, C, D, E, H 
                 B, C, D, E, I 
                 B, C, D, F, G 
                 B, C, D, F, H 
                 B, C, D, F, I 
                 B, C, D, G, H 
                 B, C, D, G, I 
                 B, C, D, H, I 
               
               
                 B, C, E, F, H 
                 B, C, E, F, I 
                 B, C, E, G, H 
                 B, C, E, G, I 
                 B, C, E, H, I 
                 B, C, F, G, H 
                 B, C, F, G, I 
                 B, C, F, H, I 
               
               
                 B, D, E, F, G 
                 B, D, E, F, H 
                 B, D, E, F, I 
                 B, D, E, G, H 
                 B, D, E, G, I 
                 B, D, E, H, I 
                 B, D, F, G, H 
                 B, D, F, G, I 
               
               
                 B, D, G, H, I 
                 B, E, F, G, H 
                 B, E, F, G, I 
                 B, E, F, H, I 
                 B, E, G, H, I 
                 B, F, G, H, I 
                 C, D, E, F, G 
                 C, D, E, F, H 
               
               
                 C, D, E, G, H 
                 C, D, E, G, I 
                 C, D, E, H, I 
                 C, D, F, G, H 
                 C, D, F, G, I 
                 C, D, F, H, I 
                 C, D, G, H, I 
                 C, E, F, G, H 
               
               
                 C, E, F, H, I 
                 C, E, G, H, I 
                 C, F, G, H, I 
                 D, E, F, G, H 
                 D, E, F, G, I 
                 D, E, F, H, I 
                 D, E, G, H, I 
                 D, F, G, H, I 
               
               
                 A, B, C, E, I 
                 A, B, D, E, H 
                 A, B, E, F, H 
                 A, C, D, E, F 
                 A, C, D, H, I 
                 A, C, F, H, I 
                 A, D, F, G, I 
                 B, C, D, E, G 
               
               
                 B, C, E, F, G 
                 B, C, G, H, I 
                 B, D, F, H, I 
                 C, D, E, F, I 
                 C, E, F, G, I 
                 E, F, G, H, I 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
               
                   
               
               
                 Four Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 A, B, C, D 
                 A, B, C, E 
                 A, B, C, F 
                 A, B, C, G 
                 A, B, C, H 
                 A, B, C, I 
                 A, B, D, E 
                 A, B, D, F 
                 D, G, H, I 
               
               
                 A, B, D, G 
                 A, B, D, H 
                 A, B, D, I 
                 A, B, E, F 
                 A, B, E, G 
                 A, B, E, H 
                 A, B, E, I 
                 A, B, F, G 
                 E, F, G, H 
               
               
                 A, B, F, H 
                 A, D, F, H 
                 A, D, F, I 
                 A, D, G, H 
                 A, D, G, I 
                 A, D, H, I 
                 A, E, F, G 
                 A, E, F, H 
                 E, F, G, I 
               
               
                 A, B, F, I 
                 A, B, G, H 
                 A, B, G, I 
                 A, B, H, I 
                 A, C, D, E 
                 A, C, D, F 
                 A, C, D, G 
                 A, C, D, H 
                 E, F, H, I 
               
               
                 A, C, D, I 
                 A, C, E, F 
                 A, C, E, G 
                 A, C, E, H 
                 A, C, E, I 
                 A, C, F, G 
                 A, C, F, H 
                 A, C, F, I 
                 E, G, H, I 
               
               
                 A, C, G, H 
                 A, C, G, I 
                 A, C, H, I 
                 A, D, E, F 
                 A, D, E, G 
                 A, D, E, H 
                 A, D, E, I 
                 A, D, F, G 
                 F, G, H, I 
               
               
                 A, E, F, I 
                 A, E, G, H 
                 A, E, G, I 
                 A, E, H, I 
                 A, F, G, H 
                 A, F, G, I 
                 A, F, H, I 
                 A, G, H, I 
                 D, E, F, H 
               
               
                 B, C, D, E 
                 B, C, D, F 
                 B, C, D, G 
                 B, C, D, H 
                 B, C, D, I 
                 B, C, E, F 
                 B, C, E, G 
                 B, C, E, H 
                 D, E, F, I 
               
               
                 B, C, E, I 
                 B, C, F, G 
                 B, C, F, H 
                 B, C, F, I 
                 B, C, G, H 
                 B, C, G, I 
                 B, C, H, I 
                 B, D, E, F 
                 D, E, G, H 
               
               
                 B, D, E, G 
                 B, D, E, H 
                 B, D, E, I 
                 B, D, F, G 
                 B, D, F, H 
                 B, D, F, I 
                 B, D, G, H 
                 B, D, G, I 
                 D, E, G, I 
               
               
                 B, D, H, I 
                 B, E, F, G 
                 B, E, F, H 
                 B, E, F, I 
                 B, E, G, H 
                 B, E, G, I 
                 B, E, H, I 
                 B, F, G, H 
                 D, E, H, I 
               
               
                 B, F, G, I 
                 B, F, H, I 
                 B, G, H, I 
                 C, D, E, F 
                 C, D, E, G 
                 C, D, E, H 
                 C, D, E, I 
                 C, D, F, G 
                 D, F, G, H 
               
               
                 C, D, F, H 
                 C, D, F, I 
                 C, D, G, H 
                 C, D, G, I 
                 C, D, H, I 
                 C, E, F, G 
                 C, E, F, H 
                 C, E, F, I 
                 D, F, G, I 
               
               
                 C, E, G, H 
                 C, E, G, I 
                 C, E, H, I 
                 C, F, G, H 
                 C, F, G, I 
                 C, F, H, I 
                 C, G, H, I 
                 D, E, F, G 
                 D, F, H, I 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
               
                   
               
               
                 Three Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 A, B, C 
                 A, B, D 
                 A, B, E 
                 A, B, F 
                 A, B, G 
                 A, B, H 
                 A, B, I 
                 A, C, D 
                 A, C, E 
                 G, H, I 
                 E, F, H 
               
               
                 A, C, F 
                 A, C, G 
                 A, C, H 
                 A, C, I 
                 A, D, E 
                 A, D, F 
                 A, D, G 
                 A, D, H 
                 A, D, I 
                 F, H, I 
                 E, F, G 
               
               
                 A, E, F 
                 A, E, G 
                 A, E, H 
                 A, E, I 
                 A, F, G 
                 A, F, H 
                 A, F, I 
                 A, G, H 
                 A, G, I 
                 F, G, I 
                 D, H, I 
               
               
                 A, H, I 
                 B, C, D 
                 B, C, E 
                 B, C, F 
                 B, C, G 
                 B, C, H 
                 B, C, I 
                 B, D, E 
                 B, D, F 
                 F, G, H 
                 D, G, I 
               
               
                 B, D, G 
                 B, D, H 
                 B, D, I 
                 B, E, F 
                 B, E, G 
                 B, E, H 
                 B, E, I 
                 B, F, G 
                 B, F, H 
                 E, H, I 
                 E, F, I 
               
               
                 B, F, I 
                 B, G, H 
                 B, G, I 
                 B, H, I 
                 C, D, E 
                 C, D, F 
                 C, D, G 
                 C, D, H 
                 C, D, I 
                 E, G, I 
                 D, G, H 
               
               
                 C, E, F 
                 C, E, G 
                 C, E, H 
                 C, E, I 
                 C, F, G 
                 C, F, H 
                 C, F, I 
                 C, G, H 
                 C, G, I 
                 E, G, H 
                 D, F, I 
               
               
                 C, H, I 
                 D, E, F 
                 D, E, G 
                 D, E, H 
                 D, E, I 
                 D, F, G 
                 D, F, H 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 12 
               
               
                   
               
               
                 Two Strain Consortia 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 A, B 
                 A, C 
                 A, D 
                 A, E 
                 A, F 
                 A, G 
                 A, H 
                 A, I 
                 B, C 
                 B, D 
                 B, E 
                 B, F 
                 B, G 
                 B, H 
                 B, I 
                 C, D 
               
               
                 C, E 
                 C, F 
                 C, G 
                 C, H 
                 C, I 
                 D, E 
                 D, F 
                 D, G 
                 D, H 
                 D, I 
                 E, F 
                 E, G 
                 E, H 
                 E, I 
                 F, G 
                 F, H 
               
               
                 F, I 
                 G, H 
                 G, I 
                 H, I 
               
               
                   
               
            
           
         
       
     
     In some embodiments, the microbial consortia may be selected from any member group from Tables 6-12. 
     In some embodiments, the microbial consortia comprises: a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 28; a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; a  Ruminococcus  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2108; and/or a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. 
     In some embodiments, the microbial consortia comprises: a  Clostridium  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 28; a  Pichia  sp. comprising an ITS nucleic acid sequence of SEQ ID NO: 32; a  Ruminococcus  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and/or a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 2067. 
     Isolated Microbes—Source Material 
     The microbes of the present disclosure were obtained, among other places, at various locales in the United States from the gastrointestinal tract of cows. 
     Isolated Microbes—Microbial Culture Techniques 
     The microbes of Table 1 and Table 3 were matched to their nearest taxonomic groups by utilizing classification tools of the Ribosomal Database Project (RDP) for 16s rRNA sequences and the User-friendly Nordic ITS Ectomycorrhiza (UNITE) database for ITS rRNA sequences. Examples of matching microbes to their nearest taxa may be found in Lan et al. (2012 . PLOS one.  7(3):e32491), Schloss and Westcott (2011 . Appl. Environ. Microbiol.  77(10):3219-3226), and Koljalg et al. (2005 . New Phytologist.  166(3):1063-1068). 
     The isolation, identification, and culturing of the microbes of the present disclosure can be effected using standard microbiological techniques. Examples of such techniques may be found in Gerhardt, P. (ed.) Methods for General and Molecular Microbiology. American Society for Microbiology, Washington, D.C. (1994) and Lennette, E. H. (ed.) Manual of Clinical Microbiology, Third Edition. American Society for Microbiology, Washington, D.C. (1980), each of which is incorporated by reference. 
     Isolation can be effected by streaking the specimen on a solid medium (e.g., nutrient agar plates) to obtain a single colony, which is characterized by the phenotypic traits described hereinabove (e.g., Gram positive/negative, capable of forming spores aerobically/anaerobically, cellular morphology, carbon source metabolism, acid/base production, enzyme secretion, metabolic secretions, etc.) and to reduce the likelihood of working with a culture which has become contaminated. 
     For example, for microbes of the disclosure, biologically pure isolates can be obtained through repeated subculture of biological samples, each subculture followed by streaking onto solid media to obtain individual colonies or colony forming units. Methods of preparing, thawing, and growing lyophilized bacteria are commonly known, for example, Gherna, R L. and C. A. Reddy. 2007. Culture Preservation, p 1019-1033. In C. A. Reddy, T. J. Beveridge, J. A. Breznak, G. A. Marzluf, T. M. Schmidt, and L. R. Snyder, eds. American Society for Microbiology, Washington, D.C., 1033 pages; herein incorporated by reference. Thus freeze dried liquid formulations and cultures stored long term at −70° C. in solutions containing glycerol are contemplated for use in providing formulations of the present disclosure. 
     The microbes of the disclosure can be propagated in a liquid medium under aerobic conditions, or alternatively anaerobic conditions. Medium for growing the bacterial strains of the present disclosure includes a carbon source, a nitrogen source, and inorganic salts, as well as specially required substances such as vitamins, amino acids, nucleic acids and the like. Examples of suitable carbon sources which can be used for growing the microbes include, but are not limited to, starch, peptone, yeast extract, amino acids, sugars such as glucose, arabinose, mannose, glucosamine, maltose, and the like; salts of organic acids such as acetic acid, fumaric acid, adipic acid, propionic acid, citric acid, gluconic acid, malic acid, pyruvic acid, malonic acid and the like; alcohols such as ethanol and glycerol and the like; oil or fat such as soybean oil, rice bran oil, olive oil, corn oil, sesame oil. The amount of the carbon source added varies according to the kind of carbon source and is typically between 1 to 100 gram(s) per liter of medium. Preferably, glucose, starch, and/or peptone is contained in the medium as a major carbon source, at a concentration of 0.1-5% (W/V). Examples of suitable nitrogen sources which can be used for growing the bacterial strains of the present disclosure include, but are not limited to, amino acids, yeast extract, tryptone, beef extract, peptone, potassium nitrate, ammonium nitrate, ammonium chloride, ammonium sulfate, ammonium phosphate, ammonia or combinations thereof. The amount of nitrogen source varies according to the type of nitrogen source, typically between 0.1 to 30 gram per liter of medium. The inorganic salts, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, disodium hydrogen phosphate, magnesium sulfate, magnesium chloride, ferric sulfate, ferrous sulfate, ferric chloride, ferrous chloride, manganous sulfate, manganous chloride, zinc sulfate, zinc chloride, cupric sulfate, calcium chloride, sodium chloride, calcium carbonate, sodium carbonate can be used alone or in combination. The amount of inorganic acid varies according to the kind of the inorganic salt, typically between 0.001 to 10 gram per liter of medium. Examples of specially required substances include, but are not limited to, vitamins, nucleic acids, yeast extract, peptone, meat extract, malt extract, dried yeast and combinations thereof. Cultivation can be effected at a temperature, which allows the growth of the microbial strains, essentially, between 20° C. and 46° C. In some aspects, a temperature range is 30° C.-39° C. For optimal growth, in some embodiments, the medium can be adjusted to pH 6.0-7.4. It will be appreciated that commercially available media may also be used to culture the microbial strains, such as Nutrient Broth or Nutrient Agar available from Difco, Detroit, Mich. It will be appreciated that cultivation time may differ depending on the type of culture medium used and the concentration of sugar as a major carbon source. 
     In some aspects, cultivation lasts between 24-96 hours. Microbial cells thus obtained are isolated using methods, which are well known in the art. Examples include, but are not limited to, membrane filtration and centrifugal separation. The pH may be adjusted using sodium hydroxide and the like and the culture may be dried using a freeze dryer, until the water content becomes equal to 4% or less. Microbial co-cultures may be obtained by propagating each strain as described hereinabove. In some aspects, microbial multi-strain cultures may be obtained by propagating two or more of the strains described hereinabove. It will be appreciated that the microbial strains may be cultured together when compatible culture conditions can be employed. 
     In some embodiments, the microorganisms of the present disclosure are subjected to a serial preservation challenge to improve microbial viability. In some embodiments, the microorganisms are subjected to a serial preservation challenge to improve stability. In some embodiments, the microorganisms of the present disclosure are subjected to at least one preservation challenge. In some embodiments, the microorganisms of the present disclosure are subjected to at least two, three, four, five, or more preservation challenges. 
     In some embodiments, the serial preservation method comprises: (a) subjecting a population of target microbial cells to a first preservation challenge to provide a first population of challenged microbial cells; (b) harvesting viable challenged microbial cells from the first population of challenged microbial cells to provide a first population of viable challenged microbial cells; (c) subjecting the first population of viable challenged microbial cells to a second preservation challenge to provide a second population of challenged microbial cells; (d) harvesting viable challenged microbial cells from the second population of challenged microbial cells to provide a second population of viable challenged microbial cells; (e) subjecting the second population of viable challenged microbial cells to a third preservation challenge to provide a third population of challenged microbial cells; (f) harvesting viable challenged microbial cells from the third population of challenged microbial cells to provide a third population of viable challenged microbial cells; (g) preserving the third population of viable challenged microbial cells to provide a population of preserved viability-enhanced microbial cells; and (h) preparing a product using the population of preserved viability-enhanced microbial cells. 
     In some embodiments, each of the preservation challenges are the same type of preservation challenge. For example, in some embodiments, the microorganisms of the present disclosure are subjected to two, three, four, five, or more preservation challenges before final preservation for storage and/or incorporation into a product, wherein each of the preservation challenges are of the same type. Types of preservation challenges include, but are not limited to, freeze drying/lyophilization, vitrification/glass formation, evaporation, foam formation, vaporization, cryopreservation, spray drying, adsorptive drying, extrusion, and fluid bed drying. Methods of microbial preservation are further described in PCT Application No. PCT/US2020/020311, herein incorporated by reference in its entirety. 
     In some embodiments, a population of target microbial cells is subjected to preservation by fluid bed drying. Fluid bed drying refers to a method in which particles are fluidized in a bed and dried. A fluidized bed is formed when a quantity of solid particulates are placed under conditions that cause a solid material to behave like a fluid. In a fluid bed drying system, inlet air provides significant air flow to support the weight of the particles. 
     In some embodiments, the preservation challenges are different types of preservation challenges. For example, in some embodiments, the microorganisms of the present disclosure are subjected to a first and a second preservation challenge, wherein the first and the second preservation challenges are different challenges types. For example, in some embodiments, the first preservation challenge is a cryopreservation challenge and the second preservation challenge is a freeze-drying preservation challenge. 
     In some embodiments, any one of the microorganisms listed in Table 1 or Table 3 may be subjected to serial preservation challenge. In some embodiments, a microorganism comprising a 16S nucleic acid sequence with at least 95% sequence identity to SEQ ID NOs: 1-30, 2045-2103, or 2108 is subjected to serial preservation challenge. In some embodiments, a microorganism comprising an ITS nucleic acid sequence with at least 95% sequence identity to SEQ ID NOs: 31-60 and 2104-2107 is subjected to serial preservation challenge. In some embodiments, the microorganism is a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 28. In some embodiments, the microorganism is a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 32. In some embodiments, the microorganism is a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 2067. In some embodiments, the microorganism is a  Ruminococcus  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 1 or 2108. In some embodiments, the microorganism is  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108. 
     In some embodiments, serial preservation results in one or more mutations in the genome of a microorganism. In some embodiments, serial preservation results in one or more mutations in the genome of any one of the microorganisms listed in Table 1 or Table 3. In some embodiments, serial preservation results in one or more mutations in a microorganism comprising a 16S nucleic acid sequence with at least 95% sequence identity to SEQ ID NOs: 1-30, 2045-2103, or 2108. In some embodiments, serial preservation results in one or more mutations in a microorganism comprising an ITS nucleic acid sequence with at least 95% sequence identity to SEQ ID NOs: 31-60 and 2104-2107. In some embodiments, the microorganism is a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 28. In some embodiments, the microorganism is a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 32. In some embodiments, the microorganism is a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 2067. In some embodiments, the microorganism is a  Ruminococcus  sp. comprising a 16S nucleic acid sequence sharing at least 95% sequence identity to SEQ ID NO: 1 or 2108. In some embodiments, the one or more mutations is a nucleotide substitution, deletion, and/or insertion in the whole genome of the microorganism. 
     In some embodiments, serial preservation results in one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108. In some embodiments, the one or more mutations are located in the whole genome of  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108. In some embodiments, the one or mutations are not located in the 16S nucleic acid sequence of SEQ ID NO: 2108 of  Ruminococcus bovis . Illustrative mutations in the whole genome of  Ruminococcus bovis  (SEQ ID NO: 2108) following serial preservation challenge are shown in Table 13 below and further described in Example 3 and Table 18. The mutations in Table 13 are in bold and underlined. 
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Illustrative mutations following serial preservation in  Ruminococcus   bovis   
               
            
           
           
               
               
               
            
               
                   
                 
                   Ruminococcus bovis 
                 
                 
                   Ruminococcus bovis 
                 
               
               
                   
                 (SEQ ID NO: 2108) 
                 (SEQ TD NO: 2108) 
               
               
                   
                 Before Serial Preservation 
                 After Serial Preservation 
               
               
                   
               
               
                 Mutation 1 
                 GCACCAAATGCAAAGGTATATTTGAT 
                 GCACCAAATGCAAAGGTATATTTGATT 
               
               
                 Melibiose 
                 TCTTGCAGGAATCTTGCCGTCAAGTC 
                 CTTGCAGGAATCTTGCCGTCAAGTCTG 
               
               
                 carrier protein, 
                 TGCGTTCAGAACTGCGTTTCATAAAA 
                 CGTTCAGAACTGCGTTTCATAAAAAAT 
               
               
                 GalR-LacI 
                 AATCCTCCTTAAATATAAAAAATGAA 
                 CCTCCTTAAATATAAAAAATGAAACTA 
               
               
                 family of 
                 ACTAACCGTACAAAATGCATAAAAGA 
                 ACCGTACAAAATGCATAAAAGAAATTA 
               
               
                 transcriptional 
                 AATTAATATTATTAATTATTAATATG 
                 ATATTATTAATTATTAATATGCTTTTT 
               
               
                 regulators 
                 CTTTTTGCTTATCTGTTAACTAAATT 
                 GCTTATCTGTTAACTAAATTATATGTT 
               
               
                   
                 ATATGTTTTGTTTCATAAAAAGTCAA 
                 TTGTTTCATAAAAAGTCAATATATTTA 
               
               
                   
                 TATATTTAGTAAACAAAATTAAAGTT 
                 GTAAACAAAATTAAAGTTTATCTATTT 
               
               
                   
                 TATCTATTTTTCACTAAACAACCCTT 
                 TTCACTAAACAACCCTTGCGTATTTAG 
               
               
                   
                 GCGTATTTAGTAAATATTCACTATAA 
                 TAAATATTCACTATAATAAGGGTAGA   T     
               
               
                   
                 TAAGGGTAGA   G    (SEQ ID NO:  
                 (SEQ ID NO: 2110) 
               
               
                   
                 2109) 
                   
               
               
                   
               
               
                 Mutations 2-3 
                 TTTCACTCAATAACTGCATTGGACTT 
                 TTTCACTCAATAACTGCATTGGACTTT 
               
               
                 Hypothetical 
                 TTGTATTCAAGTGTTCTCATTGTCTT 
                 TGTATTCAAGTGTTCTCATTGTCTTGT 
               
               
                 protein 
                 GTTATTACTCCATTCTAAATGTCCTT 
                 TATTACTCCATTCTAAATGTCCTTTTA 
               
               
                 (integrase) 
                 TTAACTTTGTATTTAATTCTTCAATA 
                 ACTTTGTATTTAATTCTTCAATATTTT 
               
               
                   
                 TTTTTGAATGTTTCCCAATCATAGAA 
                 TGAATGTTTCCCAATCATAGAAATATC 
               
               
                   
                 ATATCTTTGGTCGTTTCTATGACTTC 
                 TTTGGTCGTTTCTATGACTTCTTTCTA 
               
               
                   
                 TTTCTACCTTCCCATTGTGCCAAGGT 
                 CCTTCCCATTGTGCCAAGGTGTTCGTG 
               
               
                   
                 GTTCGTGGTGGTATTAATTTATGATT 
                 GTGGTATTAATTTATGATTTATACCTA 
               
               
                   
                 TATACCTAATTTGTTCAATTCTATTT 
                 ATTTGTTCAATTCTATTTCAAAAGGAC 
               
               
                   
                 CAAAAGGACTTTTCACTTCACTGCTT 
                 TTTTCACTTCACTGCTTTGATATTTAT 
               
               
                   
                 TGATATTTATATGTGAACTCTCTTCC 
                 ATGTGAACTCTCTTCCGTTATCTGTTT 
               
               
                   
                 GTTATCTGTTTGAA   CC   GTCT   T    (SEQ 
                 GAA   TA   GTCT   G    (SEQ ID NO: 2112) 
               
               
                   
                 ID NO: 2111) 
                   
               
               
                   
               
               
                 Mutation 4 
                 TATTCTCTAAAAGAAAATAAATTTGA 
                 TATTCTCTAAAAGAAAATAAATTTGAA 
               
               
                 Phospho- 
                 ACAATCATACAAATTACAAAAATGAA 
                 CAATCATACAAATTAGAAAAATGAAAT 
               
               
                 mannomutase 
                 ATTTTCTGTTCTGGAATAAAAAGACC 
                 TTTCTGTTCTGGAATAAAAAGACCATA 
               
               
                   
                 ATAAAAGCACCGAAAAAGCCCATGAG 
                 AAAGCACCGAAAAAGCCCATCAGAATG 
               
               
                   
                 AATGGGCTTTTCTTTATGTTATAACC 
                 GGCTTTTCTTTATGTTATAACCGACTA 
               
               
                   
                 GACTAAAAATAAGTAAAAATAAAATC 
                 AAAATAAGTAAAAATAAAATCAAAAAA 
               
               
                   
                 AAAAAATTTTAAAAAAAACTCTTTAG 
                 TTTTAAAAAAAACTCTTTAGAATACTA 
               
               
                   
                 AATACTAAAAATAGGTGAAATTATAT 
                 AAAATAGGTGAAATTATATACTTAITT 
               
               
                   
                 ACTTATTTTTATTGTATTGAACTTTG 
                 TTATTGTATTGAACTTTGTTATATTGT 
               
               
                   
                 TTATATTGTATAATAGTTTTAGAAAA 
                 ATAATAGTTTTAGAAAATTAATTTAAG 
               
               
                   
                 TTAATTTAAGGGGTATATTTTATGCT 
                 GGGTATATTTTATGCTTGATAATTTTT 
               
               
                   
                 TGATAATTTTTAT   A   A (SEQ ID NO:  
                 AT-A (SEQ ID NO: 2114) 
               
               
                   
                 2113) 
                   
               
               
                   
               
               
                 Mutation 5 
                 CGCCCCAAGAATGATAGTGTTTGCGT 
                 CGCCCCAAGAATGATAGTGTTTGCGTT 
               
               
                 Hypothetical 
                 TTTTTACTAAAATTCCGTTTTAATTC 
                 TTTTAGTAAAATTCCGTTTTAATTCTC 
               
               
                 protein 
                 TCTGCTGATTGTAGAAGGACTTCGTT 
                 TGCTGATTGTAGAAGGACTTCGTTCAA 
               
               
                 (transposase) 
                 CAAGTATTTTTGCAATTTTTCTTATG 
                 GTATTTTTGGAATTTTTCTTATGCTAT 
               
               
                   
                 CTATATCCTTT   CCA    (SEQ ID NO:  
                 ATCCTTT   TTC    (SEQ ID NO: 2116) 
               
               
                   
                 2115) 
                   
               
               
                   
               
               
                 Mutation 6 
                 TTACTAAATATTTTACATGTGCGCCC 
                 TTACTAAATATTTTACATGTGCGCCCC 
               
               
                 Hypothetical 
                 CAAGAATGATAGTGTTTGCGTTTTTT 
                 AAGAATGATAGTGTTTGCGTTTTTTAG 
               
               
                 protein 
                 ACTAAAATTCCGTTTTAATTCTCTGC 
                 TAAAATTCCGTTTTAATTCTCTGCTGA 
               
               
                 (transposase) 
                 TGATTGTAGAAGGACTTCGTTCAAGT 
                 TTGTAGAAGGACTTCGTTCAAGTATT 
               
               
                   
                 A-T (SEQ ID NO: 2117) 
                 (SEQ ID NO: 2118) 
               
               
                   
               
               
                 Mutation 7 
                 TAATCAGATTGAACGCGATATCAATT 
                 TAATCAGATTGAACGCGATATCAATTC 
               
               
                 Hypothetical 
                 CCGAAAATGCCCCGAATGTTGTTAAG 
                 CGAAAATGCCCCGAATGTTGTTAAGGA 
               
               
                 protein 
                 GATTACACAAGCAACGCGAAAATCAA 
                 TTACACAAGCAACGCGAAAATCAAAAT 
               
               
                   
                 AATCTCTCCGCTGGGTATCTCTCTTA 
                 CTCTCCGCTGGGTATCTCTCTTACGGG 
               
               
                   
                 CGGGCGAGTGTGATGAGAAATATGAC 
                 CGAGTGTGATGAGAAATATGACAAGCA 
               
               
                   
                 AAGCAAATGCCGGATTGGGGCAGTCG 
                 AATGCCGGATTGGGGCAGTCGCTGCTT 
               
               
                   
                 CTGCTTTGAGATTCCCGACACAGACG 
                 TGAGATTCCCGACACAGACGGCAAATC 
               
               
                   
                 GCAAATCAAAGGTAACAATGGATGAC 
                 AAAGGTAACAATGGATGACGGAACAGT 
               
               
                   
                 GGAACAGTTTATTATATCCTTGTAAA 
                 TTATTATATCCTTGTAAACGAGGGCGG 
               
               
                   
                 CGAGGGCGGCGAGCGCAGGACAGACG 
                 CGAGCGCAGGACAGACGACAGCGGCGT 
               
               
                   
                 ACAGCGGCGTTTTCCATGAGAATGCA 
                 TTTCCATGAGAATGCACAGCTTCAATA 
               
               
                   
                 CAGCTTCAATA   C    (SEQ ID NO:  
                     T    (SEQ ID NO: 2120) 
               
               
                   
                 2119) 
                   
               
               
                   
               
               
                 Mutation 8 
                 AAAAGGTACTGCACCATTTACTTTGT 
                 AAAAGGTACTGCACCATTTACTTTGTT 
               
               
                 Excinuclease 
                 TAGATTATTTTCCAAAGGACTTTCTG 
                 AGATTATTTTCCAAAGGACTTTCTGCT 
               
               
                 ABC subunit B 
                 CTTTTTGTTGATGAAAGCCATGTTAG 
                 TTTTGTTGATGAAAGCCATGTTACTTT 
               
               
                   
                 TTTACCTCAGGTTAGAGGTATGTATG 
                 ACCTCAGGTTAGAGGTATGTATGGTGG 
               
               
                   
                 GTGGTAACCTTTCAAGAAAGAAAAGT 
                 TAACCTTTCAAGAAAGAAAAGTCTTAT 
               
               
                   
                 CTTATTGATTATGGCTTTAGATTACC 
                 TGATTATGGCTTTAGATTACCGTCAGC 
               
               
                   
                 GTCAGCATATGACAACCGTCCTTTAA 
                 ATATGACAACCGTCCTTTAAATTTTGA 
               
               
                   
                 ATTTTGATGAATTTTATGATAGAATA 
                 TGAATTTTATGATAGAATAAATCAAGT 
               
               
                   
                 AATCAAGTCTGCTTTGTTTCAGCAAC 
                 CTGCTTTGTTTCAGCAACACCGGGCGA 
               
               
                   
                 ACCGGGCGACTTAGAACTTGAAAAGA 
                 CTTAGAACTTGAAAAGAGCAGTGTTGT 
               
               
                   
                 GCAGTGTTGTTGCAGAACAAATTATC 
                 TGCAGAACAAATTATCCGTCCAACAGG 
               
               
                   
                 CGTCCAACAGG   C    (SEQ ID NO:  
                     A    (SEQ ID NO: 2122) 
               
               
                   
                 2121) 
                   
               
               
                   
               
               
                 Mutation 9 
                 TGCCACAAAAAATATAAATATATAG-G 
                 TGCCACAAAAAATATAAATATATAGGG 
               
               
                 Hypothetical 
                 GGCAAAATTACAACTAA- 
                 GCAAAATTAGAACTAA   AC   ACACACCCA 
               
               
                 protein 
                 ACACACCCAAATAATCAAGACTTGCT 
                 AATAATCAAGACTTGCTCTACTTGTAA 
               
               
                 (stage II 
                 CTACTTGTAAAATCAGTTGGAAATAA 
                 AATCAGTTGGAAATAAAAAGTCAAAGG 
               
               
                 sporulation 
                 AAAGTCAAAGGACTTTTTAAATTCTA 
                 ACTTTTTAAATTCTAAATCGGTATTTA 
               
               
                 protein) 
                 AATCGGTATTTACCCCAAAATATATA 
                 CCCCAAAATATATACCCAGAATAAAAC 
               
               
                   
                 CCCAGAATAAAACCTACTAAAATTGA 
                 CTACTAAAATTGAAATAAGAAACATAG 
               
               
                   
                 AATAAGAAACATAGTAAAGATACCGT 
                 TAAAGATACCGTATC (SEQ ID NO: 
               
               
                   
                 ATC (SEQ ID NO: 2123) 
                 2124) 
               
               
                   
               
            
           
         
       
     
     In some embodiments, serial preservation results in one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108. In some embodiments, the one or more mutations is a G→T substitution at position 297 of SEQ ID NO: 2109. In some embodiments, the one or more mutations is a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111. In some embodiments, the one or more mutations is a T→G substitution at position 307 of SEQ ID NO: 2111. In some embodiments, the one or more mutations is a −A deletion at position 300 of SEQ ID NO: 2113. In some embodiments, the one or more mutations is a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115. In some embodiments, the one or more mutations is a +T insertion between positions 105-106 of SEQ ID NO: 2117. In some embodiments, the one or more mutations is a C→T substitution at position 298 of SEQ ID NO: 2119. In some embodiments, the one or more mutations is a C→A substitution at position 298 of SEQ ID NO: 2121. In some embodiments, the one or more mutations is a +AC insertion between positions 43-44 of SEQ ID NO; 2123. 
     In some embodiments, serial preservation results in one or more mutations in the genome of  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108. In some embodiments, the one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108 results in a change in phenotype. In some embodiments, the one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108 results in an increase in viability. In some embodiments, the one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108 results in an increase in viability by about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 50%, or more. In some embodiments, the one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108 results in an increase in stability. In some embodiments, the one or more mutations in  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108 results in an increase in stability by about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 50%, or more. 
     In some embodiments, serial preservation of the microorganisms of the present disclosure results in an increase in microbial viability of at least 5%. In other words, the viability of the population of microbes present at the conclusion of the serial preservation challenges is increased by at least 5% compared to the viability of the population of microbes that were present prior to any preservation challenges. In some embodiments, serial preservation of a microbial culture results in an increase in microbial viability between about 5% and about 300%, about 5% and about 25%, about 5% and about 20%, about 5% and about 15%, about 5% and about 10%, about 10% and about 300%, about 15% and about 30%, about 20% and about 30%, or about 25% and about 30%. In some embodiments, serial preservation of a microbial culture results in an increase in microbial viability between about 10% and about 30%, about 15% and about 30%, about 20% and about 30%, about 25% and about 30%, about 10% and about 25%, about 10% and about 20%, or about 10% and about 15%. In some embodiments, serial preservation of a microbial culture results in an increase in microbial viability of at least 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30% or more. 
     In some embodiments, serial preservation of the microorganisms of the present disclosure results in an increase in microbial stability of at least 5%. In other words, the stability of the population of microbes present at the conclusion of the serial preservation challenges is increased by at least 5% compared to the stability of the population of microbes that were present prior to any preservation challenges. In some embodiments, serial preservation of a microbial culture results in an increase in stability between about 5% and about 30%, about 5% and about 25%, about 5% and about 20%, about 5% and about 15%, about 5% and about 10%, about 10% and about 30%, about 15% and about 30%, about 20% and about 30%, or about 25% and about 30%. In some embodiments, serial preservation of a microbial culture results in an increase in stability between about 10% and about 30%, about 15% and about 30%, about 20% and about 30%, about 25% and about 30%, about 10% and about 25%, about 10% and about 20%, or about 10% and about 15%. In some embodiments, serial preservation of a microbial culture results in an increase in stability of at least 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30% or more. 
     Isolated Microbes—Microbial Strains 
     Microbes can be distinguished into a genus based on polyphasic taxonomy, which incorporates all available phenotypic and genotypic data into a consensus classification (Vandamme et al. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics.  Microbiol Rev  1996, 60:407-438). One accepted genotypic method for defining species is based on overall genomic relatedness, such that strains which share approximately 70% or more relatedness using DNA-DNA hybridization, with 5° C. or less ΔT m  (the difference in the melting temperature between homologous and heterologous hybrids), under standard conditions, are considered to be members of the same species. Thus, populations that share greater than the aforementioned 70% threshold can be considered to be variants of the same species. Another accepted genotypic method for defining species is to isolate marker genes of the present disclosure, sequence these genes, and align these sequenced genes from multiple isolates or variants. The microbes are interpreted as belonging to the same species if one or more of the sequenced genes share at least 97% sequence identity. 
     The 16S or 18S rRNA sequences or ITS sequences are often used for making distinctions between species and strains, in that if one of the aforementioned sequences share less than a specified percent sequence identity from a reference sequence, then the two organisms from which the sequences were obtained are said to be of different species or strains. 
     Thus, one could consider microbes to be of the same species, if they share at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity across the 16S or 18S rRNA sequence, or the ITS1 or ITS2 sequence. 
     Further, one could define microbial strains of a species, as those that share at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity across the 16S or 18S rRNA sequence, or the ITS1 or ITS2 sequence. 
     In one embodiment, microbial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with any one of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 2045, 2046, 2047, 2048, 2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057, 2058, 2059, 2060, 2061, 2062, 2063, 2064, 2065, 2066, 2067, 2068, 2069, 2070, 2071, 2072, 2073, 2074, 2075, 2076, 2077, 2078, 2079, 2080, 2081, 2082, 2083, 2084, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2094, 2095, 2096, 2097, 2098, 2099, 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, and 2108. In a further embodiment, microbial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with any one of SEQ ID NOs:1-2108. 
     In one embodiment, microbial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 97%, 97.1%, 97.2%, 97.3%, 97.4%, 97.5%, 97.6%, 97.7%, 97.8%, 97.9%, 98%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.60%, 99.7%, 99.8%, 99.9%, or 100% sequence identity with any one of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 2045, 2046, 2047, 2048, 2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057, 2058, 2059, 2060, 2061, 2062, 2063, 2064, 2065, 2066, 2067, 2068, 2069, 2070, 2071, 2072, 2073, 2074, 2075, 2076, 2077, 2078, 2079, 2080, 2081, 2082, 2083, 2084, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2094, 2095, 2096, 2097, 2098, 2099, 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, and 2108. 
     Comparisons may also be made with 23S rRNA sequences against reference sequences. 
     Unculturable microbes often cannot be assigned to a definite species in the absence of a phenotype determination, the microbes can be given a  candidatus  designation within a genus provided their 16S or 18S rRNA sequences or ITS sequences subscribes to the principles of identity with known species. 
     One approach is to observe the distribution of a large number of strains of closely related species in sequence space and to identify clusters of strains that are well resolved from other clusters. This approach has been developed by using the concatenated sequences of multiple core (house-keeping) genes to assess clustering patterns, and has been called multilocus sequence analysis (MLSA) or multilocus sequence phylogenetic analysis. MLSA has been used successfully to explore clustering patterns among large numbers of strains assigned to very closely related species by current taxonomic methods, to look at the relationships between small numbers of strains within a genus, or within a broader taxonomic grouping, and to address specific taxonomic questions. More generally, the method can be used to ask whether bacterial species exist—that is, to observe whether large populations of similar strains invariably fall into well-resolved clusters, or whether in some cases there is a genetic continuum in which clear separation into clusters is not observed. 
     In order to more accurately make a determination of genera, a determination of phenotypic traits, such as morphological, biochemical, and physiological characteristics are made for comparison with a reference genus archetype. The colony morphology can include color, shape, pigmentation, production of slime, etc. Features of the cell are described as to shape, size, Gram reaction, extracellular material, presence of endospores, flagella presence and location, motility, and inclusion bodies. Biochemical and physiological features describe growth of the organism at different ranges of temperature, pH, salinity and atmospheric conditions, growth in presence of different sole carbon and nitrogen sources. One of ordinary skill in the art would be reasonably apprised as to the phenotypic traits that define the genera of the present disclosure. 
     In one embodiment, the microbes taught herein were identified utilizing 16S rRNA gene sequences and ITS sequences. It is known in the art that 16S rRNA contains hypervariable regions that can provide species/strain-specific signature sequences useful for bacterial identification, and that ITS sequences can also provide species/strain-specific signature sequences useful for fungal identification. 
     Phylogenetic analysis using the rRNA genes and/or ITS sequences are used to define “substantially similar” species belonging to common genera and also to define “substantially similar” strains of a given taxonomic species. Furthermore, physiological and/or biochemical properties of the isolates can be utilized to highlight both minor and significant differences between strains that could lead to advantageous behavior in ruminants. 
     Compositions of the present disclosure may include combinations of fungal spores and bacterial spores, fungal spores and bacterial vegetative cells, fungal vegetative cells and bacterial spores, fungal vegetative cells and bacterial vegetative cells. In some embodiments, compositions of the present disclosure comprise bacteria only in the form of spores. In some embodiments, compositions of the present disclosure comprise bacteria only in the form of vegetative cells. In some embodiments, compositions of the present disclosure comprise bacteria in the absence of fungi. In some embodiments, compositions of the present disclosure comprise fungi in the absence of bacteria. 
     Bacterial spores may include endospores and akinetes. Fungal spores may include statismospores, ballistospores, autospores, aplanospores, zoospores, mitospores, megaspores, microspores, meiospores, chlamydospores, urediniospores, teliospores, oospores, carpospores, tetraspores, sporangiospores, zygospores, ascospores, basidiospores, ascospores, and asciospores. 
     In some embodiments, spores of the composition germinate upon administration to animals of the present disclosure. In some embodiments, spores of the composition germinate only upon administration to animals of the present disclosure. 
     Microbial Compositions 
     In some embodiments, the microbes of the disclosure are combined into microbial compositions. 
     In some embodiments, the microbial compositions include ruminant feed, such as cereals (barley, maize, oats, and the like); starches (tapioca and the like); oilseed cakes; and vegetable wastes. In some embodiments, the microbial compositions include vitamins, minerals, trace elements, emulsifiers, aromatizing products, binders, colorants, odorants, thickening agents, and the like. 
     In some embodiments, the microbial compositions of the present disclosure are solid. Where solid compositions are used, it may be desired to include one or more carrier materials including, but not limited to: mineral earths such as silicas, talc, kaolin, limestone, chalk, clay, dolomite, diatomaceous earth; calcium sulfate; magnesium sulfate; magnesium oxide; products of vegetable origin such as cereal meals, tree bark meal, wood meal, and nutshell meal. 
     In some embodiments, the microbial compositions of the present disclosure are liquid. In further embodiments, the liquid comprises a solvent that may include water or an alcohol, and other animal-safe solvents. In some embodiments, the microbial compositions of the present disclosure include binders such as animal-safe polymers, carboxymethylcellulose, starch, polyvinyl alcohol, and the like. 
     In some embodiments, the microbial compositions of the present disclosure comprise thickening agents such as silica, clay, natural extracts of seeds or seaweed, synthetic derivatives of cellulose, guar gum, locust bean gum, alginates, and methylcelluloses. In some embodiments, the microbial compositions comprise anti-settling agents such as modified starches, polyvinyl alcohol, xanthan gum, and the like. 
     In some embodiments, the microbial compositions of the present disclosure comprise colorants including organic chromophores classified as nitroso; nitro; azo, including monoazo, bisazo and polyazo; acridine, anthraquinone, azine, diphenylmethane, indamine, indophenol, methine, oxazine, phthalocyanine, thiazine, thiazole, triarylmethane, xanthene. In some embodiments, the microbial compositions of the present disclosure comprise trace nutrients such as salts of iron, manganese, boron, copper, cobalt, molybdenum and zinc. 
     In some embodiments, the microbial compositions of the present disclosure comprise an animal-safe virucide or nematicide. 
     In some embodiments, microbial compositions of the present disclosure comprise saccharides (e.g., monosaccharides, disaccharides, trisaccharides, polysaccharides, oligosaccharides, and the like), polymeric saccharides, lipids, polymeric lipids, lipopolysaccharides, proteins, polymeric proteins, lipoproteins, nucleic acids, nucleic acid polymers, silica, inorganic salts and combinations thereof. In a further embodiment, microbial compositions comprise polymers of agar, agarose, gelrite, gellan gumand the like. In some embodiments, microbial compositions comprise plastic capsules, emulsions (e.g., water and oil), membranes, and artificial membranes. In some embodiments, emulsions or linked polymer solutions may comprise microbial compositions of the present disclosure. See Harel and Bennett (U.S. Pat. No. 8,460,726B2). 
     In some embodiments, microbial compositions of the present disclosure occur in a solid form (e.g., dispersed lyophilized spores) or a liquid form (microbes interspersed in a storage medium). 
     In some embodiments, microbial compositions of the present disclosure comprise one or more preservatives. The preservatives may be in liquid or gas formulations. The preservatives may be selected from one or more of monosaccharide, disaccharide, trisaccharide, polysaccharide, acetic acid, ascorbic acid, calcium ascorbate, erythorbic acid, iso-ascorbic acid, erythrobic acid, potassium nitrate, sodium ascorbate, sodium erythorbate, sodium iso-ascorbate, sodium nitrate, sodium nitrite, nitrogen, benzoic acid, calcium sorbate, ethyl lauroyl arginate, methyl-p-hydroxy benzoate, methyl paraben, potassium acetate, potassium benzoate, potassium bisulphite, potassium diacetate, potassium lactate, potassium metabisulphite, potassium sorbate, propyl-p-hydroxy benzoate, propyl paraben, sodium acetate, sodium benzoate, sodium bisulphite, sodium nitrite, sodium diacetate, sodium lactate, sodium metabisulphite, sodium salt of methyl-p-hydroxy benzoic acid, sodium salt of propyl-p-hydroxy benzoic acid, sodium sulphate, sodium sulfite, sodium dithionite, sulphurous acid, calcium propionate, dimethyl dicarbonate, natamycin, potassium sorbate, potassium bisulfite, potassium metabisulfite, propionic acid, sodium diacetate, sodium propionate, sodium sorbate, sorbic acid, ascorbic acid, ascorbyl palmitate, ascorbyl stearate, butylated hydro-xyanisole, butylated hydroxytoluene (BHT), butylated hydroxyl anisole (BHA), citric acid, citric acid esters of mono- and/or diglycerides, L-cysteine, L-cysteine hydrochloride, gum guaiacum, gum guaiac, lecithin, lecithin citrate, monoglyceride citrate, monoisopropyl citrate, propyl gallate, sodium metabisulphite, tartaric acid, tertiary butyl hydroquinone, stannous chloride, thiodipropionic acid, dilauryl thiodipropionate, distearyl thiodipropionate, ethoxyquin, sulfur dioxide, formic acid, or tocopherol(s). 
     In some embodiments, microbial compositions of the present disclosure include bacterial and/or fungal cells in spore form, vegetative cell form, and/or lysed cell form. In one embodiment, the lysed cell form acts as a mycotoxin binder, e.g. mycotoxins binding to dead cells. 
     In some embodiments, the microbial compositions are shelf stable in a refrigerator (35-40° F.) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable in a refrigerator (35-40° F.) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. 
     In some embodiments, the microbial compositions are shelf stable at room temperature (68-72° F.) or between 50-77° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at room temperature (68-72° F.) or between 50-77° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. 
     In some embodiments, the microbial compositions are shelf stable at −23-35° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at −23-35° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. 
     In some embodiments, the microbial compositions are shelf stable at 77-100° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at 77-100° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. 
     In some embodiments, the microbial compositions are shelf stable at 101-213° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at 101-213° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. 
     In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of about 1 to 100, about 1 to 95, about 1 to 90, about 1 to 85, about 1 to 80, about 1 to 75, about 1 to 70, about 1 to 65, about 1 to 60, about 1 to 55, about 1 to 50, about 1 to 45, about 1 to 40, about 1 to 35, about 1 to 30, about 1 to 25, about 1 to 20, about 1 to 15, about 1 to 10, about 1 to 5, about 5 to 100, about 5 to 95, about 5 to 90, about 5 to 85, about 5 to 80, about 5 to 75, about 5 to 70, about 5 to 65, about 5 to 60, about 5 to 55, about 5 to 50, about 5 to 45, about 5 to 40, about 5 to 35, about 5 to 30, about 5 to 25, about 5 to 20, about 5 to 15, about 5 to 10, about 10 to 100, about 10 to 95, about 10 to 90, about 10 to 85, about 10 to 80, about 10 to 75, about 10 to 70, about 10 to 65, about 10 to 60, about 10 to 55, about 10 to 50, about 10 to 45, about 10 to 40, about 10 to 35, about 10 to 30, about 10 to 25, about 10 to 20, about 10 to 15, about 15 to 100, about 15 to 95, about 15 to 90, about 15 to 85, about 15 to 80, about 15 to 75, about 15 to 70, about 15 to 65, about 15 to 60, about 15 to 55, about 15 to 50, about 15 to 45, about 15 to 40, about 15 to 35, about 15 to 30, about 15 to 25, about 15 to 20, about 20 to 100, about 20 to 95, about 20 to 90, about 20 to 85, about 20 to 80, about 20 to 75, about 20 to 70, about 20 to 65, about 20 to 60, about 20 to 55, about 20 to 50, about 20 to 45, about 20 to 40, about 20 to 35, about 20 to 30, about 20 to 25, about 25 to 100, about 25 to 95, about 25 to 90, about 25 to 85, about 25 to 80, about 25 to 75, about 25 to 70, about 25 to 65, about 25 to 60, about 25 to 55, about 25 to 50, about 25 to 45, about 25 to 40, about 25 to 35, about 25 to 30, about 30 to 100, about 30 to 95, about 30 to 90, about 30 to 85, about 30 to 80, about 30 to 75, about 30 to 70, about 30 to 65, about 30 to 60, about 30 to 55, about 30 to 50, about 30 to 45, about 30 to 40, about 30 to 35, about 35 to 100, about 35 to 95, about 35 to 90, about 35 to 85, about 35 to 80, about 35 to 75, about 35 to 70, about 35 to 65, about 35 to 60, about 35 to 55, about 35 to 50, about 35 to 45, about 35 to 40, about 40 to 100, about 40 to 95, about 40 to 90, about 40 to 85, about 40 to 80, about 40 to 75, about 40 to 70, about 40 to 65, about 40 to 60, about 40 to 55, about 40 to 50, about 40 to 45, about 45 to 100, about 45 to 95, about 45 to 90, about 45 to 85, about 45 to 80, about 45 to 75, about 45 to 70, about 45 to 65, about 45 to 60, about 45 to 55, about 45 to 50, about 50 to 100, about 50 to 95, about 50 to 90, about 50 to 85, about 50 to 80, about 50 to 75, about 50 to 70, about 50 to 65, about 50 to 60, about 50 to 55, about 55 to 100, about 55 to 95, about 55 to 90, about 55 to 85, about 55 to 80, about 55 to 75, about 55 to 70, about 55 to 65, about 55 to 60, about 60 to 100, about 60 to 95, about 60 to 90, about 60 to 85, about 60 to 80, about 60 to 75, about 60 to 70, about 60 to 65, about 65 to 100, about 65 to 95, about 65 to 90, about 65 to 85, about 65 to 80, about 65 to 75, about 65 to 70, about 70 to 100, about 70 to 95, about 70 to 90, about 70 to 85, about 70 to 80, about 70 to 75, about 75 to 100, about 75 to 95, about 75 to 90, about 75 to 85, about 75 to 80, about 80 to 100, about 80 to 95, about 80 to 90, about 80 to 85, about 85 to 100, about 85 to 95, about 85 to 90, about 90 to 100, about 90 to 95, or 95 to 100 weeks 
     In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of 1 to 100, 1 to 95, 1 to 90, 1 to 85, 1 to 80, 1 to 75, 1 to 70, 1 to 65, 1 to 60, 1 to 55, 1 to 50, 1 to 45, 1 to 40, 1 to 35, 1 to 30, 1 to 25, 1 to 20, 1 to 15, 1 to 10, 1 to 5, 5 to 100, 5 to 95, 5 to 90, 5 to 85, 5 to 80, 5 to 75, 5 to 70, 5 to 65, 5 to 60, 5 to 55, 5 to 50, 5 to 45, 5 to 40, 5 to 35, 5 to 30, 5 to 25, 5 to 20, 5 to 15, 5 to 10, 10 to 100, 10 to 95, 10 to 90, 10 to 85, 10 to 80, 10 to 75, 10 to 70, 10 to 65, 10 to 60, 10 to 55, 10 to 50, 10 to 45, 10 to 40, 10 to 35, 10 to 30, 10 to 25, 10 to 20, 10 to 15, 15 to 100, 15 to 95, 15 to 90, 15 to 85, 15 to 80, 15 to 75, 15 to 70, 15 to 65, 15 to 60, 15 to 55, 15 to 50, 15 to 45, 15 to 40, 15 to 35, 15 to 30, 15 to 25, 15 to 20, 20 to 100, 20 to 95, 20 to 90, 20 to 85, 20 to 80, 20 to 75, 20 to 70, 20 to 65, 20 to 60, 20 to 55, 20 to 50, 20 to 45, 20 to 40, 20 to 35, 20 to 30, 20 to 25, 25 to 100, 25 to 95, 25 to 90, 25 to 85, 25 to 80, 25 to 75, 25 to 70, 25 to 65, 25 to 60, 25 to 55, 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 100, 30 to 95, 30 to 90, 30 to 85, 30 to 80, 30 to 75, 30 to 70, 30 to 65, 30 to 60, 30 to 55, 30 to 50, 30 to 45, 30 to 40, 30 to 35, 35 to 100, 35 to 95, 35 to 90, 35 to 85, 35 to 80, 35 to 75, 35 to 70, 35 to 65, 35 to 60, 35 to 55, 35 to 50, 35 to 45, 35 to 40, 40 to 100, 40 to 95, 40 to 90, 40 to 85, 40 to 80, 40 to 75, 40 to 70, 40 to 65, 40 to 60, 40 to 55, 40 to 50, 40 to 45, 45 to 100, 45 to 95, 45 to 90, 45 to 85, 45 to 80, 45 to 75, 45 to 70, 45 to 65, 45 to 60, 45 to 55, 45 to 50, 50 to 100, 50 to 95, 50 to 90, 50 to 85, 50 to 80, 50 to 75, 50 to 70, 50 to 65, 50 to 60, 50 to 55, 55 to 100, 55 to 95, 55 to 90, 55 to 85, 55 to 80, 55 to 75, 55 to 70, 55 to 65, 55 to 60, 60 to 100, 60 to 95, 60 to 90, 60 to 85, 60 to 80, 60 to 75, 60 to 70, 60 to 65, 65 to 100, 65 to 95, 65 to 90, 65 to 85, 65 to 80, 65 to 75, 65 to 70, 70 to 100, 70 to 95, 70 to 90, 70 to 85, 70 to 80, 70 to 75, 75 to 100, 75 to 95, 75 to 90, 75 to 85, 75 to 80, 80 to 100, 80 to 95, 80 to 90, 80 to 85, 85 to 100, 85 to 95, 85 to 90, 90 to 100, 90 to 95, or 95 to 100 weeks. 
     In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of about 1 to 36, about 1 to 34, about 1 to 32, about 1 to 30, about 1 to 28, about 1 to 26, about 1 to 24, about 1 to 22, about 1 to 20, about 1 to 18, about 1 to 16, about 1 to 14, about 1 to 12, about 1 to 10, about 1 to 8, about 1 to 6, about 1 one 4, about 1 to 2, about 4 to 36, about 4 to 34, about 4 to 32, about 4 to 30, about 4 to 28, about 4 to 26, about 4 to 24, about 4 to 22, about 4 to 20, about 4 to 18, about 4 to 16, about 4 to 14, about 4 to 12, about 4 to 10, about 4 to 8, about 4 to 6, about 6 to 36, about 6 to 34, about 6 to 32, about 6 to 30, about 6 to 28, about 6 to 26, about 6 to 24, about 6 to 22, about 6 to 20, about 6 to 18, about 6 to 16, about 6 to 14, about 6 to 12, about 6 to 10, about 6 to 8, about 8 to 36, about 8 to 34, about 8 to 32, about 8 to 30, about 8 to 28, about 8 to 26, about 8 to 24, about 8 to 22, about 8 to 20, about 8 to 18, about 8 to 16, about 8 to 14, about 8 to 12, about 8 to 10, about 10 to 36, about 10 to 34, about 10 to 32, about 10 to 30, about 10 to 28, about 10 to 26, about 10 to 24, about 10 to 22, about 10 to 20, about 10 to 18, about 10 to 16, about 10 to 14, about 10 to 12, about 12 to 36, about 12 to 34, about 12 to 32, about 12 to 30, about 12 to 28, about 12 to 26, about 12 to 24, about 12 to 22, about 12 to 20, about 12 to 18, about 12 to 16, about 12 to 14, about 14 to 36, about 14 to 34, about 14 to 32, about 14 to 30, about 14 to 28, about 14 to 26, about 14 to 24, about 14 to 22, about 14 to 20, about 14 to 18, about 14 to 16, about 16 to 36, about 16 to 34, about 16 to 32, about 16 to 30, about 16 to 28, about 16 to 26, about 16 to 24, about 16 to 22, about 16 to 20, about 16 to 18, about 18 to 36, about 18 to 34, about 18 to 32, about 18 to 30, about 18 to 28, about 18 to 26, about 18 to 24, about 18 to 22, about 18 to 20, about 20 to 36, about 20 to 34, about 20 to 32, about 20 to 30, about 20 to 28, about 20 to 26, about 20 to 24, about 20 to 22, about 22 to 36, about 22 to 34, about 22 to 32, about 22 to 30, about 22 to 28, about 22 to 26, about 22 to 24, about 24 to 36, about 24 to 34, about 24 to 32, about 24 to 30, about 24 to 28, about 24 to 26, about 26 to 36, about 26 to 34, about 26 to 32, about 26 to 30, about 26 to 28, about 28 to 36, about 28 to 34, about 28 to 32, about 28 to 30, about 30 to 36, about 30 to 34, about 30 to 32, about 32 to 36, about 32 to 34, or about 34 to 36 months. 
     In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of 1 to 36 1 to 34 1 to 32 1 to 30 1 to 28 1 to 26 1 to 24 1 to 22 1 to 20 1 to 18 1 to 16 1 to 14 1 to 12 1 to 10 1 to 8 1 to 6 1 one 4 1 to 2 4 to 36 4 to 34 4 to 32 4 to 30 4 to 28 4 to 26 4 to 24 4 to 22 4 to 20 4 to 184 to 164 to 144 to 124 to 10 4 to 8 4 to 6 6 to 36 6 to 34 6 to 32 6 to 30 6 to 28 6 to 26 6 to 24 6 to 22 6 to 20 6 to 186 to 166 to 146 to 126 to 10 6 to 8 8 to 36 8 to 34 8 to 32 8 to 30 8 to 28 8 to 26 8 to 24 8 to 22 8 to 20 8 to 18 8 to 16 8 to 14 8 to 12 8 to 10 10 to 36 10 to 34 10 to 32 10 to 30 10 to 28 10 to 26 10 to 24 10 to 22 10 to 20 10 to 18 10 to 16 10 to 14 10 to 12 12 to 36 12 to 34 12 to 32 12 to 30 12 to 28 12 to 26 12 to 24 12 to 22 12 to 20 12 to 18 12 to 16 12 to 14 14 to 36 14 to 34 14 to 32 14 to 30 14 to 28 14 to 26 14 to 24 14 to 22 14 to 20 14 to 18 14 to 16 16 to 36 16 to 34 16 to 32 16 to 30 16 to 28 16 to 26 16 to 24 16 to 22 16 to 20 16 to 18 18 to 36 18 to 34 18 to 32 18 to 30 18 to 28 18 to 26 18 to 24 18 to 22 18 to 20 20 to 36 20 to 34 20 to 32 20 to 30 20 to 28 20 to 26 20 to 24 20 to 22 22 to 36 22 to 34 22 to 32 22 to 30 22 to 28 22 to 26 22 to 24 24 to 36 24 to 34 24 to 32 24 to 30 24 to 28 24 to 26 26 to 36 26 to 34 26 to 32 26 to 30 26 to 28 28 to 36 28 to 34 28 to 32 28 to 30 30 to 36 30 to 34 30 to 32 32 to 36 32 to 34, or about 34 to 36. 
     In some embodiments, the microbial compositions of the present disclosure are shelf stable at any of the disclosed temperatures and/or temperature ranges and spans of time at a relative humidity of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, or 98%. 
     Encapsulated Compositions 
     In some embodiments, the microbes or microbial compositions of the disclosure are encapsulated in an encapsulating composition. An encapsulating composition protects the microbes from external stressors prior to entering the gastrointestinal tract of ungulates. Encapsulating compositions further create an environment that may be beneficial to the microbes, such as minimizing the oxidative stresses of an aerobic environment on anaerobic microbes. See Kalsta et al. (U.S. Pat. No. 5,104,662A), Ford (U.S. Pat. No. 5,733,568A), and Mosbach and Nilsson (U.S. Pat. No. 4,647,536A) for encapsulation compositions of microbes, and methods of encapsulating microbes. 
     In one embodiment, the encapsulating composition comprises microcapsules having a multiplicity of liquid cores encapsulated in a solid shell material. For purposes of the disclosure, a “multiplicity” of cores is defined as two or more. 
     A first category of useful fusible shell materials is that of normally solid fats, including fats which are already of suitable hardness and animal or vegetable fats and oils which are hydrogenated until their melting points are sufficiently high to serve the purposes of the present disclosure. Depending on the desired process and storage temperatures and the specific material selected, a particular fat can be either a normally solid or normally liquid material. The terms “normally solid” and “normally liquid” as used herein refer to the state of a material at desired temperatures for storing the resulting microcapsules. Since fats and hydrogenated oils do not, strictly speaking, have melting points, the term “melting point” is used herein to describe the minimum temperature at which the fusible material becomes sufficiently softened or liquid to be successfully emulsified and spray cooled, thus roughly corresponding to the maximum temperature at which the shell material has sufficient integrity to prevent release of the choline cores. “Melting point” is similarly defined herein for other materials which do not have a sharp melting point. 
     Specific examples of fats and oils useful herein (some of which require hardening) are as follows: animal oils and fats, such as beef tallow, mutton tallow, lamb tallow, lard or pork fat, fish oil, and sperm oil; vegetable oils, such as canola oil, cottonseed oil, peanut oil, corn oil, olive oil, soybean oil, sunflower oil, safflower oil, coconut oil, palm oil, linseed oil, tung oil, and castor oil; fatty acid monoglycerides and diglycerides; free fatty acids, such as stearic acid, palmitic acid, and oleic acid; and mixtures thereof. The above listing of oils and fats is not meant to be exhaustive, but only exemplary. 
     Specific examples of fatty acids include linoleic acid, γ-linoleic acid, dihomo-γ-linolenic acid, arachidonic acid, docosatetraenoic acid, vaccenic acid, nervonic acid, mead acid, erucic acid, gondoic acid, elaidic acid, oleic acid, palitoleic acid, stearidonic acid, eicosapentaenoic acid, valeric acid, caproic acid, enanthic acid, caprylic acid, pelargonic acid, capric acid, undecylic acid, lauric acid, tridecylic acid, myristic acid, pentadecylic acid, palmitic acid, margaric acid, stearic acid, nonadecyclic acid, arachidic acid, heneicosylic acid, behenic acid, tricosylic acid, lignoceric acid, pentacosylic acid, cerotic acid, heptacosylic acid, montanic acid, nonacosylic acid, melissic acid, henatriacontylic acid, lacceroic acid, psyllic acid, geddic acid, ceroplastic acid, hexatriacontylic acid, heptatriacontanoic acid, and octatriacontanoic acid. 
     Another category of fusible materials useful as encapsulating shell materials is that of waxes. Representative waxes contemplated for use herein are as follows: animal waxes, such as beeswax, lanolin, shell wax, and Chinese insect wax; vegetable waxes, such as carnauba, candelilla, bayberry, and sugar cane; mineral waxes, such as paraffin, microcrystalline petroleum, ozocerite, ceresin, and montan; synthetic waxes, such as low molecular weight polyolefin (e.g., CARBOWAX), and polyol ether-esters (e.g., sorbitol); Fischer-Tropsch process synthetic waxes; and mixtures thereof. Water-soluble waxes, such as CARBOWAX and sorbitol, are not contemplated herein if the core is aqueous. 
     Still other fusible compounds useful herein are fusible natural resins, such as rosin, balsam, shellac, and mixtures thereof. 
     Various adjunct materials are contemplated for incorporation in fusible materials according to the present disclosure. For example, antioxidants, light stabilizers, dyes and lakes, flavors, essential oils, anti-caking agents, fillers, pH stabilizers, sugars (monosaccharides, disaccharides, trisaccharides, and polysaccharides) and the like can be incorporated in the fusible material in amounts which do not diminish its utility for the present disclosure. 
     The core material contemplated herein constitutes from about 0.10% to about 50%, about 1% to about 35%. or about 5% to about 30% by weight of the microcapsules. In some embodiments, the core material contemplated herein constitutes no more than about 30% by weight of the microcapsules. In some embodiments, the core material contemplated herein constitutes about 5% by weight of the microcapsules. The core material is contemplated as either a liquid or solid at contemplated storage temperatures of the microcapsules. 
     The cores may include other additives well-known in the pharmaceutical art, including edible sugars, such as sucrose, glucose, maltose, fructose, lactose, cellobiose, monosaccharides, disaccharides, trisaccharides, polysaccharides, and mixtures thereof; artificial sweeteners, such as aspartame, saccharin, cyclamate salts, and mixtures thereof; edible acids, such as acetic acid (vinegar), citric acid, ascorbic acid, tartaric acid, and mixtures thereof; edible starches, such as corn starch; hydrolyzed vegetable protein; water-soluble vitamins, such as Vitamin C; water-soluble medicaments; water-soluble nutritional materials, such as ferrous sulfate; flavors; salts; monosodium glutamate; antimicrobial agents, such as sorbic acid; antimycotic agents, such as potassium sorbate, sorbic acid, sodium benzoate, and benzoic acid; food grade pigments and dyes; and mixtures thereof. Other potentially useful supplemental core materials will be apparent to those of ordinary skill in the art. 
     Emulsifying agents may be employed to assist in the formation of stable emulsions. Representative emulsifying agents include glyceryl monostearate, polysorbate esters, ethoxylated mono- and diglycerides, and mixtures thereof. 
     For ease of processing, and particularly to enable the successful formation of a reasonably stable emulsion, the viscosities of the core material and the shell material should be similar at the temperature at which the emulsion is formed. In particular, the ratio of the viscosity of the shell to the viscosity of the core, expressed in centipoise or comparable units, and both measured at the temperature of the emulsion, should be from about 22:1 to about 1:1, desirably from about 8:1 to about 1:1, and preferably from about 3:1 to about 1:1. A ratio of 1:1 would be ideal, but a viscosity ratio within the recited ranges is useful. 
     Encapsulating compositions are not limited to microcapsule compositions as disclosed above. In some embodiments encapsulating compositions encapsulate the microbial compositions in an adhesive polymer that can be natural or synthetic without toxic effect. In some embodiments, the encapsulating composition may be a matrix selected from sugar matrix, gelatin matrix, polymer matrix, silica matrix, starch matrix, foam matrix, etc. In some embodiments, the encapsulating composition may be selected from polyvinyl acetates; polyvinyl acetate copolymers; ethylene vinyl acetate (EVA) copolymers; polyvinyl alcohols; polyvinyl alcohol copolymers; celluloses, including ethylcelluloses, methylcelluloses, hydroxymethylcelluloses, hydroxypropylcelluloses and carboxymethylcellulose; polyvinylpyrolidones; polysaccharides, including starch, modified starch, dextrins, maltodextrins, alginate and chitosans; monosaccharides; fats; fatty acids, including oils; proteins, including gelatin and zeins; gum arabics; shellacs; vinylidene chloride and vinylidene chloride copolymers; calcium lignosulfonates; acrylic copolymers; polyvinylacrylates; polyethylene oxide; acrylamide polymers and copolymers; polyhydroxyethyl acrylate, methylacrylamide monomers; and polychloroprene. 
     In some embodiments, the encapsulating shell of the present disclosure can be up to 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm, 160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 210 μm, 220 μm, 230 μm, 240 μm, 250 μm, 260 μm, 270 μm, 280 μm, 290 μm, 300 μm, 310 μm, 320 μm, 330 μm, 340 μm, 350 μm, 360 μm, 370 μm, 380 μm, 390 μm, 400 μm, 410 μm, 420 μm, 430 μm, 440 μm, 450 μm, 460 μm, 470 μm, 480 μm, 490 μm, 500 μm, 510 μm, 520 μm, 530 μm, 540 μm, 550 μm, 560 μm, 570 μm, 580 μm, 590 μm, 600 μm, 610 μm, 620 μm, 630 μm, 640 μm, 650 μm, 660 μm, 670 μm, 680 μm, 690 μm, 700 μm, 710 μm, 720 μm, 730 μm, 740 μm, 750 μm, 760 μm, 770 μm, 780 μm, 790 μm, 800 μm, 810 μm, 820 μm, 830 μm, 840 μm, 850 μm, 860 μm, 870 μm, 880 μm, 890 μm, 900 μm, 910 μm, 920 μm, 930 μm, 940 μm, 950 μm, 960 μm, 970 μm, 980 μm, 990 μm, 1000 μm, 1010 μm, 1020 μm, 1030 μm, 1040 μm, 1050 μm, 1060 μm, 1070 μm, 1080 μm, 1090 μm, 1100 μm, 1110 μm, 1120 μm, 1130 μm, 1140 μm, 1150 μm, 1160 μm, 1170 μm, 1180 μm, 1190 μm, 1200 μm, 1210 μm, 1220 μm, 1230 μm, 1240 μm, 1250 μm, 1260 μm, 1270 μm, 1280 μm, 1290 μm, 1300 μm, 1310 μm, 1320 μm, 1330 μm, 1340 μm, 1350 μm, 1360 μm, 1370 μm, 1380 μm, 1390 μm, 1400 μm, 1410 μm, 1420 μm, 1430 μm, 1440 μm, 1450 μm, 1460 μm, 1470 μm, 1480 μm, 1490 μm, 1500 μm, 1510 μm, 1520 μm, 1530 μm, 1540 μm, 1550 μm, 1560 μm, 1570 μm, 1580 μm, 1590 μm, 1600 μm, 1610 μm, 1620 μm, 1630 μm, 1640 μm, 1650 μm, 1660 μm, 1670 μm, 1680 μm, 1690 μm, 1700 μm, 1710 μm, 1720 μm, 1730 μm, 1740 μm, 1750 μm, 1760 μm, 1770 μm, 1780 μm, 1790 μm, 1800 μm, 1810 μm, 1820 μm, 1830 μm, 1840 μm, 1850 μm, 1860 μm, 1870 μm, 1880 μm, 1890 μm, 1900 μm, 1910 μm, 1920 μm, 1930 μm, 1940 μm, 1950 μm, 1960 μm, 1970 μm, 1980 μm, 1990 μm, 2000 μm, 2010 μm, 2020 μm, 2030 μm, 2040 μm, 2050 μm, 2060 μm, 2070 μm, 2080 μm, 2090 μm, 2100 μm, 2110 μm, 2120 μm, 2130 μm, 2140 μm, 2150 μm, 2160 μm, 2170 μm, 2180 μm, 2190 μm, 2200 μm, 2210 μm, 2220 μm, 2230 μm, 2240 μm, 2250 μm, 2260 μm, 2270 μm, 2280 μm, 2290 μm, 2300 μm, 2310 μm, 2320 μm, 2330 μm, 2340 μm, 2350 μm, 2360 μm, 2370 μm, 2380 μm, 2390 μm, 2400 μm, 2410 μm, 2420 μm, 2430 μm, 2440 μm, 2450 μm, 2460 μm, 2470 μm, 2480 μm, 2490 μm, 2500 μm, 2510 μm, 2520 μm, 2530 μm, 2540 μm, 2550 μm, 2560 μm, 2570 μm, 2580 μm, 2590 μm, 2600 μm, 2610 μm, 2620 μm, 2630 μm, 2640 μm, 2650 μm, 2660 μm, 2670 μm, 2680 μm, 2690 μm, 2700 μm, 2710 μm, 2720 μm, 2730 μm, 2740 μm, 2750 μm, 2760 μm, 2770 μm, 2780 μm, 2790 μm, 2800 μm, 2810 μm, 2820 μm, 2830 μm, 2840 μm, 2850 μm, 2860 μm, 2870 μm, 2880 μm, 2890 μm, 2900 μm, 2910 μm, 2920 μm, 2930 μm, 2940 μm, 2950 μm, 2960 μm, 2970 μm, 2980 μm, 2990 μm, or 3000 μm thick. 
     Animal Feed 
     In some embodiments, compositions of the present disclosure are mixed with animal feed. In some embodiments, animal feed may be present in various forms such as pellets, capsules, granulated, powdered, liquid, or semi-liquid. 
     In some embodiments, compositions of the present disclosure are mixed into the premix at at the feed mill (e.g., Carghill or Western Millin), alone as a standalone premix, and/or alongside other feed additives such as MONENSIN, vitamins, etc. In one embodiment, the compositions of the present disclosure are mixed into the feed at the feed mill. In another embodiment, compositions of the present disclosure are mixed into the feed itself. 
     In some embodiments, feed of the present disclosure may be supplemented with water, premix or premixes, forage, fodder, beans (e.g., whole, cracked, or ground), grains (e.g., whole, cracked, or ground), bean- or grain-based oils, bean- or grain-based meals, bean- or grain-based haylage or silage, bean- or grain-based syrups, fatty acids, sugar alcohols (e.g., polyhydric alcohols), commercially available formula feeds, and mixtures thereof. 
     In some embodiments, forage encompasses hay, haylage, and silage. In some embodiments, hays include grass hays (e.g., sudangrass, orchardgrass, or the like), alfalfa hay, and clover hay. In some embodiments, haylages include grass haylages, sorghum haylage, and alfalfa haylage. In some embodiments, silages include maize, oat, wheat, alfalfa, clover, and the like. 
     In some embodiments, premix or premixes may be utilized in the feed. Premixes may comprise micro-ingredients such as vitamins, minerals, amino acids; chemical preservatives; pharmaceutical compositions such as antibiotics and other medicaments; fermentation products, and other ingredients. In some embodiments, premixes are blended into the feed. 
     In some embodiments, the feed may include feed concentrates such as soybean hulls, sugar beet pulp, molasses, high protein soybean meal, ground corn, shelled corn, wheat midds, distiller grain, cottonseed hulls, rumen-bypass protein, rumen-bypass fat, and grease. See Luhman (U.S. Publication US20150216817A1), Anderson el al. (U.S. Pat. No. 3,484,243) and Porter and Luhman (U.S. Pat. No. 9,179,694B2) for animal feed and animal feed supplements capable of use in the present compositions and methods. 
     In some embodiments, feed occurs as a compound, which includes, in a mixed composition capable of meeting the basic dietary needs, the feed itself, vitamins, minerals, amino acids, and other necessary components. Compound feed may further comprise premixes. 
     In some embodiments, microbial compositions of the present disclosure may be mixed with animal feed, premix, and/or compound feed. Individual components of the animal feed may be mixed with the microbial compositions prior to feeding to ruminants. The microbial compositions of the present disclosure may be applied into or on a premix, into or on a feed, and/or into or on a compound feed. 
     Administration of Microbial Compositions 
     In some embodiments, the microbial compositions of the present disclosure are administered to ruminants via the oral route. In some embodiments the microbial compositions are administered via a direct injection route into the gastrointestinal tract. In further embodiments, the direct injection administration delivers the microbial compositions directly to the rumen. In some embodiments, the microbial compositions of the present disclosure are administered to animals anally. In further embodiments, anal administration is in the form of an inserted suppository. 
     In some embodiments, the microbial composition is administered in a dose comprise a total of, or at least, 1 mL, 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL, 21 mL, 22 mL, 23 mL, 24 mL, 25 mL, 26 mL, 27 mL, 28 mL, 29 mL, 30 mL, 31 mL, 32 mL, 33 mL, 34 mL, 35 mL, 36 mL, 37 mL, 38 mL, 39 mL, 40 mL, 41 mL, 42 mL, 43 mL, 44 mL, 45 mL, 46 mL, 47 mL, 48 mL, 49 mL, 50 mL, 60 mL, 70 mL, 80 mL, 90 mL, 100 mL, 200 mL, 300 mL, 400 mL, 500 mL, 600 mL, 700 mL, 800 mL, 900 mL, or 1,000 mL. 
     In some embodiments, the microbial composition is administered in a dose comprising a total of, or at least, 10 18 , 10 17 , 10 16 , 10 15 , 10 14 , 10 13 , 10 12 , 10 11 , 10 10 , 10 9 , 10 8 , 10 7 , 10 6 , 10 5 , 10 4 , 10 3 , or 10 2  microbial cells. 
     In some embodiments, the microbial compositions are mixed with feed, and the administration occurs through the ingestion of the microbial compositions along with the feed. In some embodiments, the dose of the microbial composition is administered such that there exists 10 2  to 10 12 , 10 3  to 10 12 , 10 4  to 10 12 , 10 5  to 10 12 , 10 6  to 10 12 , 10 7  to 10 12 , 10 8  to 10 12 , 10 9  to 10 12 , 10 10  to 10 12 , 10 11  to 10 12 , 10 2  to 10 11 , 10 3  to 10 11 , 10 4  to 10 11 , 10 5  to 10 11 , 10 6  to 10 11 , 10 7  to 10 11 , 10 8  to 10 11 , 10 9  to 10 11 , 10 10  to 10 11 , 10 2  to 10 10 , 10 3  to 10 10 , 10 4  to 10 10 , 10 5  to 10 10 , 10 6  to 10 10 , 10 7  to 10 10 , 10 8  to 10 10 , 10 9  to 10 10 , 10 2  to 10 9 , 10 3  to 10 9 , 10 4  to 10 9 , 10 5  to 10 9 , 10 6  to 10 9 , 10 7  to 10 9 , 10 8  to 10 9 , 10 2  to 10 8 , 10 3  to 10 8 , 10 4  to 10 8 , 10 5  to 10 8 , 10 6  to 10 8 , 10 7  to 10 8 , 10 2  to 10 7 , 10 3  to 10 7 , 10 4  to 10 7 , 10 5  to 10 7 , 10 6  to 10 7 , 10 2  to 10 6 , 10 3  to 10 6 , 10 4  to 10 6 , 10 5  to 10 6 , 10 2  to 10 5 , 10 3  to 10 5 , 10 4  to 10 5 , 10 2  to 10 4 , 10 3  to 10 4 , 10 2  to 10 3 , 10 12 , 10 11 , 10 10 , 10 9 , 10 8 , 10 7 , 10 6 , 10 5 , 10 4 , 10 3 , or 10 2  total microbial cells per gram or milliliter of the composition. 
     In some embodiments, the microbial compositions are mixed with feed, and the administration occurs through the ingestion of the microbial compositions along with the feed. In some embodiments, the dose of the microbial composition is administered such that there exists 10 2  to 10 12 , 10 3  to 10 12 , 10 4  to 10 12 , 10 5  to 10 12 , 10 6  to 10 12 , 10 7  to 10 12 , 10 8  to 10 12 , 10 9  to 10 12 , 10 10  to 10 12 , 10 11  to 10 12 , 10 2  to 10 11 , 10 3  to 10 11 , 10 4  to 10 11 , 10 5  to 10 11 , 10 6  to 10 11 , 10 7  to 10 11 , 10 8  to 10 11 , 10 9  to 10 11 , 10 10  to 10 11 , 10 2  to 10 10 , 10 3  to 10 10 , 10 4  to 10 10 , 10 5  to 10 10 , 10 6  to 10 10 , 10 7  to 10 10 , 10 8  to 10 10 , 10 9  to 10 10 , 10 2  to 10 9 , 10 3  to 10 9 , 10 4  to 10 9 , 10 5  to 10 9 , 10 6  to 10 9 , 10 7  to 10 9 , 10 8  to 10 9 , 10 2  to 10 8 , 10 3  to 10 8 , 10 4  to 10 8 , 10 5  to 10 8 , 10 6  to 10 8 , 10 7  to 10 8 , 10 2  to 10 7 , 10 3  to 10 7 , 10 4  to 10 7 , 10 5  to 10 7 , 10 6  to 10 7 , 10 2  to 10 6 , 10 3  to 10 6 , 10 4  to 10 6 , 10 5  to 10 6 , 10 2  to 10 5 , 10 3  to 10 5 , 10 4  to 10 5 , 10 2  to 10 4 , 10 3  to 10 4 , 10 2  to 10 3 , 10 12 , 10 11 , 10 10 , 10 9 , 10 8 , 10 7 , 10 6 , 10 5 , 10 4 , 10 3 , or 10 2  colony forming units per gram or milliliter of the composition. 
     In some embodiments, the administered dose of the microbial composition comprises 10 2  to 10 18 , 10 3  to 10 18 , 10 4  to 10 18 , 10 5  to 10 18 , 10 6  to 10 18 , 10 7  to 10 18 , 10 8  to 10 18 , 10 9  to 10 18 , 10 10  to 10 18 , 10 11  to 10 18 , 10 12  to 10 18 , 10 13  to 10 18 , 10 14  to 10 18 , 10 15  to 10 18 , 10 16  to 10 18 , 10 17  to 10 18 , 10 2  to 10 12 , 10 3  to 10 12 , 10 4  to 10 12 , 10 5  to 10 12 , 10 6  to 10 12 , 10 7  to 10 12 , 10 8  to 10 12 , 10 9  to 10 12 , 10 10  to 10 12 , 10 11  to 10 12 , 10 2  to 10 11 , 10 3  to 10 11 , 10 4  to 10 11 , 10 5  to 10 11 , 10 6  to 10 11 , 10 7  to 10 11 , 10 8  to 10 11 , 10 9  to 10 11 , 10 10  to 10 11 , 10 2  to 10 10 , 10 3  to 10 10 , 10 4  to 10 10 , 10 5  to 10 10 , 10 6  to 10 10 , 10 7  to 10 10 , 10 8  to 10 10 , 10 9  to 10 10 , 10 2  to 10 9 , 10 3  to 10 9 , 10 4  to 10 9 , 10 5  to 10 9 , 10 6  to 10 9 , 10 7  to 10 9 , 10 8  to 10 9 , 10 2  to 10 1 , 10 3  to 10 8 , 10 4  to 10 8 , 10 5  to 10 8 , 10 6  to 10 1 , 10 7  to 10 8 , 10 2  to 10 7 , 10 3  to 10 7 , 10 4  to 10 7 , 10 5  to 10 7 , 10 6  to 10 7 , 10 2  to 10 6 , 10 3  to 10 6 , 10 4  to 10 6 , 10 5  to 10 6 , 10 2  to 10 0 , 10 3  to 10 0 , 10 4  to 10 5 , 10 2  to 10 4 , 10 3  to 10 4 , 10 2  to 10 3 , 10 18 , 10 17 , 10 16 , 10 15 , 10 14 , 10 13 , 10 12 , 10 11 , 10 10 , 10 9 , 10 8 , 10 7 , 10 6 , 10 5 , 10 4 , 10 3 , or 10 2  total microbial cells. 
     In some embodiments, the administered dose of each microbe in the microbial composition is at least about, at least about 10 3  colony forming units (CFU), at least about 10 4  CFU, at least about 10 5  CFU, at least about 10 6  CFU, at least about 10 7  CFU, at least about 10 8  CFU, at least about 10 9  CFU, at least about 10 10  CFU, at least about 10 11  CFU, at least about 10 12  CFU, at least about 10 13  CFU, at least about 10 14  CFU, at least about 10 15  CFU, at least about 10 16  CFU, at least about 10 17  CFU, at least about 10 18  CFU, at least about 10 19  CFU, or at least about 10 20  CFU. 
     In some embodiments, the composition is administered 1 or more times per day. In some aspects, the composition is administered with food each time the animal is fed. In some embodiments, the composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per day. 
     In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per week. 
     In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per month. 
     In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per year. 
     In some embodiments, the feed can be uniformly coated with one or more layers of the microbes and/or microbial compositions disclosed herein, using conventional methods of mixing, spraying, or a combination thereof through the use of treatment application equipment that is specifically designed and manufactured to accurately, safely, and efficiently apply coatings. Such equipment uses various types of coating technology such as rotary coaters, drum coaters, fluidized bed techniques, spouted beds, rotary mists, or a combination thereof. Liquid treatments such as those of the present disclosure can be applied via either a spinning “atomizer” disk or a spray nozzle, which evenly distributes the microbial composition onto the feed as it moves though the spray pattern. In some aspects, the feed is then mixed or tumbled for an additional period of time to achieve additional treatment distribution and drying. 
     In some embodiments, the feed coats of the present disclosure can be up to 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm, 160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 210 μm, 220 μm, 230 μm, 240 μm, 250 μm, 260 μm, 270 μm, 280 μm, 290 μm, 300 μm, 310 μm, 320 μm, 330 μm, 340 μm, 350 μm, 360 μm, 370 μm, 380 μm, 390 μm, 400 μm, 410 μm, 420 μm, 430 μm, 440 μm, 450 μm, 460 μm, 470 μm, 480 μm, 490 μm, 500 μm, 510 μm, 520 μm, 530 μm, 540 μm, 550 μm, 560 μm, 570 μm, 580 μm, 590 μm, 600 μm, 610 μm, 620 μm, 630 μm, 640 μm, 650 μm, 660 μm, 670 μm, 680 μm, 690 μm, 700 μm, 710 μm, 720 μm, 730 μm, 740 μm, 750 μm, 760 μm, 770 μm, 780 μm, 790 μm, 800 μm, 810 μm, 820 μm, 830 μm, 840 μm, 850 μm, 860 μm, 870 μm, 880 μm, 890 μm, 900 μm, 910 μm, 920 μm, 930 μm, 940 μm, 950 μm, 960 μm, 970 μm, 980 μm, 990 μm, 1000 μm, 1010 μm, 1020 μm, 1030 μm, 1040 μm, 1050 μm, 1060 μm, 1070 μm, 1080 μm, 1090 μm, 1100 μm, 1110 μm, 1120 μm, 1130 μm, 1140 μm, 1150 μm, 1160 μm, 1170 μm, 1180 μm, 1190 μm, 1200 μm, 1210 μm, 1220 μm, 1230 μm, 1240 μm, 1250 μm, 1260 μm, 1270 μm, 1280 μm, 1290 μm, 1300 μm, 1310 μm, 1320 μm, 1330 μm, 1340 μm, 1350 μm, 1360 μm, 1370 μm, 1380 μm, 1390 μm, 1400 μm, 1410 μm, 1420 μm, 1430 μm, 1440 μm, 1450 μm, 1460 μm, 1470 μm, 1480 μm, 1490 μm, 1500 μm, 1510 μm, 1520 μm, 1530 μm, 1540 μm, 1550 μm, 1560 μm, 1570 μm, 1580 μm, 1590 μm, 1600 μm, 1610 μm, 1620 μm, 1630 μm, 1640 μm, 1650 μm, 1660 μm, 1670 μm, 1680 μm, 1690 μm, 1700 μm, 1710 μm, 1720 μm, 1730 μm, 1740 μm, 1750 μm, 1760 μm, 1770 μm, 1780 μm, 1790 μm, 1800 μm, 1810 μm, 1820 μm, 1830 μm, 1840 μm, 1850 μm, 1860 μm, 1870 μm, 1880 μm, 1890 μm, 1900 μm, 1910 μm, 1920 μm, 1930 μm, 1940 μm, 1950 μm, 1960 μm, 1970 μm, 1980 μm, 1990 μm, 2000 μm, 2010 μm, 2020 μm, 2030 μm, 2040 μm, 2050 μm, 2060 μm, 2070 μm, 2080 μm, 2090 μm, 2100 μm, 2110 μm, 2120 μm, 2130 μm, 2140 μm, 2150 μm, 2160 μm, 2170 μm, 2180 μm, 2190 μm, 2200 μm, 2210 μm, 2220 μm, 2230 μm, 2240 μm, 2250 μm, 2260 μm, 2270 μm, 2280 μm, 2290 μm, 2300 μm, 2310 μm, 2320 μm, 2330 μm, 2340 μm, 2350 μm, 2360 μm, 2370 μm, 2380 μm, 2390 μm, 2400 μm, 2410 μm, 2420 μm, 2430 μm, 2440 μm, 2450 μm, 2460 μm, 2470 μm, 2480 μm, 2490 μm, 2500 μm, 2510 μm, 2520 μm, 2530 μm, 2540 μm, 2550 μm, 2560 μm, 2570 μm, 2580 μm, 2590 μm, 2600 μm, 2610 μm, 2620 μm, 2630 μm, 2640 μm, 2650 μm, 2660 μm, 2670 μm, 2680 μm, 2690 μm, 2700 μm, 2710 μm, 2720 μm, 2730 μm, 2740 μm, 2750 μm, 2760 μm, 2770 μm, 2780 μm, 2790 μm, 2800 μm, 2810 μm, 2820 μm, 2830 μm, 2840 μm, 2850 μm, 2860 μm, 2870 μm, 2880 μm, 2890 μm, 2900 μm, 2910 μm, 2920 μm, 2930 μm, 2940 μm, 2950 μm, 2960 μm, 2970 μm, 2980 μm, 2990 μm, or 3000 μm thick. 
     In some embodiments, the microbial cells can be coated freely onto any number of compositions or they can be formulated in a liquid or solid composition before being coated onto a composition. For example, a solid composition comprising the microorganisms can be prepared by mixing a solid carrier with a suspension of the spores until the solid carriers are impregnated with the spore or cell suspension. This mixture can then be dried to obtain the desired particles. 
     In some other embodiments, it is contemplated that the solid or liquid microbial compositions of the present disclosure further contain functional agents e.g., activated carbon, minerals, vitamins, and other agents capable of improving the quality of the products or a combination thereof. 
     Methods of coating and compositions in use of said methods that are known in the art can be particularly useful when they are modified by the addition of one of the embodiments of the present disclosure. Such coating methods and apparatus for their application are disclosed in, for example: U.S. Pat. Nos. 8,097,245, and 7,998,502; and PCT Pat. App. Publication Nos. WO 2008/076975, WO 2010/138522, WO 2011/094469, WO 2010/111347, and WO 2010/111565 each of which is incorporated by reference herein. 
     In some embodiments, the microbes or microbial consortia of the present disclosure exhibit a synergistic effect, on one or more of the traits described herein, in the presence of one or more of the microbes or consortia coming into contact with one another. The synergistic effect obtained by the taught methods can be quantified, for example, according to Colby&#39;s formula (i.e., (E)=X+Y−(X*Y/100)). See Colby, R. S., “Calculating Synergistic and Antagonistic Responses of Herbicide Combinations,” 1967. Weeds. Vol. 15, pp. 20-22, incorporated herein by reference in its entirety. Thus, “synergistic” is intended to reflect an outcome/parameter/effect that has been increased by more than an additive amount. 
     In some embodiments, the microbes or microbial consortia of the present disclosure may be administered via bolus. In one embodiment, a bolus (e.g., capsule containing the composition) is inserted into a bolus gun, and the bolus gun is inserted into the buccal cavity and/or esophagus of the animal, followed by the release/injection of the bolus into the animal&#39;s digestive tract. In one embodiment, the bolus gun/applicator is a BOVIKALC bolus gun/applicator. In another embodiment, the bolus gun/applicator is a QUADRICAL gun/applicator. 
     In some embodiments, the microbes or microbial consortia of the present disclosure may be administered via drench. In one embodiment, the drench is an oral drench. A drench administration comprises utilizing a drench kit/applicator/syringe that injects/releases a liquid comprising the microbes or microbial consortia into the buccal cavity and/or esophagus of the animal. 
     In some embodiments, the microbes or microbial consortia of the present disclosure may be administered in a time-released fashion. The composition may be coated in a chemical composition, or may be contained in a mechanical device or capsule that releases the microbes or microbial consortia over a period of time instead all at once. In one embodiment, the microbes or microbial consortia are administered to an animal in a time-release capsule. In one embodiment, the composition may be coated in a chemical composition, or may be contained in a mechanical device or capsule that releases the microbes or microbial consortia all at once a period of time hours post ingestion. 
     In some embodiments, the microbes or microbial consortia are administered in a time-released fashion between 1 to 5, 1 to 10, 1 to 15, 1 to 20, 1 to 24, 1 to 25, 1 to 30, 1 to 35, 1 to 40, 1 to 45, 1 to 50, 1 to 55, 1 to 60, 1 to 65, 1 to 70, 1 to 75, 1 to 80, 1 to 85, 1 to 90, 1 to 95, or 1 to 100 hours. 
     In some embodiments, the microbes or microbial consortia are administered in a time-released fashion between 1 to 2, 1 to 3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, 1 to 10, 1 to 11, 1 to 12, 1 to 13, 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 29, or 1 to 30 days. 
     Microorganisms 
     As used herein the term “microorganism” should be taken broadly. It includes, but is not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as eukaryotic fungi, protists, and viruses. 
     By way of example, the microorganisms may include species of the genera of:  Clostridium, Ruminococcus, Roseburia, Hydrogenoanaerobacterium, Saccharofermentans, Papillibacter, Pelotomaculum, Butyricicoccus, Tannerella, Prevotella, Butyricimonas, Piromyces, Pichia, Candida, Vrystaatia, Orpinomyces, Neocallimastix , and  Phyllosticta . The microorganisms may further include species belonging to the family of Lachnospiraceae, and the order of Saccharomycetales. In some embodiments, the microorganisms may include species of any genera disclosed herein. 
     In certain embodiments, the microorganism is unculturable. This should be taken to mean that the microorganism is not known to be culturable or is difficult to culture using methods known to one skilled in the art. 
     In one embodiment, the microbes are obtained from animals (e.g., mammals, reptiles, birds, and the like), soil (e.g., rhizosphere), air, water (e.g., marine, freshwater, wastewater sludge), sediment, oil, plants (e.g., roots, leaves, stems), agricultural products, and extreme environments (e.g., acid mine drainage or hydrothermal systems). In a further embodiment, microbes obtained from marine or freshwater environments such as an ocean, river, or lake. In a further embodiment, the microbes can be from the surface of the body of water, or any depth of the body of water (e.g., a deep sea sample). 
     The microorganisms of the disclosure may be isolated in substantially pure or mixed cultures. They may be concentrated, diluted, or provided in the natural concentrations in which they are found in the source material. For example, microorganisms from saline sediments may be isolated for use in this disclosure by suspending the sediment in fresh water and allowing the sediment to fall to the bottom. The water containing the bulk of the microorganisms may be removed by decantation after a suitable period of settling and either administered to the GI tract of an ungulate, or concentrated by filtering or centrifugation, diluted to an appropriate concentration and administered to the GI tract of an ungulate with the bulk of the salt removed. By way of further example, microorganisms from mineralized or toxic sources may be similarly treated to recover the microbes for application to the ungulate to minimize the potential for damage to the animal. 
     In another embodiment, the microorganisms are used in a crude form, in which they are not isolated from the source material in which they naturally reside. For example, the microorganisms are provided in combination with the source material in which they reside; for example, fecal matter, cud, or other composition found in the gastrointestinal tract. In this embodiment, the source material may include one or more species of microorganisms. 
     In some embodiments, a mixed population of microorganisms is used in the methods of the disclosure. 
     In embodiments of the disclosure where the microorganisms are isolated from a source material (for example, the material in which they naturally reside), any one or a combination of a number of standard techniques which will be readily known to skilled persons may be used. However, by way of example, these in general employ processes by which a solid or liquid culture of a single microorganism can be obtained in a substantially pure form, usually by physical separation on the surface of a solid microbial growth medium or by volumetric dilutive isolation into a liquid microbial growth medium. These processes may include isolation from dry material, liquid suspension, slurries or homogenates in which the material is spread in a thin layer over an appropriate solid gel growth medium, or serial dilutions of the material made into a sterile medium and inoculated into liquid or solid culture media. 
     Whilst not essential, in one embodiment, the material containing the microorganisms may be pre-treated prior to the isolation process in order to either multiply all microorganisms in the material. Microorganisms can then be isolated from the enriched materials as disclosed above. 
     In certain embodiments, as mentioned herein before, the microorganism(s) may be used in crude form and need not be isolated from an animal or a media. For example, cud, feces, or growth media which includes the microorganisms identified to be of benefit to increased milk production in ungulates may be obtained and used as a crude source of microorganisms for the next round of the method or as a crude source of microorganisms at the conclusion of the method. For example, fresh feces could be obtained and optionally processed. 
     Microbiome Shift and Abundance of Microbes 
     In some embodiments, the microbiome of a ruminant, including the rumen microbiome, comprises a diverse arrive of microbes with a wide variety of metabolic capabilities. The microbiome is influenced by a range of factors including diet, variations in animal metabolism, and breed, among others. Most bovine diets are plant-based and rich in complex polysaccharides that enrich the gastrointestinal microbial community for microbes capable of breaking down specific polymeric components in the diet. The end products of primary degradation sustains a chain of microbes that ultimately produce a range of organic acids together with hydrogen and carbon dioxide. Because of the complex and interlinked nature of the microbiome, changing the diet and thus substrates for primary degradation may have a cascading effect on rumen microbial metabolism, with changes in both the organic acid profiles and the methane levels produced, thus impacting the quality and quantity of animal production and or the products produced by the animal. See Menezes et al. (2011 . FEMS Microbiol. Ecol.  78(2):256-265.) 
     In some aspects, the present disclosure is drawn to administering microbial compositions described herein to modulate or shift the microbiome of a ruminant. 
     In some embodiments, the microbiome is shifted through the administration of one or more microbes to the gastrointestinal tract. In further embodiments, the one or more microbes are those selected from Table 1 or Table 3. In some embodiments, the microbiome shift or modulation includes a decrease or loss of specific microbes that were present prior to the administration of one or more microbes of the present disclosure. In some embodiments, the microbiome shift or modulation includes an increase in microbes that were present prior to the administration of one or more microbes of the present disclosure. In some embodiments, the microbiome shift or modulation includes a gain of one or more microbes that were not present prior to the administration of one or more microbes of the present disclosure. In a further embodiment, the gain of one or more microbes is a microbe that was not specifically included in the administered microbial consortium. 
     In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. 
     In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks. 
     In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. 
     In some embodiments, the presence of the administered microbes are detected by sampling the gastrointestinal tract and using primers to amplify the 16S or 18S rDNA sequences, or the ITS rDNA sequences of the administered microbes. In some embodiments, the administered microbes are one or more of those selected from Table 1 or Table 3, and the corresponding rDNA sequences are those selected from SEQ ID NOs:1-60, SEQ ID NOs: 2045-2108 and the SEQ ID NOs identified in Table 3. 
     In some embodiments, the microbiome of a ruminant is measured by amplifying polynucleotides collected from gastrointestinal samples, wherein the polynucleotides may be 16S or 18S rDNA fragments, or ITS rDNA fragments of microbial rDNA. In one embodiment, the microbiome is fingerprinted by a method of denaturing gradient gel electrophoresis (DGGE) wherein the amplified rDNA fragments are sorted by where they denature, and form a unique banding pattern in a gel that may be used for comparing the microbiome of the same ruminant over time or the microbiomes of multiple ruminants. In another embodiment, the microbiome is fingerprinted by a method of terminal restriction fragment length polymorphism (T-RFLP), wherein labelled PCR fragments are digested using a restriction enzyme and then sorted by size. In a further embodiment, the data collected from the T-RFLP method is evaluated by nonmetric multidimensional scaling (nMDS) ordination and PERMANOVA statistics identify differences in microbiomes, thus allowing for the identification and measurement of shifts in the microbiome. See also Shanks et al. (2011 . Appl. Environ. Microbiol.  77(9):2992-3001), Petri et al. (2013 . PLOS one.  8(12):e83424), and Menezes et al. (2011 . FEMS Microbiol. Ecol.  78(2):256-265.) 
     In some embodiments, the administration of microbes of the present disclosure results in a modulation or shift of the microbiome which further results in a desired phenotype or improved trait. 
     According to the methods provided herein, a sample is processed to detect the presence of one or more microorganism types in the sample ( FIG.  1 ,  1001   ;  FIG.  2 ,  2001   ). The absolute number of one or more microorganism organism type in the sample is determined ( FIG.  1 ,  1002   ;  FIG.  2 ,  2002   ). The determination of the presence of the one or more organism types and the absolute number of at least one organism type can be conducted in parallel or serially. For example, in the case of a sample comprising a microbial community comprising bacteria (i.e., one microorganism type) and fungi (i.e., a second microorganism type), the user in one embodiment detects the presence of one or both of the organism types in the sample ( FIG.  1 ,  1001   ;  FIG.  2 ,  2001   ). The user, in a further embodiment, determines the absolute number of at least one organism type in the sample—in the case of this example, the number of bacteria, fungi or combination thereof, in the sample ( FIG.  1 ,  1002   ;  FIG.  2 ,  2002   ). 
     In one embodiment, the sample, or a portion thereof is subjected to flow cytometry (FC) analysis to detect the presence and/or number of one or more microorganism types ( FIG.  1 ,  1001 ,  1002   ;  FIG.  2 ,  2001 ,  2002   ). In one flow cytometer embodiment, individual microbial cells pass through an illumination zone, at a rate of at least about 300*s −1 , or at least about 500*s −1 , or at least about 1000*s −1 . However, one of ordinary skill in the art will recognize that this rate can vary depending on the type of instrument is employed. Detectors which are gated electronically measure the magnitude of a pulse representing the extent of light scattered. The magnitudes of these pulses are sorted electronically into “bins” or “channels,” permitting the display of histograms of the number of cells possessing a certain quantitative property (e.g., cell staining property, diameter, cell membrane) versus the channel number. Such analysis allows for the determination of the number of cells in each “bin” which in embodiments described herein is an “microorganism type” bin, e.g., a bacteria, fungi, nematode, protozoan, archaea, algae, dinoflagellate, virus, viroid, etc. 
     In one embodiment, a sample is stained with one or more fluorescent dyes wherein a fluorescent dye is specific to a particular microorganism type, to enable detection via a flow cytometer or some other detection and quantification method that harnesses fluorescence, such as fluorescence microscopy. The method can provide quantification of the number of cells and/or cell volume of a given organism type in a sample. In a further embodiment, as described herein, flow cytometry is harnessed to determine the presence and quantity of a unique first marker and/or unique second marker of the organism type, such as enzyme expression, cell surface protein expression, etc. Two- or three-variable histograms or contour plots of, for example, light scattering versus fluorescence from a cell membrane stain (versus fluorescence from a protein stain or DNA stain) may also be generated, and thus an impression may be gained of the distribution of a variety of properties of interest among the cells in the population as a whole. A number of displays of such multiparameter flow cytometric data are in common use and are amenable for use with the methods described herein. 
     In one embodiment of processing the sample to detect the presence and number of one or more microorganism types, a microscopy assay is employed ( FIG.  1 ,  1001 ,  1002   ). In one embodiment, the microscopy is optical microscopy, where visible light and a system of lenses are used to magnify images of small samples. Digital images can be captured by a charge-couple device (CCD) camera. Other microscopic techniques include, but are not limited to, scanning electron microscopy and transmission electron microscopy. Microorganism types are visualized and quantified according to the aspects provided herein. 
     In another embodiment of in order to detect the presence and number of one or more microorganism types, the sample, or a portion thereof is subjected to fluorescence microscopy. Different fluorescent dyes can be used to directly stain cells in samples and to quantify total cell counts using an epifluorescence microscope as well as flow cytometry, described above. Useful dyes to quantify microorganisms include but are not limited to acridine orange (AO), 4,6-di-amino-2 phenylindole (DAPI) and 5-cyano-2,3 Dytolyl Tetrazolium Chloride (CTC). Viable cells can be estimated by a viability staining method such as the LIVE/DEAD® Bacterial Viability Kit (Bac-Light™) which contains two nucleic acid stains: the green-fluorescent SYTO 9™ dye penetrates all membranes and the red-fluorescent propidium iodide (PI) dye penetrates cells with damaged membranes. Therefore, cells with compromised membranes will stain red, whereas cells with undamaged membranes will stain green. Fluorescent in situ hybridization (FISH) extends epifluorescence microscopy, allowing for the fast detection and enumeration of specific organisms. FISH uses fluorescent labelled oligonucleotides probes (usually 15-25 basepairs) which bind specifically to organism DNA in the sample, allowing the visualization of the cells using an epifluorescence or confocal laser scanning microscope (CLSM). Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) improves upon the FISH method by using oligonucleotide probes labelled with a horse radish peroxidase (HRP) to amplify the intensity of the signal obtained from the microorganisms being studied. FISH can be combined with other techniques to characterize microorganism communities. One combined technique is high affinity peptide nucleic acid (PNA)-FISH, where the probe has an enhanced capability to penetrate through the Extracellular Polymeric Substance (EPS) matrix. Another example is LIVE/DEAD-FISH which combines the cell viability kit with FISH and has been used to assess the efficiency of disinfection in drinking water distribution systems. 
     In another embodiment, the sample, or a portion thereof is subjected to Raman micro-spectroscopy in order to determine the presence of a microorganism type and the absolute number of at least one microorganism type ( FIG.  1 ,  1001 - 1002   ;  FIG.  2 ,  2001 - 2002   ). Raman micro-spectroscopy is a non-destructive and label-free technology capable of detecting and measuring a single cell Raman spectrum (SCRS). A typical SCRS provides an intrinsic biochemical “fingerprint” of a single cell. A SCRS contains rich information of the biomolecules within it, including nucleic acids, proteins, carbohydrates and lipids, which enables characterization of different cell species, physiological changes and cell phenotypes. Raman microscopy examines the scattering of laser light by the chemical bonds of different cell biomarkers. A SCRS is a sum of the spectra of all the biomolecules in one single cell, indicating a cell&#39;s phenotypic profile. Cellular phenotypes, as a consequence of gene expression, usually reflect genotypes. Thus, under identical growth conditions, different microorganism types give distinct SCRS corresponding to differences in their genotypes and can thus be identified by their Raman spectra. 
     In yet another embodiment, the sample, or a portion thereof is subjected to centrifugation in order to determine the presence of a microorganism type and the number of at least one microorganism type ( FIG.  1 ,  1001 - 1002   ;  FIG.  2 ,  2001 - 2002   ). This process sediments a heterogeneous mixture by using the centrifugal force created by a centrifuge. More dense components of the mixture migrate away from the axis of the centrifuge, while less dense components of the mixture migrate towards the axis. Centrifugation can allow fractionation of samples into cytoplasmic, membrane and extracellular portions. It can also be used to determine localization information for biological molecules of interest. Additionally, centrifugation can be used to fractionate total microbial community DNA. Different prokaryotic groups differ in their guanine-plus-cytosine (G+C) content of DNA, so density-gradient centrifugation based on G+C content is a method to differentiate organism types and the number of cells associated with each type. The technique generates a fractionated profile of the entire community DNA and indicates abundance of DNA as a function of G+C content. The total community DNA is physically separated into highly purified fractions, each representing a different G+C content that can be analyzed by additional molecular techniques such as denaturing gradient gel electrophoresis (DGGE)/amplified ribosomal DNA restriction analysis (ARDRA) (see discussion herein) to assess total microbial community diversity and the presence/quantity of one or more microorganism types. 
     In another embodiment, the sample, or a portion thereof is subjected to staining in order to determine the presence of a microorganism type and the number of at least one microorganism type ( FIG.  1 ,  1001 - 1002   ;  FIG.  2 ,  2001 - 2002   ). Stains and dyes can be used to visualize biological tissues, cells or organelles within cells. Staining can be used in conjunction with microscopy, flow cytometry or gel electrophoresis to visualize or mark cells or biological molecules that are unique to different microorganism types. In vivo staining is the process of dyeing living tissues, whereas in vitro staining involves dyeing cells or structures that have been removed from their biological context. Examples of specific staining techniques for use with the methods described herein include, but are not limited to: gram staining to determine gram status of bacteria, endospore staining to identify the presence of endospores, Ziehl-Neelsen staining, haematoxylin and eosin staining to examine thin sections of tissue, papanicolaou staining to examine cell samples from various bodily secretions, periodic acid-Schiff staining of carbohydrates, Masson&#39;s trichome employing a three-color staining protocol to distinguish cells from the surrounding connective tissue, Romanowsky stains (or common variants that include Wright&#39;s stain, Jenner&#39;s stain, May-Grunwald stain, Leishman stain and Giemsa stain) to examine blood or bone marrow samples, silver staining to reveal proteins and DNA, Sudan staining for lipids and Conklin&#39;s staining to detect true endospores. Common biological stains include acridine orange for cell cycle determination; bismarck brown for acid mucins; carmine for glycogen; carmine alum for nuclei; Coomassie blue for proteins; Cresyl violet for the acidic components of the neuronal cytoplasm; Crystal violet for cell walls; DAPI for nuclei; eosin for cytoplasmic material, cell membranes, some extracellular structures and red blood cells; ethidium bromide for DNA; acid fuchsine for collagen, smooth muscle or mitochondria; haematoxylin for nuclei; Hoechst stains for DNA; iodine for starch; malachite green for bacteria in the Gimenez staining technique and for spores; methyl green for chromatin; methylene blue for animal cells; neutral red for Nissl substance; Nile blue for nuclei; Nile red for lipohilic entities; osmium tetroxide for lipids; rhodamine is used in fluorescence microscopy; safranin for nuclei. Stains are also used in transmission electron microscopy to enhance contrast and include phosphotungstic acid, osmium tetroxide, ruthenium tetroxide, ammonium molybdate, cadmium iodide, carbohydrazide, ferric chloride, hexamine, indium trichloride, lanthanum nitrate, lead acetate, lead citrate, lead(II) nitrate, periodic acid, phosphomolybdic acid, potassium ferricyanide, potassium ferrocyanide, ruthenium red, silver nitrate, silver proteinate, sodium chloroaurate, thallium nitrate, thiosemicarbazide, uranyl acetate, uranyl nitrate, and vanadyl sulfate. 
     In another embodiment, the sample, or a portion thereof is subjected to mass spectrometry (MS) in order to determine the presence of a microorganism type and the number of at least one microorganism type ( FIG.  1 ,  1001 - 1002   ;  FIG.  2 ,  2001 - 2002   ). MS, as discussed below, can also be used to detect the presence and expression of one or more unique markers in a sample ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ). MS is used for example, to detect the presence and quantity of protein and/or peptide markers unique to microorganism types and therefore to provide an assessment of the number of the respective microorganism type in the sample. Quantification can be either with stable isotope labelling or label-free. De novo sequencing of peptides can also occur directly from MS/MS spectra or sequence tagging (produce a short tag that can be matched against a database). MS can also reveal post-translational modifications of proteins and identify metabolites. MS can be used in conjunction with chromatographic and other separation techniques (such as gas chromatography, liquid chromatography, capillary electrophoresis, ion mobility) to enhance mass resolution and determination. 
     In another embodiment, the sample, or a portion thereof is subjected to lipid analysis in order to determine the presence of a microorganism type and the number of at least one microorganism type ( FIG.  1 ,  1001 - 1002   ;  FIG.  2 ,  2001 - 2002   ). Fatty acids are present in a relatively constant proportion of the cell biomass, and signature fatty acids exist in microbial cells that can differentiate microorganism types within a community. In one embodiment, fatty acids are extracted by saponification followed by derivatization to give the respective fatty acid methyl esters (FAMEs), which are then analyzed by gas chromatography. The FAME profile in one embodiment is then compared to a reference FAME database to identify the fatty acids and their corresponding microbial signatures by multivariate statistical analyses. 
     In the aspects of the methods provided herein, the number of unique first makers in the sample, or portion thereof (e.g., sample aliquot) is measured, as well as the abundance of each of the unique first markers ( FIG.  1 ,  1003   ;  FIG.  2 ,  2003   ). A unique marker is a marker of a microorganism strain. It should be understood by one of ordinary skill in the art that depending on the unique marker being probed for and measured, the entire sample need not be analyzed. For example, if the unique marker is unique to bacterial strains, then the fungal portion of the sample need not be analyzed. As described above, in some embodiments, measuring the absolute abundance of one or more organism types in a sample comprises separating the sample by organism type, e.g., via flow cytometry. 
     Any marker that is unique to an organism strain can be employed herein. For example, markers can include, but are not limited to, small subunit ribosomal RNA genes (16S/18S rDNA), large subunit ribosomal RNA genes (23S/25S/28S rDNA), intercalary 5.8S gene, cytochrome c oxidase, beta-tubulin, elongation factor, RNA polymerase and internal transcribed spacer (ITS). 
     Ribosomal RNA genes (rDNA), especially the small subunit ribosomal RNA genes, i.e., 18S rRNA genes (18S rDNA) in the case of eukaryotes and 16S rRNA (16S rDNA) in the case of prokaryotes, have been the predominant target for the assessment of organism types and strains in a microbial community. However, the large subunit ribosomal RNA genes, 28S rDNAs, have been also targeted. rDNAs are suitable for taxonomic identification because: (i) they are ubiquitous in all known organisms; (ii) they possess both conserved and variable regions; (iii) there is an exponentially expanding database of their sequences available for comparison. In community analysis of samples, the conserved regions serve as annealing sites for the corresponding universal PCR and/or sequencing primers, whereas the variable regions can be used for phylogenetic differentiation. In addition, the high copy number of rDNA in the cells facilitates detection from environmental samples. 
     The internal transcribed spacer (ITS), located between the 18S rDNA and 28S rDNA, has also been targeted. The ITS is transcribed but spliced away before assembly of the ribosomes The ITS region is composed of two highly variable spacers, ITS1 and ITS2, and the intercalary 5.8S gene. This rDNA operon occurs in multiple copies in genomes. Because the ITS region does not code for ribosome components, it is highly variable. 
     In one embodiment, the unique RNA marker can be an mRNA marker, an siRNA marker or a ribosomal RNA marker. 
     Protein-coding functional genes can also be used herein as a unique first marker. Such markers include but are not limited to: the recombinase A gene family (bacterial RecA, archaea RadA and RadB, eukaryotic Rad51 and Rad57, phage UvsX); RNA polymerase p subunit (RpoB) gene, which is responsible for transcription initiation and elongation, chaperonins. Candidate marker genes have also been identified for bacteria plus archaea: ribosomal protein S2 (rpsB), ribosomal protein S10 (rpsJ), ribosomal protein L1 rplA), translation elongation factor EF-2, translation initiation factor IF-2, metalloendopeptidase, ribosomal protein L22, ffh signal recognition particle protein, ribosomal protein L4/Lle (rplD), ribosomal protein L2 (rplB), ribosomal protein S9 (rpsI), ribosomal protein L3 (rplC), phenylalanyl-tRNA synthetase beta subunit, ribosomal protein L14b/L23e (rplN), ribosomal protein S5, ribosomal protein S19 (rpsS), ribosomal protein S7, ribosomal protein L16/L10E (rplP), ribosomal protein S13 (rpsM), phenylalanyl-tRNA synthetase a subunit, ribosomal protein L15, ribosomal protein L25/L23, ribosomal protein L6 (rplF), ribosomal protein L11 (rplK), ribosomal protein L5 (rplE), ribosomal protein S12/S23, ribosomal protein L29, ribosomal protein S3 (rpsC), ribosomal protein S11 (rpsK), ribosomal protein L10, ribosomal protein S8, tRNA pseudouridine synthase B, ribosomal protein L18P/L5E, ribosomal protein S15P/S13e, Porphobilinogen deaminase, ribosomal protein S17, ribosomal protein L13 (rplM), phosphoribosylformylglycinamidine cyclo-ligase (rpsE), ribonuclease HII and ribosomal protein L24. Other candidate marker genes for bacteria include: transcription elongation protein NusA (nusA), rpoB DNA-directed RNA polymerase subunit beta (rpoB), GTP-binding protein EngA, rpoC DNA-directed RNA polymerase subunit beta′, priA primosome assembly protein, transcription-repair coupling factor, CTP synthase (pyrG), secY preprotein translocase subunit SecY, GTP-binding protein Obg/CgtA, DNA polymerase 1, rpsF 30S ribosomal protein S6, poA DNA-directed RNA polymerase subunit alpha, peptide chain release factor 1, rplI 50S ribosomal protein L9, polyribonucleotide nucleotidyltransferase, tsf elongation factor Ts (tsf), rplQ 50S ribosomal protein L17, tRNA (guanine-N(1)-)-methyltransferase (rplS), rplY probable 50S ribosomal protein L25, DNA repair protein RadA, glucose-inhibited division protein A, ribosome-binding factor A, DNA mismatch repair protein MutL, smpB SsrA-binding protein (smpB), N-acetylglucosaminyl transferase, S-adenosyl-methyltransferase MraW, UDP-N-acetylmuramoylalanine-D-glutamate ligase, rplS 50S ribosomal protein L19, rplT 50S ribosomal protein L20 (rplT), ruvA Holliday junction DNA helicase, ruvB Holliday junction DNA helicase B, serS seryl-tRNA synthetase, rplU 50S ribosomal protein L21, rpsR 30S ribosomal protein S18, DNA mismatch repair protein MutS, rpsT 30S ribosomal protein S20, DNA repair protein RecN, frr ribosome recycling factor (frr), recombination protein RecR, protein of unknown function UPF0054, miaA tRNA isopentenyltransferase, GTP-binding protein YchF, chromosomal replication initiator protein DnaA, dephospho-CoA kinase, 16S rRNA processing protein RimM, ATP-cone domain protein, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, fatty acid/phospholipid synthesis protein PlsX, tRNA(Ile)-lysidine synthetase, dnaG DNA primase (dnaG), ruvC Holliday junction resolvase, rpsP 30S ribosomal protein S16, Recombinase A recA, riboflavin biosynthesis protein RibF, glycyl-tRNA synthetase beta subunit, trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, rpmI 50S ribosomal protein L35, hemE uroporphyrinogen decarboxylase, Rod shape-determining protein, rpmA 50S ribosomal protein L27 (rpmA), peptidyl-tRNA hydrolase, translation initiation factor IF-3 (infC), UDP-N-acetylmuramyl-tripeptide synthetase, rpmF 50S ribosomal protein L32, rplL 50S ribosomal protein L7/L12 (rpIL), leuS leucyl-tRNA synthetase, ligA NAD-dependent DNA ligase, cell division protein FtsA, GTP-binding protein TypA, ATP-dependent Clp protease, ATP-binding subunit CIpX, DNA replication and repair protein RecF and UDP-N-acetylenolpyruvoylglucosamine reductase. 
     Phospholipid fatty acids (PLFAs) may also be used as unique first markers according to the methods described herein. Because PLFAs are rapidly synthesized during microbial growth, are not found in storage molecules and degrade rapidly during cell death, it provides an accurate census of the current living community. All cells contain fatty acids (FAs) that can be extracted and esterified to form fatty acid methyl esters (FAMEs). When the FAMEs are analyzed using gas chromatography-mass spectrometry, the resulting profile constitutes a ‘fingerprint’ of the microorganisms in the sample. The chemical compositions of membranes for organisms in the domains Bacteria and Eukarya are comprised of fatty acids linked to the glycerol by an ester-type bond (phospholipid fatty acids (PLFAs)). In contrast, the membrane lipids of Archaea are composed of long and branched hydrocarbons that are joined to glycerol by an ether-type bond (phospholipid ether lipids (PLELs)). This is one of the most widely used non-genetic criteria to distinguish the three domains. In this context, the phospholipids derived from microbial cell membranes, characterized by different acyl chains, are excellent signature molecules, because such lipid structural diversity can be linked to specific microbial taxa. 
     As provided herein, in order to determine whether an organism strain is active, the level of expression of one or more unique second markers, which can be the same or different as the first marker, is measured ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). Unique first unique markers are described above. The unique second marker is a marker of microorganism activity. For example, in one embodiment, the mRNA or protein expression of any of the first markers described above is considered a unique second marker for the purposes of this invention. 
     In one embodiment, if the level of expression of the second marker is above a threshold level (e.g., a control level) or at a threshold level, the microorganism is considered to be active ( FIG.  1 ,  1005   ;  FIG.  2 ,  2005   ). Activity is determined in one embodiment, if the level of expression of the second marker is altered by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, or at least about 30%, as compared to a threshold level, which in some embodiments, is a control level. 
     Second unique markers are measured, in one embodiment, at the protein, RNA or metabolite level. A unique second marker is the same or different as the first unique marker. 
     As provided above, a number of unique first markers and unique second markers can be detected according to the methods described herein. Moreover, the detection and quantification of a unique first marker is carried out according to methods known to those of ordinary skill in the art ( FIG.  1 ,  1003 - 1004   ,  FIG.  2 ,  2003 - 2004   ). 
     Nucleic acid sequencing (e.g., gDNA, cDNA, rRNA, mRNA) in one embodiment is used to determine absolute abundance of a unique first marker and/or unique second marker. Sequencing platforms include, but are not limited to, Sanger sequencing and high-throughput sequencing methods available from Roche/454 Life Sciences, Illumina/Solexa, Pacific Biosciences, Ion Torrent and Nanopore. The sequencing can be amplicon sequencing of particular DNA or RNA sequences or whole metagenome/transcriptome shotgun sequencing. 
     Traditional Sanger sequencing (Sanger et al. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl. Acad. Sci. USA, 74, pp. 5463-5467, incorporated by reference herein in its entirety) relies on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication and is amenable for use with the methods described herein. 
     In another embodiment, the sample, or a portion thereof is subjected to extraction of nucleic acids, amplification of DNA of interest (such as the rRNA gene) with suitable primers and the construction of clone libraries using sequencing vectors. Selected clones are then sequenced by Sanger sequencing and the nucleotide sequence of the DNA of interest is retrieved, allowing calculation of the number of unique microorganism strains in a sample. 
     454 pyrosequencing from Roche/454 Life Sciences yields long reads and can be harnessed in the methods described herein (Margulies et al. (2005) Nature, 437, pp. 376-380; U.S. Pat. Nos. 6,274,320; 6,258,568; 6,210,891, each of which is herein incorporated in its entirety for all purposes). Nucleic acid to be sequenced (e.g., amplicons or nebulized genomic/metagenomic DNA) have specific adapters affixed on either end by PCR or by ligation. The DNA with adapters is fixed to tiny beads (ideally, one bead will have one DNA fragment) that are suspended in a water-in-oil emulsion. An emulsion PCR step is then performed to make multiple copies of each DNA fragment, resulting in a set of beads in which each bead contains many cloned copies of the same DNA fragment. Each bead is then placed into a well of a fiber-optic chip that also contains enzymes necessary for the sequencing-by-synthesis reactions. The addition of bases (such as A, C, G, or T) trigger pyrophosphate release, which produces flashes of light that are recorded to infer the sequence of the DNA fragments in each well. About 1 million reads per run with reads up to 1,000 bases in length can be achieved. Paired-end sequencing can be done, which produces pairs of reads, each of which begins at one end of a given DNA fragment. A molecular barcode can be created and placed between the adapter sequence and the sequence of interest in multiplex reactions, allowing each sequence to be assigned to a sample bioinformatically. 
     Illumina/Solexa sequencing produces average read lengths of about 25 basepairs (bp) to about 300 bp (Bennett et al. (2005) Pharmacogenomics, 6:373-382; Lange et al. (2014). BMC Genomics 15, p. 63; Fadrosh et al. (2014) Microbiome 2, p. 6; Caporaso et al. (2012) ISME J, 6, p. 1621-1624; Bentley et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456:53-59). This sequencing technology is also sequencing-by-synthesis but employs reversible dye terminators and a flow cell with a field of oligos attached. DNA fragments to be sequenced have specific adapters on either end and are washed over a flow cell filled with specific oligonucleotides that hybridize to the ends of the fragments. Each fragment is then replicated to make a cluster of identical fragments. Reversible dye-terminator nucleotides are then washed over the flow cell and given time to attach. The excess nucleotides are washed away, the flow cell is imaged, and the reversible terminators can be removed so that the process can repeat and nucleotides can continue to be added in subsequent cycles. Paired-end reads that are 300 bases in length each can be achieved. An Illumina platform can produce 4 billion fragments in a paired-end fashion with 125 bases for each read in a single run. Barcodes can also be used for sample multiplexing, but indexing primers are used. 
     The SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) process is a “sequencing-by-ligation” approach, and can be used with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ) (Peckham et al. SOLID™ Sequencing and 2-Base Encoding. San Diego, Calif.: American Society of Human Genetics, 2007; Mitra et al. (2013) Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics, 14(Suppl 5): S16; Mardis (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 9:387-402; each incorporated by reference herein in its entirety). A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare clonal bead populations, where only one species of fragment will be present on the surface of each magnetic bead. The fragments attached to the magnetic beads will have a universal P1 adapter sequence so that the starting sequence of every fragment is both known and identical. Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently labelled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. The SOLiD platform can produce up to 3 billion reads per run with reads that are 75 bases long. Paired-end sequencing is available and can be used herein, but with the second read in the pair being only 35 bases long. Multiplexing of samples is possible through a system akin to the one used by Illumina, with a separate indexing run. 
     The Ion Torrent system, like 454 sequencing, is amenable for use with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ). It uses a plate of microwells containing beads to which DNA fragments are attached. It differs from all of the other systems, however, in the manner in which base incorporation is detected. When a base is added to a growing DNA strand, a proton is released, which slightly alters the surrounding pH. Microdetectors sensitive to pH are associated with the wells on the plate, and they record when these changes occur. The different bases (A, C, G, T) are washed sequentially through the wells, allowing the sequence from each well to be inferred. The Ion Proton platform can produce up to 50 million reads per run that have read lengths of 200 bases. The Personal Genome Machine platform has longer reads at 400 bases. Bidirectional sequencing is available. Multiplexing is possible through the standard in-line molecular barcode sequencing. 
     Pacific Biosciences (PacBio) SMRT sequencing uses a single-molecule, real-time sequencing approach and in one embodiment, is used with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ). The PacBio sequencing system involves no amplification step, setting it apart from the other major next-generation sequencing systems. In one embodiment, the sequencing is performed on a chip containing many zero-mode waveguide (ZMW) detectors. DNA polymerases are attached to the ZMW detectors and phospholinked dye-labeled nucleotide incorporation is imaged in real time as DNA strands are synthesized. The PacBio system yields very long read lengths (averaging around 4,600 bases) and a very high number of reads per run (about 47,000). The typical “paired-end” approach is not used with PacBio, since reads are typically long enough that fragments, through CCS, can be covered multiple times without having to sequence from each end independently. Multiplexing with PacBio does not involve an independent read, but rather follows the standard “in-line” barcoding model. 
     In one embodiment, where the first unique marker is the ITS genomic region, automated ribosomal intergenic spacer analysis (ARISA) is used in one embodiment to determine the number and identity of microorganism strains in a sample ( FIG.  1 ,  1003   ,  FIG.  2 ,  2003   ) (Ranjard et al. (2003). Environmental Microbiology 5, pp. 1111-1120, incorporated by reference in its entirety for all purposes). The ITS region has significant heterogeneity in both length and nucleotide sequence. The use of a fluorescence-labeled forward primer and an automatic DNA sequencer permits high resolution of separation and high throughput. The inclusion of an internal standard in each sample provides accuracy in sizing general fragments. 
     In another embodiment, fragment length polymorphism (RFLP) of PCR-amplified rDNA fragments, otherwise known as amplified ribosomal DNA restriction analysis (ARDRA), is used to characterize unique first markers and the abundance of the same in samples ( FIG.  1 ,  1003   ,  FIG.  2 ,  2003   ) (Massol-Deya et al. (1995). Mol. Microb. Ecol. Manual. 3.3.2, pp. 1-18, incorporated by reference in its entirety for all purposes). rDNA fragments are generated by PCR using general primers, digested with restriction enzymes, electrophoresed in agarose or acrylamide gels, and stained with ethidium bromide or silver nitrate. 
     One fingerprinting technique used in detecting the presence and abundance of a unique first marker is single-stranded-conformation polymorphism (SSCP) (Lee et al. (1996). Appl Environ Microbiol 62, pp. 3112-3120; Scheinert et al. (1996). J. Microbiol. Methods 26, pp. 103-117; Schwieger and Tebbe (1998). Appl. Environ. Microbiol. 64, pp. 4870-4876, each of which is incorporated by reference herein in its entirety). In this technique, DNA fragments such as PCR products obtained with primers specific for the 16S rRNA gene, are denatured and directly electrophoresed on a non-denaturing gel. Separation is based on differences in size and in the folded conformation of single-stranded DNA, which influences the electrophoretic mobility. Reannealing of DNA strands during electrophoresis can be prevented by a number of strategies, including the use of one phosphorylated primer in the PCR followed by specific digestion of the phosphorylated strands with lambda exonuclease and the use of one biotinylated primer to perform magnetic separation of one single strand after denaturation. To assess the identity of the predominant populations in a given consortium, in one embodiment, bands are excised and sequenced, or SSCP-patterns can be hybridized with specific probes. Electrophoretic conditions, such as gel matrix, temperature, and addition of glycerol to the gel, can influence the separation. 
     In addition to sequencing based methods, other methods for quantifying expression (e.g., gene, protein expression) of a second marker are amenable for use with the methods provided herein for determining the level of expression of one or more second markers ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). For example, quantitative RT-PCR, microarray analysis, linear amplification techniques such as nucleic acid sequence based amplification (NASBA) are all amenable for use with the methods described herein, and can be carried out according to methods known to those of ordinary skill in the art. 
     In another embodiment, the sample, or a portion thereof is subjected to a quantitative polymerase chain reaction (PCR) for detecting the presence and abundance of a first marker and/or a second marker ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ). Specific microorganism strains activity is measured by reverse transcription of transcribed ribosomal and/or messenger RNA (rRNA and mRNA) into complementary DNA (cDNA), followed by PCR (RT-PCR). 
     In another embodiment, the sample, or a portion thereof is subjected to PCR-based fingerprinting techniques to detect the presence and abundance of a first marker and/or a second marker ( FIG.  1 ,  1003 - 1004   ;  FIG.  2 ,  2003 - 2004   ). PCR products can be separated by electrophoresis based on the nucleotide composition. Sequence variation among the different DNA molecules influences the melting behaviour, and therefore molecules with different sequences will stop migrating at different positions in the gel. Thus electrophoretic profiles can be defined by the position and the relative intensity of different bands or peaks and can be translated to numerical data for calculation of diversity indices. Bands can also be excised from the gel and subsequently sequenced to reveal the phylogenetic affiliation of the community members. Electrophoresis methods include, but are not limited to: denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-stranded-conformation polymorphism (SSCP), restriction fragment length polymorphism analysis (RFLP) or amplified ribosomal DNA restriction analysis (ARDRA), terminal restriction fragment length polymorphism analysis (T-RFLP), automated ribosomal intergenic spacer analysis (ARISA), randomly amplified polymorphic DNA (RAPD), DNA amplification fingerprinting (DAF) and Bb-PEG electrophoresis. 
     In another embodiment, the sample, or a portion thereof is subjected to a chip-based platform such as microarray or microfluidics to determine the abundance of a unique first marker and/or presence/abundance of a unique second marker ( FIG.  1 ,  1003 - 1004   ,  FIG.  2 , 2003 - 2004   ). The PCR products are amplified from total DNA in the sample and directly hybridized to known molecular probes affixed to microarrays. After the fluorescently labeled PCR amplicons are hybridized to the probes, positive signals are scored by the use of confocal laser scanning microscopy. The microarray technique allows samples to be rapidly evaluated with replication, which is a significant advantage in microbial community analyses. In general, the hybridization signal intensity on microarrays is directly proportional to the abundance of the target organism. The universal high-density 16S microarray (PhyloChip) contains about 30,000 probes of 16SrRNA gene targeted to several cultured microbial species and “candidate divisions”. These probes target all 121 demarcated prokaryotic orders and allow simultaneous detection of 8,741 bacterial and archaeal taxa. Another microarray in use for profiling microbial communities is the Functional Gene Array (FGA). Unlike PhyloChips, FGAs are designed primarily to detect specific metabolic groups of bacteria. Thus, FGA not only reveal the community structure, but they also shed light on the in situ community metabolic potential. FGA contain probes from genes with known biological functions, so they are useful in linking microbial community composition to ecosystem functions. An FGA termed GeoChip contains &gt;24,000 probes from all known metabolic genes involved in various biogeochemical, ecological, and environmental processes such as ammonia oxidation, methane oxidation, and nitrogen fixation. 
     A protein expression assay, in one embodiment, is used with the methods described herein for determining the level of expression of one or more second markers ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). For example, in one embodiment, mass spectrometry or an immunoassay such as an enzyme-linked immunosorbant assay (ELISA) is utilized to quantify the level of expression of one or more unique second markers, wherein the one or more unique second markers is a protein. 
     In one embodiment, the sample, or a portion thereof is subjected to Bromodeoxyuridine (BrdU) incorporation to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). BrdU, a synthetic nucleoside analog of thymidine, can be incorporated into newly synthesized DNA of replicating cells. Antibodies specific for BRdU can then be used for detection of the base analog. Thus BrdU incorporation identifies cells that are actively replicating their DNA, a measure of activity of a microorganism according to one embodiment of the methods described herein. BrdU incorporation can be used in combination with FISH to provide the identity and activity of targeted cells. 
     In one embodiment, the sample, or a portion thereof is subjected to microautoradiography (MAR) combined with FISH to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). MAR-FISH is based on the incorporation of radioactive substrate into cells, detection of the active cells using autoradiography and identification of the cells using FISH. The detection and identification of active cells at single-cell resolution is performed with a microscope. MAR-FISH provides information on total cells, probe targeted cells and the percentage of cells that incorporate a given radiolabelled substance. The method provides an assessment of the in situ function of targeted microorganisms and is an effective approach to study the in vivo physiology of microorganisms. A technique developed for quantification of cell-specific substrate uptake in combination with MAR-FISH is known as quantitative MAR (QMAR). 
     In one embodiment, the sample, or a portion thereof is subjected to stable isotope Raman spectroscopy combined with FISH (Raman-FISH) to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). This technique combines stable isotope probing, Raman spectroscopy and FISH to link metabolic processes with particular organisms. The proportion of stable isotope incorporation by cells affects the light scatter, resulting in measurable peak shifts for labelled cellular components, including protein and mRNA components. Raman spectroscopy can be used to identify whether a cell synthesizes compounds including, but not limited to: oil (such as alkanes), lipids (such as triacylglycerols (TAG)), specific proteins (such as heme proteins, metalloproteins), cytochrome (such as P450, cytochrome c), chlorophyll, chromophores (such as pigments for light harvesting carotenoids and rhodopsins), organic polymers (such as polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB)), hopanoids, steroids, starch, sulfide, sulfate and secondary metabolites (such as vitamin B12). 
     In one embodiment, the sample, or a portion thereof is subjected to DNA/RNA stable isotope probing (SIP) to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). SIP enables determination of the microbial diversity associated with specific metabolic pathways and has been generally applied to study microorganisms involved in the utilization of carbon and nitrogen compounds. The substrate of interest is labelled with stable isotopes (such as  3 C or  15 N) and added to the sample. Only microorganisms able to metabolize the substrate will incorporate it into their cells. Subsequently,  13 C-DNA and  15 N-DNA can be isolated by density gradient centrifugation and used for metagenomic analysis. RNA-based SIP can be a responsive biomarker for use in SIP studies, since RNA itself is a reflection of cellular activity. 
     In one embodiment, the sample, or a portion thereof is subjected to isotope array to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). Isotope arrays allow for functional and phylogenetic screening of active microbial communities in a high-throughput fashion. The technique uses a combination of SIP for monitoring the substrate uptake profiles and microarray technology for determining the taxonomic identities of active microbial communities. Samples are incubated with a  14 C-labeled substrate, which during the course of growth becomes incorporated into microbial biomass. The  14 C-labeled rRNA is separated from unlabeled rRNA and then labeled with fluorochromes. Fluorescent labeled rRNA is hybridized to a phylogenetic microarray followed by scanning for radioactive and fluorescent signals. The technique thus allows simultaneous study of microbial community composition and specific substrate consumption by metabolically active microorganisms of complex microbial communities. 
     In one embodiment, the sample, or a portion thereof is subjected to a metabolomics assay to determine the level of a second unique marker ( FIG.  1 ,  1004   ;  FIG.  2 ,  2004   ). Metabolomics studies the metabolome which represents the collection of all metabolites, the end products of cellular processes, in a biological cell, tissue, organ or organism. This methodology can be used to monitor the presence of microorganisms and/or microbial mediated processes since it allows associating specific metabolite profiles with different microorganisms. Profiles of intracellular and extracellular metabolites associated with microbial activity can be obtained using techniques such as gas chromatography-mass spectrometry (GC-MS). The complex mixture of a metabolomic sample can be separated by such techniques as gas chromatography, high performance liquid chromatography and capillary electrophoresis. Detection of metabolites can be by mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, ion-mobility spectrometry, electrochemical detection (coupled to HPLC) and radiolabel (when combined with thin-layer chromatography). 
     According to the embodiments described herein, the presence and respective number of one or more active microorganism strains in a sample are determined ( FIG.  1 ,  1006   ;  FIG.  2 ,  2006   ). For example, strain identity information obtained from assaying the number and presence of first markers is analyzed to determine how many occurrences of a unique first marker are present, thereby representing a unique microorganism strain (e.g., by counting the number of sequence reads in a sequencing assay). This value can be represented in one embodiment as a percentage of total sequence reads of the first maker to give a percentage of unique microorganism strains of a particular microorganism type. In a further embodiment, this percentage is multiplied by the number of microorganism types (obtained at step  1002  or  2002 , see  FIG.  1    and  FIG.  2   ) to give the absolute abundance of the one or more microorganism strains in a sample and a given volume. 
     The one or more microorganism strains are considered active, as described above, if the level of second unique marker expression at a threshold level, higher than a threshold value, e.g., higher than at least about 5%, at least about 10%, at least about 20% or at least about 30% over a control level. 
     In another aspect of the invention, a method for determining the absolute abundance of one or more microorganism strains is determined in a plurality of samples ( FIG.  2   , see in particular, 2007). For a microorganism strain to be classified as active, it need only be active in one of the samples. The samples can be taken over multiple time points from the same source, or can be from different environmental sources (e.g., different animals). 
     The absolute abundance values over samples are used in one embodiment to relate the one or more active microorganism strains, with an environmental parameter ( FIG.  2 ,  2008   ). In one embodiment, the environmental parameter is the presence of a second active microorganism strain. Relating the one or more active microorganism strains to the environmental parameter, in one embodiment, is carried out by determining the co-occurrence of the strain and parameter by correlation or by network analysis. 
     In one embodiment, determining the co-occurrence of one or more active microorganism strains with an environmental parameter comprises a network and/or cluster analysis method to measure connectivity of strains or a strain with an environmental parameter within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In another embodiment, the network and/or cluster analysis method may be applied to determining the co-occurrence of two or more active microorganism strains in a sample ( FIG.  2 ,  2008   ). In another embodiment, the network analysis comprises nonparametric approaches including mutual information to establish connectivity between variables. In another embodiment, the network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof ( FIG.  2 ,  2009   ). In another embodiment, the cluster analysis method comprises building a connectivity model, subspace model, distribution model, density model, or a centroid model and/or using community detection algorithms such as the Louvain, Bron-Kerbosch, Girvan-Newman, Clauset-Newman-Moore, Pons-Latapy, and Wakita-Tsurumi algorithms ( FIG.  2 ,  2010   ). 
     In one embodiment, the cluster analysis method is a heuristic method based on modularity optimization. In a further embodiment, the cluster analysis method is the Louvain method. &amp;e, e.g., the method described by Blondel et al. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment, Volume 2008, October 2008, incorporated by reference herein in its entirety for all purposes. 
     In another embodiment, the network analysis comprises predictive modeling of network through link mining and prediction, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, the network analysis comprises differential equation based modeling of populations. In another embodiment, the network analysis comprises Lotka-Volterra modeling. 
     In one embodiment, relating the one or more active microorganism strains to an environmental parameter (e.g., determining the co-occurrence) in the sample comprises creating matrices populated with linkages denoting environmental parameter and microorganism strain associations. 
     In one embodiment, the multiple sample data obtained at step  2007  (e.g., over two or more samples which can be collected at two or more time points where each time point corresponds to an individual sample), is compiled. In a further embodiment, the number of cells of each of the one or more microorganism strains in each sample is stored in an association matrix (which can be in some embodiments, an abundance matrix). In one embodiment, the association matrix is used to identify associations between active microorganism strains in a specific time point sample using rule mining approaches weighted with association (e.g., abundance) data. Filters are applied in one embodiment to remove insignificant rules. 
     In one embodiment, the absolute abundance of one or more, or two or more active microorganism strains is related to one or more environmental parameters ( FIG.  2 ,  2008   ), e.g., via co-occurrence determination. Environmental parameters are chosen by the user depending on the sample(s) to be analyzed and are not restricted by the methods described herein. The environmental parameter can be a parameter of the sample itself, e.g., pH, temperature, amount of protein in the sample. Alternatively, the environmental parameter is a parameter that affects a change in the identity of a microbial community (i.e., where the “identity” of a microbial community is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is affected by a change in the identity of a microbial community. For example, an environmental parameter in one embodiment, is the food intake of an animal or the amount of milk (or the protein or fat content of the milk) produced by a lactating ruminant In one embodiment, the environmental parameter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample. 
     In some embodiments described herein, an environmental parameter is referred to as a metadata parameter. 
     Other examples of metadata parameters include but are not limited to genetic information from the host from which the sample was obtained (e.g., DNA mutation information), sample pH, sample temperature, expression of a particular protein or mRNA, nutrient conditions (e.g., level and/or identity of one or more nutrients) of the surrounding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, susceptibility or resistance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of natural products, or a combination thereof. 
     For example, according to one embodiment, microorganism strain number changes are calculated over multiple samples according to the method of  FIG.  2    (i.e., at  2001 - 2007 ). Strain number changes of one or more active strains over time is compiled (e.g., one or more strains that have initially been identified as active according to step  2006 ), and the directionality of change is noted (i.e., negative values denoting decreases, positive values denoting increases). The number of cells over time is represented as a network, with microorganism strains representing nodes and the abundance weighted rules representing edges. Markov chains and random walks are leveraged to determine connectivity between nodes and to define clusters. Clusters in one embodiment are filtered using metadata in order to identify clusters associated with desirable metadata ( FIG.  2 ,  2008   ). 
     In a further embodiment, microorganism strains are ranked according to importance by integrating cell number changes over time and strains present in target clusters, with the highest changes in cell number ranking the highest. 
     Network and/or cluster analysis method in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof. In another embodiment, network analysis comprises predictive modeling of network through link mining and prediction, social network theory, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, network analysis comprises differential equation based modeling of populations. In yet another embodiment, network analysis comprises Lotka-Volterra modeling. 
     Cluster analysis method comprises building a connectivity model, subspace model, distribution model, density model, or a centroid model. 
     Network and cluster based analysis, for example, to carry out method step  2008  of  FIG.  2   , can be carried out via a module. As used herein, a module can be, for example, any assembly, instructions and/or set of operatively-coupled electrical components, and can include, for example, a memory, a processor, electrical traces, optical connectors, software (executing in hardware) and/or the like. 
     Bovine Pathogen Resistance and Clearance 
     In some aspects, the present disclosure is drawn to administering one or more microbial compositions described herein to cows to clear the gastrointestinal tract of pathogenic microbes. In some embodiments, the present disclosure is further drawn to administering microbial compositions described herein to prevent colonization of pathogenic microbes in the gastrointestinal tract. In some embodiments, the administration of microbial compositions described herein further clears pathogens from the integument and the respiratory tract of cows, and/or prevent colonization of pathogens on the integument and in the respiratory tract. In some embodiments, the administration of microbial compositions described herein reduce leaky gut/intestinal permeability, inflammation, and/or incidence of liver disease. 
     In some embodiments, the microbial compositions of the present disclosure comprise one or more microbes that are present in the gastrointestinal tract of cows at a relative abundance of less than 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, or 0.01%. 
     In some embodiments, after administration of microbial compositions of the present disclosure the one or more microbes are present in the gastrointestinal tract of the cow at a relative abundance of at least 0.5%, 1%, 5%, 10)%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. 
     Pathogenic microbes of cows may include the following:  Clostridium perfringens, Clostridium botulinum, Salmonella typi, Salmonella typhimurium, Salmonella enterica, Salmonella pullorum, Erysipelothrix insidiosa, Campylobacter jejuni, Campylobacter coli, Campylobacter lari, Listeria monocytogenes, Streptococcus agalactiae, Streptococcus dysgalactiae, Corynebacterium bovis, Mycoplasma  sp.,  Citrobacter  sp.,  Enterobacter  sp.,  Pseudomonas aeruginosa, Pasteurella  sp.,  Bacillus cereus, Bacillus licheniformis, Streptococcus uberis, Staphylococcus aureus , and pathogenic strains of  Escherichia coli  and  Staphylococcus aureus . In some embodiments, the pathogenic microbes include viral pathogens. In some embodiments, the pathogenic microbes are pathogenic to both cows and humans. In some embodiments, the pathogenic microbes are pathogenic to either cows or humans. 
     In some embodiments, the administration of compositions of the present disclosure to cows modulate the makeup of the gastrointestinal microbiome such that the administered microbes outcompete microbial pathogens present in the gastrointestinal tract. In some embodiments, the administration of compositions of the present disclosure to cows harboring microbial pathogens outcompetes the pathogens and clears cows of the pathogens. In some embodiments, the administration of compositions of the present disclosure results in the stimulation of host immunity, and aid in clearance of the microbial pathogens. In some embodiments, the administration of compositions of the present disclosure introduce microbes that produce bacteriostatic and/or bactericidal components that decrease or clear the cows of the microbial pathogens. (U.S. Pat. No. 8,345,010). 
     In some embodiments, challenging cows with a microbial colonizer or microbial pathogen after administering one or more compositions of the present disclosure prevents the microbial colonizer or microbial pathogen from growing to a relative abundance of greater than 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, or 0.01%. In further embodiments, challenging cows with a microbial colonizer or microbial pathogen after administering one or more compositions of the present disclosure prevents the microbial colonizer or microbial pathogen from colonizing cows. 
     In some embodiments, clearance of the microbial colonizer or microbial pathogen occurs in less than 25 days, less than 24 days, less than 23 days, less than 22 days, less than 21 days, less than 20 days, less than 19 days, less than 18 days, less than 17 days, less than 16 days, less than 15 days, less than 14 days, less than 13 days, less than 12 days, less than 11 days, less than 10 days, less than 9 days, less than 8 days, less than 7 days, less than 6 days, less than 5 days, less than 4 days, less than 3 days, or less than 2 days post administration of the one or more compositions of the present disclosure. 
     In some embodiments, clearance of the microbial colonizer or microbial pathogen occurs within 1-30 days, 1-25 days, 1-20 day, 1-15 days, 1-10 days, 1-5 days, 5-30 days, 5-25 days, 5-20 days, 5-15 days, 5-10 days, 10-30 days, 10-25 days, 10-20 days, 10-15 days, 15-30 days, 15-25 days, 15-20 days, 20-30 days, 20-25 days, or 25-30 days post administration of the one or more compositions of the present disclosure. 
     Improved Traits 
     In some aspects, the present disclosure is drawn to administering microbial compositions described herein to ruminants to improve one or more traits through the modulation of aspects of milk production, milk quantity, milk quality, ruminant digestive chemistry, and efficiency of feed utilization and digestibility. 
     In some embodiments, improving the quantity of milk fat produced by a ruminant is desirable, wherein milk fat includes triglycerides, triacylglycerides, diacylglycerides, monoacylglycerides, phospholipids, cholesterol, glycolipids, and free fatty acids. In further embodiments, free fatty acids include short chain fatty acids (i.e., C4:0, C6:0, and C8:0), medium chain fatty acids (i.e., C10:0, C10:1, C12:0, C14:0, C14:1, and C15:0), and long chain fatty acids (i.e., C16:0, C16:1, C17:0, C17:1, C18:0, C18:1, C18:2, C18:3, and C20:0). In further embodiments, it is desirable to achieve an increase in milk fat efficiency, which is measured by the total weight of milk fat produced, divided by the weight of feed ingested. The weight of milk fat produced is calculated from the measured fat percentage multiplied by the weight of milk produced. 
     In some embodiments, improving the quantity of carbohydrates in milk produced by a ruminant is desirable, wherein carbohydrates include lactose, glucose, galactose, and oligosaccharides. Tao et al. (2009 . J. Dairy Sci.  92:2991-3001) disclose numerous oligosaccharides that may be found in bovine milk. 
     In some embodiments, improving the quantity of proteins in milk produced by a ruminant, wherein proteins include caseins and whey. In some embodiments, proteins of interest are only those proteins produced in milk. In other embodiments, proteins of interest are not required to be produced only in milk. Whey proteins include immunoglobulins, serum albumin, beta-lactoglobulin, and alpha-lactoglobulin. 
     In some embodiments, improving the quantity of vitamins in milk produced by a ruminant is desirable. Vitamins found in milk include the fat-soluble vitamins of A, D, E, and K; as well as the B vitamins found in the aqueous phase of the milk. 
     In some embodiments, improving the quantity of minerals in milk produced by a ruminant is desirable. Minerals found in milk include iron, zinc, copper, cobalt, magnesium, manganese, molybdenum, calcium, phosphorous, potassium, sodium, chlorine, and citric acid. Trace amounts of the following may be found in milk: aluminum, arsenic, boron, bromine, cadmium, chromium, fluorine, iodine, lead, nickel, selenium, silicon, silver, strontium, and vanadium. 
     In some embodiments, improving the milk yield and milk volume produced by a ruminant is desirable. In some embodiments, it is further desirable if the increase in milk yield and volume is not accompanied by simply an increase in solute volume. 
     In some embodiments improving energy-corrected milk (ECM) is desirable. In further embodiments, improving ECM amounts to increasing the calculated ECM output. In some embodiments, the ECM is calculated as follows: ECM=(0.327×milk pounds)+(12.95×fat pounds)+(7.2×protein pounds). 
     In some embodiments, improving the efficiency and digestibility of animal feed is desirable. In some embodiments, increasing the degradation of lignocellulosic components from animal feed is desirable. Lignocellulosic components include lignin, cellulose, and hemicellulose. 
     In some embodiments, increasing the concentration of fatty acids in the rumen of ruminants is desirable. Fatty acids include acetic acid, propionic acid, and butyric acid. In some embodiments, maintaining the pH balance in the rumen to prevent lysis of beneficial microbial consortia is desirable. In some embodiments, maintaining the pH balance in the rumen to prevent a reduction of beneficial microbial consortia is desirable. 
     In some embodiments, decreasing the amount of methane and manure produced by ruminants is desirable. 
     In some embodiments, improving the dry matter intake is desirable. In some embodiments, improving the efficiency of nitrogen utilization of the feed and dry matter ingested by ruminants is desirable. 
     In some embodiments, the improved traits of the present disclosure are the result of the administration of the presently described microbial compositions. It is thought that the microbial compositions modulate the microbiome of the ruminants such that the biochemistry of the rumen is changed in such a way that the ruminal liquid and solid substratum are more efficiently and more completely degraded into subcomponents and metabolites than the rumens of ruminants not having been administered microbial compositions of the present disclosure. 
     In some embodiments, the increase in efficiency and the increase of degradation of the ruminal substratum result in an increase in improved traits of the present disclosure. 
     Mode of Action: Digestibility Improvement in Ruminants 
     The rumen is a specialized stomach dedicated to the digestion of feed components in ruminants. A diverse microbial population inhabits the rumen, where their primary function revolves around converting the fibrous and non-fibrous carbohydrate components into useable sources of energy and protein ( FIG.  16   ). Cellulose, in particular, forms up to 40% of plant biomass and is considered indigestible by mammals. It also is tightly associated with other structural carbohydrates, including hemicellulose, pectin, and lignin. The cellulolytic microbes in the rumen leverage extensive enzymatic activity in order break these molecules down into simple sugars and volatile fatty acids. This enzymatic activity is critical to the extraction of energy from feed, and more efficient degradation ultimately provides more energy to the animal. The soluble sugars found in the non-fibrous portion of the feed are also fermented into gases and volatile fatty acids such as butyrate, propionate, and acetate. Volatile fatty acids arising from the digestion of both the fibrous and non-fibrous components of feed are ultimately the main source of energy of the ruminant. 
     Individual fatty acids have been tested in ruminants in order to identify their impacts on varying aspects of production. 
     Acetate: Structural carbohydrates produce large amounts of acetate when degraded. An infusion of acetate directly into the rumen was shown to improve the yield of milk, as well as the amount of milk fat produced. Acetate represents at least 90% of acids in the peripheral blood—it is possible that acetate can be directly utilized by mammary tissue as a source of energy. See Rook and Balch. 1961. Brit. J. Nutr. 15:361-369. 
     Propionate: Propionate has been shown to increase milk protein production, but decrease milk yield. See Rook and Balch. 1961. Brit. J. Nutr. 15:361-369. 
     Butyrate: An infusion of butyrate directly into the rumen of dairy cows increases milk fat production without changing milk yield. See Huhtanen et al. 1993. J. Dairy Sci. 76:1114-1124. 
     Network Analysis 
     A network and/or cluster analysis method, in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof. In another embodiment, network analysis comprises predictive modeling of network through link mining and prediction, social network theory, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, network analysis comprises mutual information, maximal information coefficient (MIC) calculations, or other nonparametric methods between variables to establish connectivity. In another embodiment, network analysis comprises differential equation based modeling of populations. In yet another embodiment, network analysis comprises Lotka-Volterra modeling. 
     The environmental parameter can be a parameter of the sample itself, e.g., pH, temperature, amount of protein in the sample. Alternatively, the environmental parameter is a parameter that affects a change in the identity of a microbial community (i.e., where the “identity” of a microbial community is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is affected by a change in the identity of a microbial community. For example, an environmental parameter in one embodiment, is the food intake of an animal or the amount of milk (or the protein or fat content of the milk) produced by a lactating ruminant In one embodiment, the environmental parameter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample. In some embodiments, an environmental parameter is referred to as a metadata parameter. 
     Other examples of metadata parameters include but are not limited to genetic information from the host from which the sample was obtained (e.g., DNA mutation information), sample pH, sample temperature, expression of a particular protein or mRNA, nutrient conditions (e.g., level and/or identity of one or more nutrients) of the surrounding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, susceptibility or resistance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of natural products, or a combination thereof. 
     Bovine Somatotropin/Bovine Growth Hormone 
     Bovine somatotropin (bST), also known as bovine growth hormone, is an animal drug approved by FDA to increase milk production in dairy cows. This drug is based on the somatotropin naturally produced in cattle. Somatotropin is a protein hormone produced in the pituitary gland of animals, including humans, and is essential for normal growth, development, and health maintenance. 
     FDA approved a bST product in 1993 with the brand name “Posilac™” (sometribove zinc suspension). Posilac™ is approved for over-the-counter use in dairy cows starting at around 2 months after the cow has a calf until the end of the lactation period. During this time, cows are injected with Posilac™ subcutaneously (under the skin) every 14 days. A cow&#39;s typical lactation period is approximately 10 months long, starting right after she has a calf Thus, treated dairy cows are typically given Posilac™ for about 8 months of the year. 
     Dairy cows treated with Posilac™ exhibit a milk yield of approximately 9.9 pounds and energy corrected milk of approximately 8.72 pounds post-peak (greater than 90 days in milk) compared to control. As shown below in Example 4, dairy cows supplemented with Treatment 2 resulted in improved milk yield and milk compositional characteristics compared to control animals in weeks 6 to 24 of the trial. The trial is still ongoing and it is expected that cows supplemented with Treatment 2 will reach milk yields similar to Posilac™ by the end of the trial. Therefore, microbial supplementation in dairy cows is the same or better than the industry standard Posilac™. 
     In some embodiments, the present disclosure provides microbial compositions that perform the same or better than bovine growth hormone (e.g., Posilac™) in dairy cows. In some embodiments, the composition comprises one or more microorganisms from Table 1 and/or Table 3. In some embodiments, the composition comprises: a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO; 28; a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 32; a  Ruminococcus  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2108; and/or a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97% sequence identity to SEQ ID NO: 2067. In some embodiments, the composition comprises: a  Clostridium  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 28; a  Pichia  sp. comprising an ITS nucleic acid sequence of SEQ ID NO: 32; a  Ruminococcus  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and/or a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence of SEQ ID NO: 2067. 
     EXAMPLES 
     Example 1. Identification and Characterization of  Ruminococcus bovis    
     Applicant has identified a novel  Ruminococcus  sp. referred to herein as  Ruminococcus bovis . This microorganism was recovered from the rumen content of a healthy, Holstein dairy cow and was taxonomically predicted to be  Ruminococcus bromii  based on sequencing of the 16S rRNA gene. However, upon further characterization, Applicant discovered that this was a novel species and named the species  Ruminococcus bovis.    
     Applicant originally experienced difficulty obtaining a pure culture of the novel  Ruminococcus  sp. and therefore, it was deposited at the Bigelow depository as an enriched culture. The Bigelow deposit accession numbers and 16S rRNA sequence of this novel  Ruminococcus  sp. was first described in PCT Application No. PCT/US2017/012573 (incorporated by reference herein) and was identified in the application as SEQ ID NO: 1. 
     Applicant was eventually able to isolate  Ruminococcus bovis  into pure culture and characterized the isolate as described in Example 2 below. Isolated  Ruminococcus bovis  comprises a 16S rRNA sequence that differs by two nucleotides to the original  Ruminococcus bovis  of SEQ ID NO: 1. The isolate was deposited at the USDA, ATCC, and NCTC depositories. Isolated  Ruminococcus bovis  is described for the first time in the present application and is identified as SEQ ID NO: 2108. 
     Isolated  Ruminococcus bovis  (SEQ ID NO: 2108) underwent a series of preservation challenges and recoveries in order to improve yield, which is further described in Example 3 below. The  Ruminococcus bovis  strain recovered from this serial preservation challenge had a number of mutations in whole genome compared to the  Ruminococcus bovis  strain before the serial preservation challenge (see, Table 18 in Example 3). This novel  Ruminococcus bovis  strain exhibited a dramatic increase in survival compared to the  Ruminococcus bovis  strain before the serial preservation challenge (see, Table 17 in Example 3). 
     Therefore, the present application describes for the first time novel  Ruminococcus bovis  strains with unique characteristics. 
     Example 2 . Ruminococcus bovis  sp. Nov., a Novel Species of Amylolytic  Ruminococcus  Isolated from the Rumen of a Dairy Cow 
     This study presents JE7A12 T , an isolate from the ruminal content of a dairy cow. The genus  Ruminococcus  was first described by A. Kaars Sijpesteijn with  Ruminococcus flavefaciens  as the type strain (Sijpesteijn A K, Kaars Sijpesteijn A. Vol. 15, Antonie van Leeuwenhoek. 1949. p. 49-52; Sijpesteijn A K. J Gen Microbiol. 1951 November; 5(5 Suppl.):869-79). Previously,  Ruminococcus  have been isolated from the rumen and gastrointestinal tract of a wide variety of animals including humans (Ezaki T.  Ruminococcus  [Internet]. Bergey&#39;s Manual of Systematics of Archaea and Bacteria. 2015. p. 1-5). The genus is polyphyletic and divided into two groups.  Ruminococcus  group 1 includes the type strain  Ruminococcus flavefaciens, Ruminococcus albus, Ruminococcus bromii , and  Ruminococcus callidus. Ruminococcus  group 2 species have recently undergone taxonomic re-classification with many species being reassigned to different genera. It is now believed that true members of the genus  Ruminococcus  are the species found in group 1 (Liu C et al. Vol. 58, International Journal of Systematic and Evolutionary Microbiology. 2008. p. 1896-902). The following description pertains to the isolation and the classification of a novel group 1 amylolytic species, strain JE7A12 T , of the genus  Ruminococcus.    
     Isolation and Phenotypic Characterization 
     JE7A12 T  was recovered from the rumen content of a healthy, Holstein dairy cow obtained from Dairy Experts (Tulare, Calif., USA). After 48 hours of anaerobic incubation at 37-39° C., JE7A12 T  displays off-white-colored colonies on supplemented Bacto Tryptic Soy Broth (TSB-FAC) (BD, San Jose, Calif., USA). Gram-staining was performed as described by Jones et al. (Jones D. Manual of Methods for General Bacteriology [Internet]. Vol. 34, Journal of Clinical Pathology. 1981. p. 1069-1069). Cell morphology was observed under Accu-Scope EXC-350 light microscope at 1000× magnification using cells grown for 48 h at 37° C. on TSB+FAC. Consistent with previous descriptions of the genus, JE7A12 T  is a strictly anaerobic coccoid, commonly found in pairs and chains (Ezaki T.  Ruminococcus  [Internet]. Bergey&#39;s Manual of Systematics of Archaea and Bacteria. 2015. p. 1-5). Although isolated from rumen content, JE7A12 T  does not require rumen fluid for growth. 
     Carbohydrate fermentation of JE7A12 T  was qualitatively measured using the API 50CH carbon panel (BioMérieux, Marcy-l&#39;Étoile, France). JE7A12 T  cells were grown to late exponential phase and recovered by centrifugation at 3,000×g for 10 minutes. Cells were resuspended and 0.017% (wt/vol) bromocresol purple added as a pH indicator for acidification of carbohydrates (Avgustin G et al. Int J Syst Bacteriol. 1997 April; 47(2):284-8.). Closely related  Ruminococcus  strains derived from the bovine rumen are unable to ferment glucose, fructose, galactose while their human derived counterparts are able to utilize these carbon sources (Mukhopadhya I et al. Environ Microbiol. 2018 January; 20(1):324-36). Therefore, fermentation of glucose, fructose, and galactose in combination with genomic data could act to differentiate JE7A12 T  from closely related, rumenally derived,  Ruminococcus.    
     Metabolite production was measured using a Waters Acquity UPLC Q System with RI detector. The column used was a Phenomenex 00H-0138-KO Rezex ROA Organic Acid H+(8%) operated at 60° C. The mobile phase was 0.00325 N H2S04 at 0.5 mL/min. Pure standards were used for calibration at varying concentrations. JE7A12 T  produces acetate as a major fermentation product as well as ethanol and glycerol as minor products. Major fermentation product comparison between JE7A12 T  and other species in the genus  Ruminococcus  are shown in Table 14 below. 
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Major Fermentation Products of JE7A12 T  and 
               
               
                 other members of the genus  Ruminococcus   
               
            
           
           
               
               
               
            
               
                   
                 Organism 
                 Product 
               
               
                   
                   
               
               
                   
                 JE7A12 T   
                 Acetate 
               
               
                   
                 
                   R. albus 
                 
                 Acetate, Formate 
               
               
                   
                 
                   R. bromii 
                 
                 Acetate 
               
               
                   
                 
                   R. callidus 
                 
                 Succinate 
               
               
                   
                 
                   R. champanellensis 
                 
                 Acetate, Succinate 
               
               
                   
                 
                   R. flavefaciens 
                 
                 Acetate, Formate, Succinate 
               
               
                   
                 
                   R. gauvreauii 
                 
                 Acetate 
               
               
                   
                 
                   R. gnavus 
                 
                 Acetate, Formate 
               
               
                   
                 
                   R. lactaris 
                 
                 Acetate, Formate 
               
               
                   
                 
                   R. torques 
                 
                 Lactate 
               
               
                   
                   
               
            
           
         
       
     
     The data shown in Table A for  R. albus, R. bromii, R. flavefaciens, R. callidus, R. gnavus, R. lactaris, R. torques  as represented in paper from Ezaki (Ezaki T.  Ruminococcus  [Internet]. Bergey&#39;s Manual of Systematics of Archaea and Bacteria. 2015. p. 1-5).  R. champanellensis  data as represented by Chassard et al. (Chassard C et al.  Ruminococcus champanellensis  sp. nov., a cellulose-degrading bacterium from human gut microbiota [Internet], Vol. 62, International Journal of Systematic and Evolutionary Microbiology. 2012. p. 138-43).  R. gauvreauii  data as represented by Domingo et al. (Domingo M-C et al.  Ruminococcus gauvreauii  sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen [Internet]. Vol. 58, International Journal of Systematic and Evolutionary Microbiology. 2008. p. 1393-7). 
     Genomic Characterization 
     The 16S rRNA gene was amplified from JE7A12 T  using 27F and 534R primers (Lane et al., 1991; Muyzer et al., 1992) and paired-end sequenced (2×300 bp) on an Illumina Miseq. The resulting sequence was quality trimmed and compared to the NCBI database. The closest neighbors to JE7A12 T  based on sequence similarity were  Ruminococcus bromii  (90°),  Butyricicoccus pullicaecorum  (89%), and  Colidextribacter massiliensis  (89%). Whole genome sequence of JE7A12 T  was generated using hybrid methods as described by Jain et al. Nat Biotechnol. 2018 April; 36(4):338-45.). Whole genome size and GC content were compared between JE7A12 T  and phylogenetically close neighbors as well as other members of the genus  Ruminococcus . The results are shown in Table 15 below. GC content of JE7A12 T  should act as a differentiating characteristic for the species as it is lower than the any other member in the genus. 
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Comparison of genome size and GC content between 
               
               
                 JE7A12 T  and members of the genus  Ruminococcus   
               
               
                 as well as phylogenetically close organisms 
               
            
           
           
               
               
               
            
               
                   
                 Genome 
                 GC 
               
               
                   
                 Size 
                 Content 
               
               
                 Genus species (GenBank Accession #) 
                 (Mbp) 
                 (%) 
               
               
                   
               
            
           
           
               
               
               
            
               
                   Ruminococcus bovis  JE7A12 T   
                 2.44 
                 34.6 
               
               
                   Anaeromassilibacillus  sp. An172 (GCA_002160515) 
                 2.81 
                 49.1 
               
               
                   Clostridium  sp. (GCA_000431855) 
                 2.25 
                 35.9 
               
               
                   Clostridium  sp. (GCA_000435335) 
                 2.11 
                 35.9 
               
               
                   Eubacterium  sp. (GCA_000436775 ) 
                 1.97 
                 38 
               
               
                   Eubacterium  sp. (GCA_000437975 ) 
                 1.9 
                 38 
               
               
                 Ruminococcaceae bacterium P7 (GCA_900100595) 
                 3.06 
                 50.3 
               
               
                   Ruminococcus albus  DSM 20455 (GCA_000179635) 
                 4.48 
                 44.5 
               
               
                   Ruminococcus bromii  YE282 (GCA_900101355) 
                 2.54 
                 40.7 
               
               
                   Ruminococcus callidus  ATCC 27760 
                 3.01 
                 49 
               
               
                 (GCA_000468015) 
               
               
                   Ruminococcus champanellensis  DSM 18848 
                 2.57 
                 53.33 
               
               
                 (GCA_000210095) 
               
               
                   Ruminococcus flavefaciens  ATCC 19208 
                 3.59 
                 45.9 
               
               
                 (GCA_000518765) 
               
               
                   Ruminococcus gauvreauii  DSM 19829 
                 4.09 
                 47.6 
               
               
                 (GCA_000425525) 
               
               
                   Ruminococcus gnavus  AGR2154 (GCA_000526735) 
                 3.72 
                 42.5 
               
               
                   Ruminococcus lactaris  ATCC 29176 
                 2.73 
                 42.7 
               
               
                 (GCA_000155205) 
               
               
                   Ruminococcus  sp. (GCA_000433495) 
                 2.09 
                 44.2 
               
               
                   Ruminococcus torques  ATCC 27756 
                 2.74 
                 42 
               
               
                 (GCA_000153925) 
               
               
                   
               
            
           
         
       
     
     To further investigate taxonomic identity whole genome average nucleotide identity (AM) was compared between JE7A12 T  and closely related whole genomes (Richter M K Rosselló-Móra R Proc Natl Acad Sci USA. 2009 Nov. 10; 106(45):19126-31.). Genomes used for comparison were selected based on phylogenetic proximity. Additionally, all current species of  Ruminococcus  were included in the ANI analysis. The results are shown in  FIG.  4   . Of the genomes with cultured representatives, there were no matches at the suggested 95% cutoff for defining a species (Yoon et al. Antonie Van Leeuwenhoek. 2017 October; 110(10):1281-6; and Goris J et al. Int J Syst Evol Microbiol. 2007 Jan. 1; 57(1):81-91). 
     The best match from a cultured genome with standing nomenclature was  Ruminococcus bromii . Though the two strains are still genetically distant, with 88% sequence similarity between the two, but with only 2.1% coverage of the genome. The closest overall match is an uncultured  Eubacterium  with no standing nomenclature. Whole genome nucleotide dissimilarity should be used as a strong differentiator of JE7A12 T  from the other taxa in the genus. 
     Phylogeny 
     16S based phylogeny was computed by the neighbor-joining method using MEGA X (Kumar S et al. Mol Biol Evol. 2018 Jun. 1; 35(6):1547-9.). JE7A12 T  was placed in a dendrogram of all  Ruminococcus  isolates available in the RDP database (Cole J R et al. Nucleic Acids Res. 2014 January; 4:D633-42.). The resulting dendrogram is presented in  FIG.  5   . Whole Genome phylogeny was inferred by PhyloPhlan (Segata N et al. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013; 4:2304) using JE7A12 T  whole genome amino acid sequence. JE7A12 T  was placed in a dendrogram with whole genome sequences from the NCBI database. The resulting dendrogram is presented in  FIG.  6   . 
     Description of  Ruminococcus bovis  sp. nov. 
       Ruminococcus bovis  (bo.vis. bos,  bovis  L. m. gen. n. of the cow) 
       Ruminococcus bovis  is an obligate anaerobe, catalase negative, and oxidase negative bacterium. It gram stains gram-variable ( FIG.  7   ) and forms chains of small cocci when cultured in liquid medium ( FIG.  8   ). When cultured on TSB+FAC solid medium, it forms small, slightly opaque, off-white, circular colonies with even margins. The genome GC content is 34.6%. API 50CH carbon panel results are shown in Table 16 below. The major fermentation product is acetate, ethanol and glycerol are minor fermentation products. No lactate, butyrate, butanol, propionate, succinate, or pyruvate is produced. 
     The type strain (PTA-125917, NRRL B-67764) originally collected as JE7A12, was isolated from rumen content of a healthy, Holstein cow from Dairy Experts (Tulare, Calif., USA). 
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 JE7A12 T  API 50CH carbon panel 
               
            
           
           
               
               
               
               
               
               
            
               
                 Component 
                 JE7A12 T   
                 Component 
                 JE7A12 T   
                 Component 
                 JE7A12 T   
               
               
                   
               
               
                 Glycerol 
                 No Growth 
                 D-Adonitol 
                 No Growth 
                 L-Rhamnose 
                 No Growth 
               
               
                 Erythritol 
                 No Growth 
                 Methyl-BD- 
                 No Growth 
                 Dulcitol 
                 No Growth 
               
               
                   
                   
                 xylopyranoside 
               
               
                 D-Arabinose 
                 No Growth 
                 D-Galactose 
                 Growth 
                 Inositol 
                 No Growth 
               
               
                 L-Arabinose 
                 No Growth 
                 D-Glucose 
                 Growth 
                 D-Mannitol 
                 No Growth 
               
               
                 D-Ribose 
                 No Growth 
                 D-Fructose 
                 Growth 
                 D-Sorbitol 
                 No Growth 
               
               
                 D-xylose 
                 No Growth 
                 D-Mannose 
                 No Growth 
                 Methyl-aD- 
                 No Growth 
               
               
                   
                   
                   
                   
                 Mannopyranoside 
               
               
                 Amygdalin 
                 No Growth 
                 L-Sorbose 
                 No Growth 
                 Methyl-aD- 
                 No Growth 
               
               
                   
                   
                   
                   
                 Glucopyranoside 
               
               
                 Arbutin 
                 No Growth 
                 D-Saccharose 
                 No Growth 
                 N- 
                 No Growth 
               
               
                   
                   
                   
                   
                 AcetylGlucosamine 
               
               
                 Esculin/Ferric 
                 No Growth 
                 D-Trehalose 
                 No Growth 
                 D-Lyxose 
                 No Growth 
               
               
                 Citrate 
               
               
                 Salicin 
                 No Growth 
                 Inulin 
                 No Growth 
                 D-Tagatose 
                 No Growth 
               
               
                 D-Cellobiose 
                 No Growth 
                 D-Melezitose 
                 No Growth 
                 D-Fucose 
                 No Growth 
               
               
                 D-Maltose 
                 Growth 
                 D-Raffinose 
                 No Growth 
                 L-Fucose 
                 No Growth 
               
               
                 D-Lactose 
                 No Growth 
                 Starch 
                 Growth 
                 D-Arabitol 
                 No Growth 
               
               
                   
                   
                 Glycogen 
                 Growth 
                 L-Arabitol 
                 No Growth 
               
               
                 Potassium 5- 
                 No Growth 
                 Xylitol 
                 No Growth 
                 D-Turanose 
                 Growth 
               
               
                 KetoGluconate 
               
               
                 Potassium 
                 No Growth 
                 Gentiobiose 
                 No Growth 
                 D-Melibiose 
                 No Growth 
               
               
                 Gluconate 
               
               
                 Potassium 2- 
                 No Growth 
               
               
                 KetoGluconate 
               
               
                   
               
            
           
         
       
     
     CONCLUSION 
     This study presents JE7A12 T , an isolate from the ruminal content of a dairy cow. Phenotypic and genotypic traits of the isolate were explored. JE7A12 T  was found to be a strictly anaerobic, catalase negative, oxidase negative, coccoid bacterium that grows in chains. API 50 CH carbon source assay showed growth on D-glucose, D-fructose, D-galactose, glycogen, and starch. HPLC showed acetate as the major fermentation product as result of carbohydrate fermentation. Phylogenetic analysis of JE7A12 T  based on 16S rRNA nucleotide sequence and whole genome amino acid sequence show a divergent lineage from the closest neighbors in the genus  Ruminococcus.  16S sequence comparison, whole genome average nucleotide identity (ANI), and GC content data suggest that JE7A12 T  represents a novel species for which we propose the name  Ruminococcus bovis  sp nov. with JE7A12 T  as the type strain. 
     Example 3. Serial Preservation Challenges of  Ruminococcus bovis    
       R. bovis  (Ascusb_5) was subjected to a series of preservation challenges and recoveries in order to improve yield through a serial preservation process. 
     Methods 
       R. bovis  was subjected to three rounds of Preservation by Vaporization (PBV) challenges. Briefly, an aliquot from a glycerol stock was streaked onto a growth plate. After an appropriate incubation time, a single colony was selected and used to inoculate a seed tube of Tryptic Soy Broth. The seed tube inoculate was cultured to allow bacterial expansion and the expanded bacterial culture was then used to inoculate the main fermentation culture. The bacterial cells were cultured in the main fermentation culture until mid-stationary phase. Loading sugars are included, if necessary. After 40 hours, cells were harvested and combined with preservation solutions to produce a preservation mixture. 
     For preservation, 100 μL of each preservation mixture was dispensed into a 2 mL serum vial, which was then sealed with a lyophilization cap and placed the vials in an aluminum lyophilizer block. The vials were frozen at −80° C. for at least one hour and then the vials were transferred to the lyophilizer in the aluminum block. Lypholization caps were changed to the open position and the following lyophilization program was executed: 
     (a) Freeze at −17° C. at atmospheric pressure for 30 minutes 
     (b) Freeze at −17° C. at 1000 mTorr for 15 minutes 
     (c) Freeze at −17° C. at 300 mTorr for 15 minutes 
     (d) Incubate at 30° C. at 300 mTorr for 24 hours 
     (e) Incubate at 40° C. at 300 mTorr for 24 hours 
     (f) Hold at 25° C. 
     All vials are then removed from the lyophilizer and rehydrated in the following manner: 
     (a) 1 mL of sterile PBS is added to each vial (effectively a 10× dilution to the initial preservation mixture) and reconstituted by slowly pipetting up and down. This mixture was then diluted 6 additional logs (for a total dilution of E-07) and a 5 μL aliquot from each vial was spot plated for CFU determination. 
     (b) A separate aliquot of the reconstituted PBV product was streaked onto a plate as the starting plate (a “rescue” plate) for re-inoculation in subsequent. 
     A second and third round of PBV is then performed according to the protocol described above, using the “rescue” plates as the initial source of bacteria for inoculation of the seed tube. 
     Results 
     The results from Round 1-3 for Ascusb_5 are presented in Table 17 below. As shown, there was a dramatic increase in the Survival % of Colony Forming Units (CFU)/mL for Ascusb_5 of SEQ ID NO: 2108 from Round 1 (RCB) to Round 2 (Rescue 1). 
     
       
         
           
               
             
               
                 TABLE 17 
               
             
            
               
                   
               
               
                 CFU Titer and PBV survival of  R. bovis   
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 Titer 
                 PBV 
               
               
                 Round 
                 Microbe 
                 Inoculant source 
                 (CFU/mL) 
                 Survival (%) 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 1 
                 Ascusb_5 
                 RCB 
                 7.70E+08 
                 0.0013%    
               
               
                 2 
                 Ascusb_5 
                 Rescue plate Round 1 
                 6.70E+08 
                 30% 
               
               
                 3 
                 Ascusb_5 
                 Rescue plate Round 2 
                 4.93E+08 
                 20% 
               
               
                   
               
            
           
         
       
     
     The genomes of the RCB isolate and the Round 3 isolate of Ascusb_5 were sequenced to determine any genomic changes as a result of the serial passage. Briefly, DNA was isolated from  R. bovis  using a Qiagen Powersoil Pro kit. Short read sequencing libraries were prepared from the isolated DNA using the Nextera XT kit (Illumina, San Diego, Calif.) by the manufacturer&#39;s recommended protocol. Libraries were sequenced on an Illumina MiSeq (1×300 bp). Reads were mapped to the reference genome using bowtie2 (Langmead B, Salzberg S. (2012) Fast gapped-read alignment with Bowtie 2 . Nature Methods.  9: 357-359) and analyzed for mutations using breseq (Deatherage D E, Barrick J E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.  Methods Mol. Biol.  1151: 165-188). 
     A summary of the mutations is presented in Table 18 below. Mutations 7 and 8 are silent mutations and unlikely to result in significant effects. Mutations 2, 3, 5, and 6 affect either integrases or transposases and are unlikely to affect preservation tolerance. Mutation 1 is likely the key mutation resulting in the improvement of preservation tolerance in Ascusb_5. It occurs 4 bp upstream of the Galactose operon repressor, GalR-LacI. This key protein represses transcription of a host of genes related to carbohydrate uptake and metabolism. As cryoprotectant uptake, often in the form of non-reducing sugars, is a key step in preservation tolerance, a change in the regulation of sugar uptake could result in a dramatic improvement in preservation tolerance. The phosphomannomutase could provide another key mutation, perhaps disrupting the metabolism of preservation sugars and enabling intracellular accumulation. The Ascusb_5 microbe from round 3 did not exhibit any mutations in its 16S nucleic acid sequence (SEQ ID NO: 2108). 
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                   R. bovis  mutation summary 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Mutation 
                   
                   
                   
               
               
                   
                 position 
                 Change 
                 Description 
                 Protein Description 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                 1 
                 676,590 
                 G→T 
                 intergenic (−223/−4) 
                 Melibiose carrier protein, Na+, 
               
               
                   
                   
                   
                   
                 melibiose symporter/Galactose 
               
               
                   
                   
                   
                   
                 operon repressor, GalR-LacI 
               
               
                   
                   
                   
                   
                 family of transcriptional regulators 
               
               
                 2 
                 759,729 
                 2 bp→TA 
                 coding (306-307/633 nt) 
                 hypothetical protein (integrase) 
               
               
                 3 
                 759,735 
                 T→G 
                 K101Q ( A AG→ C AG) 
                 hypothetical protein (integrase) 
               
               
                 4 
                 1,403,355 
                 (A) 5→4   
                 coding (23/1503 nt) 
                 Phosphomannomutase 
               
               
                 5 
                 1,450,594 
                 3 bp→TTC 
                 coding (55-57/300 nt) 
                 hypothetical protein (transposase) 
               
               
                 6 
                 1,546,754 
                 +T 
                 coding (84/126 nt) 
                 hypothetical protein (transposase) 
               
               
                 7 
                 1,667,526 
                 C→T 
                 Y399Y (TA C →TA T ) 
                 hypothetical protein 
               
               
                 8 
                 2,124,083 
                 C→A 
                 G414G (GG C →GG A ) 
                 Excinuclease ABC subunit B 
               
               
                 9 
                 2,437,094 
                 +AC 
                 coding (233/240 nt) 
                 hypothetical protein 
               
               
                   
                   
                   
                   
                 (stage II sporulation protein) 
               
               
                   
               
            
           
         
       
     
     Example 4. Microbial Supplementation in Dairy Cows 
     This study examines the effect of microbial supplementation on feed efficiency, milk yield, and milk compositional characteristics in dairy cows. 
     Materials and Methods 
     A total of 90 multi-parous cows were brought to the Research Barn at least 10 days prior the experimental phase of the study to adapt to facilities and feeding system. Thereafter, cows were blocked based on milk yield and assigned to 1 of 3 groups and followed for 150 days. 
     The treatment groups are shown in Table 19 below. The control group received a total mixed ration without microbial supplementation. 
     
       
         
           
               
             
               
                 TABLE 19 
               
             
            
               
                   
               
               
                 Treatment Groups 
               
            
           
           
               
               
               
               
            
               
                 Group 
                 Microorganisms 
                 Dose 
                 Carrier 
               
               
                   
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E6 CFU/g 
                 Calcium 
               
               
                 ment 1 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E7 CFU/g 
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E6 CFU/g 
                 Calcium 
               
               
                 ment 2 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E7 CFU/g 
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                   
                   Ruminococcus bovis  (SEQ ID NO: 
                 2E7 CFU/g 
               
               
                   
                 2108) 
               
               
                   
                   Butyrivibrio fibrisolvens  (SEQ ID 
                 2E7 CFU/g 
               
               
                   
                 NO: 2067) 
               
               
                 Control 
                 None 
                 None 
                 Calcium 
               
               
                   
                   
                   
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                   
               
            
           
         
       
     
     Cows in all treatment groups shared the same housing space, which is a roof covered pen bedded with sand. Adjacent to this area was a cow traffic alley with feed mangers and waterers providing ad libitum feed and water. Cows were milked twice a day in a double 10 parallel parlor. 
     All cows were fed the same ration other than the microorganisms included in the feed. A total mixed ration (TMR) was delivered twice a day into 48 feed mangers of which 16 were assigned to each group (Treatment 1, Treatment 2, and control) following a sequential order. 
     A TMR load was prepared once a day using a feed mixing wagon. The amount of TMR prepared every day for cows in the study was 105% of the previous day average intake. First, feed to be fed to cows assigned to Treatment 1 (105% of the previous day average intake for the study group) was unloaded into a long strip over the floor and 150 g of product was spread along the top of the strip. Second, feed from the same load to be fed to cows assigned to Treatment 2 was unloaded into another feed strip over the floor and 150 g of product was spread along the top of the strip. Third, the last portion of the feed from the same load to be fed to cows assigned to Control was delivered into feed mangers assigned to that study group. An empty wagon returned to the feed preparation area and the strip of feed assigned to Treatment 1 cows was loaded into the wagon, mixed for a minimum of 10 minutes, and delivered into mangers assigned to Treatment 1. Finally, an empty wagon returned to the feed preparation area and the strip of feed assigned to Treatment 2 cows was loaded into the wagon, mixed for a minimum of 10 minutes, and delivered into mangers assigned to Treatment 2. 
     Feed intake was recorded individually for each cow and continuously with automatic feed mangers placed on weighing cells using the BioControl Controlling and Recording Feed Intake (CRFT) system (Biocontrol, CRFI, Rakkestad, Norway). The CRFI system limits the access of cows to the different mangers depending on the treatment to which were assigned. It allows all cows assigned to the same treatment group to access all feed mangers with that treatment. Records were available from three days before until the end of the experimental phase of the study. 
     Milk yield: Individual cow milk yield was recorded at each milking using an electronic milk meter (AfiMilk MPC, Afikim, Israel). Records were available from three days before until the end of the experimental phase of the study. 
     Milk composition: Individual cow milk fat, protein and lactose was measured at each milking by an optical in-line milk component analyzer (AfiLab, Afikim, Israel). Records were available from three days before until the end of the experimental phase of the study. In addition, a composite milk sample was collected from milk meters to be analyzed for milk fat, protein and lactose by the local DHIA association (Tulare DHIA, Tulare, Calif.). Records were available for milk collected at the morning milking the three days before commencement of the experimental phase of the study, and twice a week thereafter. 
     Body Condition Score and Weight: Cows were weighed individually after the morning milking using a PS-2000 scale (Salter Brecknell, Fairmont, Minn.) on the last day of adaptation phase, and then on experimental days 30, 60, 90, 120 and 150. A 1-5 scoring was assigned for body condition. 
     Feed analysis: Individual ingredients from the ration and TMR representative samples were analyzed for nutritional and mineral content at DairyExperts Feeds Lab (DairyExperts, Inc, Tulare, Calif.). Ingredients were sampled once during adaptation and once during the experimental phase. TMR was sampled once during adaptation and once a week during the Intervention period. 
     A number of outcomes were evaluated, including: 
     (a) Dry Matter Intake (DMI): the feed consumed (Kg) per cow in an as fed basis times the dry matter percentage of the feed obtained from the laboratory analysis; 
     (b) Daily Milk Yield: calculated as the sum of both morning and afternoon milk weights (Kg); 
     (c) 3.5% Fat Corrected Milk (FCM): milk yield value corrected for 3.5% fat using formula from NRC (2001): [(0.4324×kg of milk)+(16.216×kg of fat)]; 
     (d) Energy Corrected Milk (ECM): milk yield value corrected for 3.5% fat and 3.2% true protein using formula from NRC (2001): [(0.3246×kg of milk)+(12.86×kg of fat)+(7.04×kg of true protein)]; 
     (e) Milk Components Percentage: daily milk crude protein (%), fat (%), and lactose (%) was calculated as the average of both morning and afternoon readings from the in-line sensor. Also, DHIA results were available from the samples collected at the morning milking on the days previously listed; 
     (f) Milk Components Yield: obtained by multiplying daily milk crude protein (%), fat (%), lactose (%) by the daily milk yield (Kg); 
     (g) Feed Efficiency: defined as Kg of 3.5% FCM produced per Kg of DM consumed; and 
     (h) Body Condition Score and Weight: these variables were analyzed for the measurements taken at different time points. 
     Table 20 below shows a summary of parameters from cows in control, Treatment 1, and Treatment 2 at the beginning of the trial. ECM, energy corrected milk; DIM, days in milk; and FE, feed efficiency. 
     
       
         
           
               
             
               
                 TABLE 20 
               
             
            
               
                   
               
               
                 Summary of Parameters at the Beginning of the Trial 
               
            
           
           
               
               
               
               
            
               
                   
                 Control 
                 Treatment 1 
                 Treatment 2 
               
               
                   
                   
               
            
           
           
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 92.27 ± 1.09  
                 92.66 ± 1.32 
                 93.11 ± 1.2  
               
               
                 ECM (lbs) 
                 86.5 ± 1.12 
                 87.92 ± 1.25 
                 85.01 ± 1.18  
               
               
                 Lactation 
                 2.34 ± 0.09 
                  2.48 ± 0.09 
                 2.31 ± 0.09 
               
               
                 Fat (lbs) 
                 2.94 ± 0.05 
                  3.06 ± 0.05 
                 2.81 ± 0.05 
               
               
                 Protein (lbs) 
                 2.52 ± 0.03 
                  2.51 ± 0.04 
                 2.52 ± 0.04 
               
               
                 DIM 
                 36.41 ± 1.17  
                 36.59 ± 1.12 
                 35.93 ± 1.27  
               
               
                 Intake (lbs) 
                 82.9 ± 1.36 
                 88.94 ± 1.15 
                 84.83 ± 1.13  
               
               
                 Body weight (kg) 
                 652.31 ± 8.97  
                 665.86 ± 11.13 
                 654.03 ± 6.67  
               
               
                 Body Condition 
                 2.98 ± 0.04 
                  2.94 ± 0.06 
                 2.97 ± 0.04 
               
               
                   
               
            
           
         
       
     
     Results 
     Table 21 below shows a summary of the trial results from cows in control, Treatment 1, and Treatment 2. Overall, cows in Treatment 2 performed better than cows in Treatment 1. Trt, treatment; ECM, energy corrected milk; DMI, dry matter intake; and FE, feed efficiency. 
     
       
         
           
               
             
               
                 TABLE 21 
               
             
            
               
                   
               
               
                 Summary of Trial Results 
               
            
           
           
               
               
            
               
                   
                 P value 
               
            
           
           
               
               
               
               
            
               
                   
                 % Difference 
                   
                 Trt 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Control 
                 Trt 1 
                 Trt 2 
                 Trt 1 
                 Trt 2 
                 Trt 
                 *Time 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 87.36 ± 1.8  
                 87.97 ± 1.8  
                 92.32 ± 1.79  
                 0.7 
                 5.67 
                 0.909 
                 &lt;0.001 
               
               
                 ECM (lbs) 
                 89.26 ± 1.74  
                 89.94 ± 1.74  
                 95.06 ± 1.73  
                 0.77 
                 6.5 
                 0.888 
                 &lt;0.001 
               
               
                 Fat (%) 
                 3.78 ± 0.05 
                 3.83 ± 0.05 
                 3.69 ± 0.05 
                 1.2.7 
                 −2.42 
                 0.114 
                 0.67 
               
               
                 Fat (lbs) 
                 3.24 ± 0.07 
                 3.26 ± 0.07 
                 3.45 ± 0.07 
                 0.74 
                 6.69 
                 0.883 
                 &lt;0.001 
               
               
                 Protein (%) 
                 3.01 ± 0.02 
                 3.05 ± 0.02 
                 2.99 ± 0.02 
                 1.49 
                 −0.42 
                 0.765 
                 &lt;0.001 
               
               
                 Protein (lbs) 
                 2.61 ± 0.06 
                 2.65 ± 0.06 
                 2.76 ± 0.06 
                 1.63 
                 5.72 
                 0.966 
                 &lt;0.001 
               
               
                 Lactose (%) 
                 4.59 ± 0.04 
                 4.59 ± 0.04 
                 4.64 ± 0.04 
                 0.05 
                 1.02 
                 0.674 
                 0.967 
               
               
                 Lactose (lbs) 
                 3.99 ± 0.09 
                 4.04 ± 0.09 
                  4.3 ± 0.09 
                 1.14 
                 7.75 
                 0.884 
                 &lt;0.001 
               
               
                 DMI (lbs) 
                 59.27 ± 1.0  
                 59.41 ± 1.01  
                 61.32 ± 1.0  
                 0.23 
                 3.45 
                 0.825 
                 &lt;0.001 
               
               
                 FE (ECM:DMI) 
                 1.57 ± 0.03 
                 1.59 ± 0.03 
                 1.58 ± 0.03 
                 1.41 
                 0.49 
                 0.401 
                 0.001 
               
               
                 Body weight (kg) 
                 1512.13 ± 10.18  
                 1490.65 ± 10.15  
                 1495.71 ± 10.06  
                 −1.42 
                 −1.09 
                 0.997 
                 0.533 
               
               
                 Body Condition 
                 3.13 ± 0.04 
                 3.15 ± 0.04 
                 3.05 ± 0.04 
                 0.64 
                 −2.41 
                 0.929 
                 0.441 
               
               
                   
               
            
           
         
       
     
     Table 22 below shows a summary of the trial results pre-peak (less than 90 days in milk) from cows in control, Treatment 1, and Treatment 2. ECM, energy corrected milk; DMI, dry matter intake, and FE, feed efficiency. 
     
       
         
           
               
             
               
                 TABLE 22 
               
             
            
               
                   
               
               
                 Summary of Trial Results Pre-Peak 
               
            
           
           
               
               
            
               
                   
                 % Difference 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Control 
                 Treatment 1 
                 Treatment 2 
                 Treatment 1 
                 Treatment 2 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 96.31 ± 1.8  
                 99.55 ± 1.8  
                 98.17 ± 1.79  
                 3.37 
                 1.93 
               
               
                 ECM (lbs) 
                 91.13 ± 1.74  
                 94.62 ± 1.74  
                 93.83 ± 1.74  
                 3.83 
                 2.97 
               
               
                 Fat (%) 
                 3.28 ± 0.05 
                 3.33 ± 0.05 
                 3.21 ± 0.05 
                 1.4 
                 −2.03 
               
               
                 Fat (lbs) 
                 3.11 ± 0.07 
                 3.25 ± 0.07 
                 3.22 ± 0.07 
                 4.46 
                 3.37 
               
               
                 Protein (%) 
                 2.79 ± 0.02 
                  2.8 ± 0.02 
                 2.78 ± 0.02 
                 0.56 
                 −0.4 
               
               
                 Protein (lbs) 
                 2.68 ± 0.06 
                 2.79 ± 0.06 
                 2.74 ± 0.06 
                 3.8 
                 1.97 
               
               
                 Lactose (%) 
                 4.62 ± 0.04 
                 4.63 ± 0.04 
                 4.69 ± 0.04 
                 0.01 
                 1.39 
               
               
                 Lactose (lbs) 
                 4.42 ± 0.09 
                 4.59 ± 0.09 
                 4.61 ± 0.09 
                 3.8 
                 4.3 
               
               
                 DMI (lbs) 
                 56.12 ± 1.0  
                 57.57 ± 1.01  
                 57.61 ± 1.0  
                 2.59 
                 2.66 
               
               
                 FE (ECM:DMI) 
                 1.66 ± 0.03 
                 1.67 ± 0.03 
                 1.63 ± 0.03 
                 1.01 
                 −1.52 
               
               
                 Body weight (kg) 
                 1466.26 ± 10.14  
                 1459.61 ± 10.11  
                 1454.53 ± 10.06  
                 −0.45 
                 −0.8 
               
               
                 Body Condition 
                 3.0.5 ± 0.04  
                  3.1 ± 0.04 
                 3.02 ± 0.04 
                 1.38 
                 −1.23 
               
               
                   
               
            
           
         
       
     
     Table 23 below shows a summary of the trial results post-peak (greater than 90 days in milk) from cows in control, Treatment 1, and Treatment 2. ECM, energy corrected milk; DMI, dry matter intake, and FE, feed efficiency. 
     
       
         
           
               
             
               
                 TABLE 23 
               
             
            
               
                   
               
               
                 Summary of Trial Results Post-Peak 
               
            
           
           
               
               
            
               
                   
                 % Difference 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Control 
                 Treatment 1 
                 Treatment 2 
                 Treatment 1 
                 Treatment 2 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 83.91 ± 1.8  
                 83.36 ± 1.81  
                 90.32 ± 1.79  
                 −0.66 
                 7.64 
               
               
                 ECM (lbs) 
                 89.05 ± 1.74  
                 88.51 ± 1.74  
                 96.28 ± 1.73  
                 −0.61 
                 8.12 
               
               
                 Fat (%) 
                 4.02 ± 0.05 
                 4.06 ± 0.05 
                 3.91 ± 0.05 
                 1.22 
                 −2.52 
               
               
                 Fat (lbs) 
                 3.32 ± 0.07 
                 3.29 ± 0.07 
                 3.59 ± 0.07 
                 −0.8 
                 8.07 
               
               
                 Protein (%) 
                  3.1 ± 0.02 
                 3.16 ± 0.02 
                 3.09 ± 0.02 
                 1.88 
                 −0.49 
               
               
                 Protein (lbs) 
                  2.6 ± 0.06 
                 2.61 ± 0.06 
                 2.79 ± 0.06 
                 0.66 
                 7.4 
               
               
                 Lactose (%) 
                 4.58 ± 0.04 
                 4.58 ± 0.04 
                 4.62 ± 0.04 
                 0.02 
                 0.81 
               
               
                 Lactose (lbs) 
                 3.83 ± 0.09 
                 3.82 ± 0.09 
                 4.19 ± 0.09 
                 −0.24 
                 9.54 
               
               
                 DMI (lbs) 
                 61.41 ± 1.0  
                 60.7 ± 1.01 
                 63.81 ± 1.0  
                 −1.16 
                 3.9 
               
               
                 FE (ECM:DMI) 
                 1.52 ± 0.03 
                 1.54 ± 0.03 
                 1.55 ± 0.03 
                 1.77 
                 1.81 
               
               
                 Body weight (kg) 
                 1523.6 ± 10.2  
                 1498.41 ± 10.16  
                 1506.01 ± 10.06  
                 −1.65 
                 −1.15 
               
               
                 Body Condition 
                 3.15 ± 0.04 
                 3.16 ± 0.04 
                 3.06 ± 0.04 
                 0.46 
                 −2.69 
               
               
                   
               
            
           
         
       
     
       FIG.  9    shows milk yield in cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  10    shows energy corrected milk (ECM) in cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  11 A  shows percent fat in milk from cows administered control, treatment 1, or treatment 2 over time.  FIG.  11 B  shows pounds (lbs) of fat in milk from cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  12 A  shows percent protein in milk from cows administered control, treatment 1, or treatment 2 over time.  FIG.  12 B  shows pounds (lbs) of protein in milk from cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  13 A  shows percent lactose in milk from cows administered control, treatment 1, or treatment 2 over time.  FIG.  13 B  shows pounds (lbs) of lactose in milk in cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  14 A  shows dry matter intake in cows administered control, treatment 1, or treatment 2 over time.  FIG.  14 B  shows feed efficiency (energy corrected milk to dry matter intake) in cows administered control, treatment 1, or treatment 2 over time. 
       FIG.  15 A  shows body weight of cows administered control, treatment 1, or treatment 2 over time.  FIG.  15 B  shows body condition of cows administered control, treatment 1, or treatment 2 over time. 
     Overall, cows administered treatment 1 showed an increase in milk yield and energy corrected milk, and an increase in milk fat and protein from weeks 1-9 of the trial. Cows administered treatment 1 also showed increased feed efficiency consistently across the entire trial. Cows administered treatment 2 showed an increase in milk yield and energy corrected milk from weeks 6-24 of the trial, and an increase in milk fat and protein from weeks 5-24 of the trial. Cows administered treatment 2 also showed no significant decreases in body weight and condition scores. 
     Example 5. Microbial Supplementation in Dairy Cows 
     This study examines the effect of microbial supplementation on feed efficiency, milk yield, and milk compositional characteristics. 
     Materials and Methods 
     Seventy-two Holstein dairy cows, between 28-100 days in milk were assigned to one of three treatments (n=24 cows/trt; Control, Treatment 1, and Treatment 2). Animals were evaluated for soundness and removed before beginning trial if they exhibited feet and leg issues, were a three quartered animal or had more than one case of mastitis during calving to beginning of covariate period. 
     Treatments were blocked and balanced for parity, days in milk, and current milk yield. Parity was defined as primiparous (no more 30% of animals), or multiparous (2 nd  or greater). Animals were within a range of 15-20 days in milk within the block. The level of milk production was as tight as possible with the goal being within a range of 10 lbs of milk within a block. 
     Cows were adapted to tie-stalls and then baseline data (covariate) was collected for 2 weeks prior to start of treatments for all cows. Cows remained on their respective treatment diets for 140 days. 
     The treatment groups are shown in Table 24 below. The control group received a total mixed ration without microbial supplementation. 
     
       
         
           
               
             
               
                 TABLE 24 
               
             
            
               
                   
               
               
                 Treatment Groups 
               
            
           
           
               
               
               
               
            
               
                 Group 
                 Microorganisms 
                 Dose 
                 Carrier 
               
               
                   
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E6 CFU/g 
                 Calcium 
               
               
                 ment 1 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E7 CFU/g 
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E6 CFU/g 
                 Calcium 
               
               
                 ment 2 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E7 CFU/g 
                 carbonate 
               
               
                   
                   Ruminococcus bovis  (SEQ ID NO: 
                 2E7 CFU/g 
                 and zeolite 
               
               
                   
                 2108) 
               
               
                   
                   Butyrivibrio fibrisolvens  (SEQ ID 
                 2E7 CFU/g 
               
               
                   
                 NO: 2067) 
               
               
                 Control 
                 None 
                 None 
                 Calcium 
               
               
                   
                   
                   
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                   
               
            
           
         
       
     
     A top-dress for each cow was produced daily by adding the 5 g treatment to approximately 150 g of the carrier ground corn. Treatments were top-dressed on the feed and mixed into the top 3-6 inches of the total mixed ration (TMR). Treatments were color-coded and marked on the stalls and containers delivering the top-dress to the cows. Personnel changed gloves between treatments. 
     Treatments were packed into a daily packet of approximately 132 g, with each packet containing enough product for each cow in the treatment group plus 10% overage. Packets were stored at 4° C. 
     Each day, a fresh packet was opened. 5 g was weighed out for each cow individually and mixed into approximately 150 g of ground corn. Once completed, the packet was resealed and labeled with the date opened before storing at 4° C. Approximately every 50 days, one unused packet was assayed for quality control. 
     The basal TMR was delivered to the barn and CALAN Data Rangers were used to weigh out individual animal feedings. Animals were given approximately 60% of food at first feeding. Cows were fed at a reasonably consistent time each day (approximately 9 am), and then the rest of feed was put in a barrel in front of cows and fed later in day to ensure feed is always available. Individual cow dry matter intake (DMI) was adjusted daily to allow for a 10% feed refusal rate. Cow feeding areas were separated using plastic panels approximately 34 in. high near cows to 20 in. at back of manger area to prevent cross contamination of feed. The test products were hand-fed once daily by top-dressing on each cow&#39;s individual TMR diet. Treatments were mixed into the top 3-6 inches of TMR 
     Dry Matter Intake: Dry matter intakes from −14 to 140 treatment (daily, summarized by week). Diets were offered at ad libitum intake with 10% refusals. Orts were weighed daily and daily intakes were calculated for the duration of the study. 
     Body Weights: Double body weights were collected at beginning and end of covariate period, every 28 days and at removal from trial. More frequent body weights were allowed and were defined by each trial site but the double body weights were a requirement. Average body weight change was calculated by 28 day periods and overall body weight change was based on body weight at end of covariate. 
     Body Condition Score (BCS): BCS scores were determined using the 1-5 Elanco scoring system. Two scorers at beginning and end of covariate, every 28 days and at removal from experiment. Average BCS were determined and used for analysis. If BCS was ≥0.5 between scorers, then scorers independently rescored animal. 
     Milk composition: Once a week on the trial, a milk sample was collected at each milking during a 24 hour period. Milk samples were collected on the same day(s) of the week. Milk samples were not be composited but were sent to DHIA laboratories in Dubuque, Iowa for analysis of milk fat, protein, lactose, total solids, MUN and somatic cell counts. 
     Milk production: Cows were milked daily at approximately 4:00 am and 3:30 μm in a D-12 parallel milking parlor. Daily milk weights were captured by DairyPlan software. A milking system maintenance including calibration of the meters were performed prior to start of trial. Average daily milk and ECM by week and total treatment period was calculated based on milk and milk composition data collected on the trial. 
     Feed efficiency: Average daily milk and ECM by week and total treatment period was calculated based on milk and milk composition data collected on the trial. Weekly feed efficiency was calculated as milk/DMI and ECM/DMI. 
     Feed sampling: Weekly silage samples were collected and composited monthly. Dry matter determinations was conducted on corn silage and wet forages weekly. TMR was adjusted based on these dry matter determinations. Concentrate mixes, forages, and TMR was sampled weekly, composited by months and analyzed for model profile nutrients by chemical methods at Dairy One Forage Laboratory, Ithaca, N.Y. 
     Health and Reproduction: All health (including mastitis) and reproductive events and treatments was recorded throughout the trial and summarized by treatment. Cows were let out once a day for about 2 hours for exercise and estrus observations were captured during this and other times animals moving to parlor and back. 
     Rumen Fluid Collection: Rumen fluid was collected from 10 blocks of animals on the experiment. The samples were collected by esophageal tube or rumen canula. For samples collected using an esophageal tube, the first 200-300 mL was discarded to minimize saliva contamination. The pH of the sample was then determined and if the pH was greater than 6.9 than the animal was resampled due to possible saliva contamination. 
     Results 
     Table 25 below shows a summary of the trial results from cows in control, Treatment 1, and Treatment 2. Overall, cows in Treatment 2 performed better than cows in Treatment 1. Trt, treatment; trt*time, treatment over time; and ECM, energy corrected milk. 
     
       
         
           
               
             
               
                 TABLE 25 
               
             
            
               
                   
               
               
                 Summary of Trial Results 
               
            
           
           
               
               
            
               
                   
                 P value 
               
            
           
           
               
               
               
               
            
               
                   
                 % Difference 
                   
                 Trt 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Control 
                 Trt 1 
                 Trt 2 
                 Trt 1 
                 Trt 2 
                 Trt 
                 *Time 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 77.18 ± 2.09  
                 79.99 ± 2.1  
                 78.7 ± 1.98 
                 3.65 
                 1.97 
                 0.994 
                 0.261 
               
               
                 ECM (lbs) 
                 80.34 ± 5.01  
                 81.32 ± 5.1  
                 83.51 ± 4.77  
                 1.21 
                 3.94 
                 0.849 
                 0.835 
               
               
                 Fat (%) 
                 3.68 ± 0.23 
                 3.87 ± 0.23 
                  4.0 ± 0.22 
                 5.11 
                 8.54 
                 0.504 
                 0.557 
               
               
                 Fat (lbs) 
                  2.8 ± 0.25 
                 2.94 ± 0.25 
                 3.05 ± 0.24 
                 4.82 
                 8.67 
                 0.507 
                 0.863 
               
               
                 Protein (%) 
                 3.31 ± 0.04 
                 3.27 ± 0.04 
                 3.32 ± 0.03 
                 −1.35 
                 0.31 
                 0.976 
                 0.649 
               
               
                 Protein (lbs) 
                 2.56 ± 0.14 
                 2.46 ± 0.14 
                 2.52 ± 0.13 
                 −4.03 
                 −1.52 
                 0.971 
                 0.55 
               
               
                 Lactose (%) 
                 4.73 ± 0.05 
                 4.78 ± 0.05 
                 4.75 ± 0.05 
                 1.08 
                 0.47 
                 0.709 
                 0.641 
               
               
                 Lactose (lbs) 
                 3.73 ± 0.2  
                 3.68 ± 0.21 
                 3.73 ± 0.19 
                 −1.34 
                 −0.04 
                 0.879 
                 0.583 
               
               
                   
               
            
           
         
       
     
       FIG.  16 A  shows energy corrected milk in cows administered control, treatment 1, or treatment over time.  FIG.  16 B  shows milk fat in cows administered control, treatment 1, or treatment over time. 
     Example 6. Microbial Supplementation in Dairy Cows 
     This study examines the effect of microbial supplementation on feed efficiency, milk yield, and milk compositional characteristics. 
     Materials and Methods 
     Ninety Holstein dairy cows, between 70-114 days in milk were assigned to one of three treatments (n=30 cows/trt; Control, Treatment 1 and Treatment 2). Animals were evaluated for soundness and removed before beginning the trial if they had feet or leg issues, were a three quartered animal or had more than one case of mastitis during calving to beginning of covariate period. 
     Treatments were blocked and balanced for parity, days in milk, and current milk yield. Parity was defined as primiparous (no more 30% of animals) or multiparous (2nd or greater). Animals were within a range of 15-20 days in milk within the block. The level of milk production was as tight as possible with the goal being within a range of 10 lbs of milk within a block. 
     Cows were adapted to tie-stalls and then a baseline data (covariate) was collected for 2 weeks prior to the start of treatment for all cows. Cows remained on their respective treatment diets for 112 days. 
     The treatment groups are shown in Table 26 below. The control group received a total mixed ration without microbial supplementation. 
     
       
         
           
               
             
               
                 TABLE 26 
               
             
            
               
                   
               
               
                 Treatment Groups 
               
            
           
           
               
               
               
               
            
               
                 Group 
                 Microorganisms 
                 Dose 
                 Carrier 
               
               
                   
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E6 CFU/g 
                 Calcium 
               
               
                 ment 1 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E7 CFU/g 
                 carbonate 
               
               
                   
                   Ruminococcus bovis  (SEQ ID NO: 
                 2E7 CFU/g 
                 and zeolite 
               
               
                   
                 2108) 
               
               
                   
                   Butyrivibrio fibrisolvens  (SEQ ID 
                 2E7 CFU/g 
               
               
                   
                 NO: 2067) 
               
               
                 Treat- 
                   Clostridium  sp. (SEQ ID NO: 28) 
                 2E7 CFU/g 
                 Calcium 
               
               
                 ment 2 
                   Pichia kudriavzevii  (SEQ ID NO: 32) 
                 2E8 CFU/g 
                 carbonate 
               
               
                   
                   Ruminococcus bovis  (SEQ ID NO: 
                 2E7 CFU/g 
                 and zeolite 
               
               
                   
                 2108) 
               
               
                   
                   Butyrivibrio fibrisolvens  (SEQ ID 
                 2E7 CFU/g 
               
               
                   
                 NO: 2067) 
               
               
                 Control 
                 None 
                 None 
                 Calcium 
               
               
                   
                   
                   
                 carbonate 
               
               
                   
                   
                   
                 and zeolite 
               
               
                   
               
            
           
         
       
     
     Treatments were packed into a daily packet of approximately 165 g with each packet containing enough product for each cow in the treatment group plus 10% overage. Packets were be stored at 4° C. 
     Each day, a fresh packet was opened. 5 g was weighed out for each cow individually and mixed into approximately 150 g of ground corn. Once completed, the packet was resealed and labeled with the date opened before storing at 4° C. Approximately every 50 days, one unused packet was assayed for quality control. 
     The basal diet was formulated to meet or exceed dairy NRC nutrient requirements for protein, minerals and vitamins. The basal TMR was formulated based on a 2:1 ratio of corn silage to alfalfa haylage and include 10-20% byproducts, as well as ground corn and protein sources to provide 20% forage NDF, 28-32% total NDF, and 30% starch. The basal TMR was delivered to the barn and CALAN Data Rangers were used to weigh out individual animal feedings. Animals were given all of their daily allotment of food at one feeding. Cows were fed at a reasonably consistent time each day (approximately 9 am). Individual cow dry matter intake (DMI) was adjusted daily to allow for a 10% feed refusal rate. Cow feeding areas were separated by hard plastic dividers in the feed manger between cows to prevent cross contamination of feed and the feed mangers were blocked when cows were being released or being brought back to tie stalls. The test products were hand-fed once daily by top-dressing on each cow&#39;s individual TMR diet. Treatments were mixed into the top 3-6 inches of TMR. 
     Dry Matter Intakes: Dry matter intakes from −14 to 112 days of treatment (daily/weekly). Diets were offered at ad libitum intake with 10% refusals. Orts were weighed daily and daily intakes calculated for the duration of the study. 
     Body Weights: Body weights were collected 3 times per week. The average of body weights collected were used as the body weights for the time periods. Average body weight change was calculated by 28-day periods and overall body weight change based on body weight at end of covariate to end of trial 
     Body Condition Score (BCS): BCS scores were determined using the 1-5 Elanco scoring system. Two scorers at beginning and end of covariate, every 28 days and at removal from experiment. Average BCS were determined and used for analysis. If BCS was ≥0.5 between scorers, then scorers independently rescored animal. 
     Milk Composition: Once a week on the trial, a milk sample was collected at each milking of a 48-hour period. Milk samples were collected on the same day(s) of the week. Milk samples were not composited but were sent to DHIA laboratories in East Lansing for analysis of milk fat, protein, lactose, solids not fat, total solids, MUN and somatic cell counts. 
     Milk Production: Cows were milked daily at approximately 3:00 am and 2:00 μm in a D-7 herringbone milking parlor. Daily milk weights were captured by the Boumatic software. A milking system maintenance including calibration of the meters was performed prior to start of trial. Average daily milk and ECM by week and total treatment period was calculated based on milk and milk composition data collected on the trial. 
     Feed Efficiency: Average daily milk and ECM by week and total treatment period was calculated based on milk and milk composition data collected during the trial. Weekly feed efficiency was calculated as milk/DMI, ECM/DMI, and total energy captured as milk and body tissue/DMI. 
     Feed Sampling: Weekly silage samples were collected and composited monthly. A NIR nutrient analysis was determined. Dry matter determinations were conducted on corn silage and wet forages twice weekly by Koster tester. TMR may be adjusted based on these dry matter determinations. Samples of all feeds were collected weekly, composited monthly and analyzed by wet chemistry for DM, NDF, starch, CP, lipid, and ash. 
     Health and Reproduction; All health (including mastitis) and reproductive events and treatments were recorded throughout the trial and summarized by treatment. Cows were let out once a day for about 2 hours for exercise and estrus observations are captured during this and other times animals moving to parlor and back. 
     Other Measurements: Total tract digestibility of dry matter, neutral detergent fiber, starch, protein, and lipid was determined on 20 cows from each treatment group at approximately 30 to 50 days on treatment. A total of 8 samples for each cow was collected over 5 consecutive days. During the sampling period, blood glucose, insulin, and non-esterified fatty acids were collected and also on one other day at −1, +2 and +6 h of feeding time as metabolic indicators. 
     Rumen samples were collected via oro-ruminal sampling on 12 cows per treatment group during pretreatment, approximately 50-60 days on treatment and 90-100 days on treatment. 
     Results 
     Table 27 below shows a summary of the trial results from cows in control, Treatment 1, and Treatment 2. Overall, cows in Treatment 2 performed better than cows in Treatment 1. Trt, treatment; and ECM, energy corrected milk. 
     
       
         
           
               
             
               
                 TABLE 27 
               
             
            
               
                   
               
               
                 Summary of Trial Results 
               
            
           
           
               
               
            
               
                   
                 P value 
               
            
           
           
               
               
               
               
            
               
                   
                 % Difference 
                   
                 Trt 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Control 
                 Trt 1 
                 Trt 2 
                 Trt 1 
                 Trt 2 
                 Trt 
                 *Time 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Milk Yield (lbs) 
                 86.54 ± 1.97  
                 85.8 ± 1.98 
                 91.09 ± 2.0  
                 −0.85 
                 5.26 
                 0.859 
                 0.005 
               
               
                 ECM (lbs) 
                 90.77 ± 2.62  
                 91.79 ± 2.63  
                 97.31 ± 2.78  
                 1.13 
                 7.21 
                 0.899 
                 0.12 
               
               
                 Fat (%) 
                 3.95 ± 0.09 
                 3.76 ± 0.1  
                 3.85 ± 0.09 
                 −4.75 
                 −2.68 
                 0.054 
                 0.131 
               
               
                 Fat (lbs) 
                 3.36 ± 0.1  
                 3.32 ± 0.11 
                 3.51 ± 0.11 
                 4.3 
                 4.24 
                 0.751 
                 0.267 
               
               
                 Protein (%) 
                 3.16 ± 0.04 
                 3.18 ± 0.05 
                 3.25 ± 0.04 
                 0.58 
                 3 
                 0.217 
                 0.36 
               
               
                 Protein (lbs) 
                 2.69 ± 0.09 
                 2.79 ± 0.09 
                 2.97 ± 0.1  
                 4.03 
                 10.66 
                 0.404 
                 0.066 
               
               
                 Lactose (%) 
                 4.97 ± 0.02 
                 4.99 ± 0.02 
                 4.98 ± 0.02 
                 0.32 
                 0.08 
                 0.068 
                 0.233 
               
               
                 Lactose (lbs) 
                 4.21 ± 0.13 
                  4.4 ± 0.13 
                 4.62 ± 0.13 
                 4.38 
                 9.53 
                 0.716 
                 0.067 
               
               
                 DMI (lbs) 
                 76.59 ± 1.85  
                 75.83 ± 1.85  
                 77.97 ± 1.87  
                 −0.99 
                 1.81 
                 0.364 
                 0.696 
               
               
                 FE (ECM:DMI) 
                 1.14 ± 0.03 
                 1.15 ± 0.03 
                 1.19 ± 0.04 
                 0.81 
                 4.41 
                 0.213 
                 0.111 
               
               
                 Body weight (kg) 
                 1414.01 ± 8.74   
                 1419.59 ± 8.87   
                 1416.04 ± 8.93   
                 0.39 
                 0.14 
                 &lt;0.001 
                 0.924 
               
               
                   
               
            
           
         
       
     
       FIG.  17 A  shows milk yield in cows administered control, treatment 1, or treatment over time.  FIG.  17 B  shows energy corrected milk in cows administered control, treatment 1, or treatment over time. 
     INCORPORATION BY REFERENCE 
     All references, articles, publications, patents, patent publications, and patent applications cited herein are incorporated by reference in their entireties for all purposes, including PCT Application Nos. PCT/US2017/012573 and PCT/US2020/020311. 
     However, mention of any reference, article, publication, patent, patent publication, and patent application cited herein is not, and should not be taken as, an acknowledgment or any form of suggestion that they constitute valid prior art or form part of the common general knowledge in any country in the world. 
     NUMBERED EMBODIMENTS 
     Other subject matter contemplated by the present disclosure is set out in the following numbered embodiments: 
     Embodiment 1. An orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising:
         a)  Ruminococcus  bois comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 2. The composition of embodiment 1, wherein the  Ruminococcus bovis  is deposited as PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479.
 
Embodiment 3. The composition of embodiment 1 or 2, wherein the composition comprises:
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 4. The composition of any one of embodiments 1-3, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 5. The composition of embodiment 4, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 6. The composition of any one of embodiments 1-5, wherein the  Ruminococcus bovis  comprises one or more mutations in the whole genome following serial preservation.
 
Embodiment 7. The composition of embodiment 6, wherein the one or more mutations are selected from the group consisting of:
   a) a G→T substitution at position 297 of SEQ ID NO; 2109;   b) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111;   c) a T→G substitution at position 307 of SEQ ID NO; 2111;   d) a −A deletion at position 300 of SEQ ID NO: 2113;   e) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115;   f) a +T insertion between positions 105-106 of SEQ ID NO: 2117;   g) a C→T substitution at position 298 of SEQ ID NO: 2119;   h) a C→A substitution at position 298 of SEQ ID NO: 2121; and   i) a +AC insertion between positions 43-44 of SEQ ID NO: 2123.
 
Embodiment 8. An orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising:
   a)  Ruminococcus bovis  comprising one or more mutations selected from the group consisting of:
           i) a G→T substitution at position 297 of SEQ ID NO: 2109;   ii) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111;   iii) a T→G substitution at position 307 of SEQ ID NO: 2111;   iv) a −A deletion at position 300 of SEQ ID NO: 2113;   v) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115;   vi) a +T insertion between positions 105-106 of SEQ ID NO: 2117;   vii) a C→T substitution at position 298 of SEQ ID NO: 2119;   viii) a C→A substitution at position 298 of SEQ ID NO: 2121; and   ix) a +AC insertion between positions 43-44 of SEQ ID NO: 2123; and   
           b) a carrier suitable for oral ruminant administration.
 
Embodiment 9. The composition of embodiment 8, wherein the composition comprises.
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 10. The composition of embodiment 9, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 990%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 11. The composition of embodiment 10, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 12. An orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising:
   a)  Ruminococcus bovis  comprising a nucleic acid sequence selected from any one of SEQ ID NOs: 2110, 2112, 2114, 2116, 2118, 2120, 2122, or 2124; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 13. The composition of embodiment 12, wherein the composition comprises:
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 14. The composition of embodiment 13, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 15. The composition of embodiment 14, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 16. An orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising:
   a) a  Ruminococcus bovis  with a deposit accession number PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 17. The composition of embodiment 16, wherein the composition comprises:
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 18. The composition of embodiment 17, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 19. The composition of embodiment 18, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 20. An orally deliverable composition for increasing milk production or improving milk compositional characteristics in a ruminant, comprising:
   a)  Ruminococcus bovis ; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 21. The composition of embodiment 20, wherein the composition comprises:
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 22. The composition of embodiment 21, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 23. The composition of embodiment 22, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 24. A composition, comprising:
   a)  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 25. A composition, comprising:
   a)  Ruminococcus bovis  comprising one or more mutations selected from the group consisting of:
           i) a G→T substitution at position 297 of SEQ ID NO: 2109;   ii) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111;   iii) a T→G substitution at position 307 of SEQ ID NO: 2111;   iv) a −A deletion at position 300 of SEQ ID NO: 2113;   v) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115;   vi) a +T insertion between positions 105-106 of SEQ ID NO: 2117;   vii) a C→T substitution at position 298 of SEQ ID NO: 2119;   viii) a C→A substitution at position 298 of SEQ ID NO: 2121; and   ix) a +AC insertion between positions 43-44 of SEQ ID NO: 2123; and   
           b) a carrier suitable for oral ruminant administration.
 
Embodiment 26. A composition, comprising:
   a)  Ruminococcus bovis  comprising a nucleic acid sequence selected from any one of SEQ ID NOs: 2110, 2112, 2114, 2116, 2118, 2120, 2122, or 2124; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 27. A composition, comprising:
   a) a  Ruminococcus bovis  with the deposit accession number PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 28. A composition, comprising:
   a)  Ruminococcus bovis ; and   b) a carrier suitable for ruminant administration.
 
Embodiment 29. The composition of any one of embodiments 1-28, wherein the composition is formulated to protect the bacteria and/or fungi from external stressors prior to entering the gastrointestinal tract of the ruminant.
 
Embodiment 30. The composition of any one of embodiments 1-28, wherein the ruminant is a cow.
 
Embodiment 31. The composition of any one of embodiments 1-28, wherein a ruminant administered the composition exhibits an increase in milk production that leads to an increase in milk yield or an increase in energy-corrected milk.
 
Embodiment 32. The composition of any one of embodiments 1-28, wherein a ruminant administered the composition exhibits an improved milk compositional characteristic selected from the group consisting of: an increase in milk fat(s), an increase in milk protein(s), an increase of carbohydrates in milk, an increase of vitamins in milk, an increase of minerals in milk, or combinations thereof.
 
Embodiment 33. The composition of any one of embodiments 1-28, wherein a ruminant administered the composition exhibits at least one improved phenotypic trait, selected from the group consisting of: an improved efficiency in feed utilization, improved digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in manure production, improved dry matter intake, an improved efficiency of nitrogen utilization, or combinations thereof.
 
Embodiment 34. The composition of any one of embodiments 1-28, wherein the composition is formulated to protect the bacteria and/or fungi from oxidative stress.
 
Embodiment 35. The composition of any one of embodiments 1-28, wherein the composition is formulated to protect the bacteria and/or fungi from moisture.
 
Embodiment 36. The composition of any one of embodiments 1-28, wherein the composition is dry.
 
Embodiment 37. The composition of any one of embodiments 1-28, wherein the composition is combined with food.
 
Embodiment 38. The composition of any one of embodiments 1-28, wherein the composition is combined with cereal, starch, oilseed cake, or vegetable waste.
 
Embodiment 39. The composition of any one of embodiments 1-28, wherein the composition is combined with hay, haylage, silage, livestock feed, forage, fodder, beans, grains, micro-ingredients, fermentation compositions, mixed ration, total mixed ration, or a mixture thereof.
 
Embodiment 40. The composition of any one of embodiments 1-28, wherein the composition is formulated as a solid, liquid, or mixture thereof.
 
Embodiment 41. The composition of any one of embodiments 1-28, wherein the composition is formulated as a pellet, capsule, granulate, or powder.
 
Embodiment 42. The composition of any one of embodiments 1-28, wherein the composition is combined with water, medicine, vaccine, or a mixture thereof.
 
Embodiment 43. The composition of any one of embodiments 1-28, wherein the composition is encapsulated.
 
Embodiment 44. The composition of embodiment 43, wherein the composition is encapsulated in a polymer or carbohydrate.
 
Embodiment 45. The composition of any one of embodiments 1-44, wherein the bacteria and/or fungi is present in the composition in an amount of at least 10 2  cells.
 
Embodiment 46. A method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of the composition from any one of embodiments 1-45.
 
Embodiment 47. A method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of a ruminant supplement comprising:
   a)  Ruminococcus bovis ; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 48. A method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of a ruminant supplement comprising:
   a)  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 49. A method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of a ruminant supplement comprising:
   a) a  Ruminococcus bovis  with the deposit accession number PTA-125917, NRRL B-67764, TSD-225, or NCTC 14479; and   b) a carrier suitable for oral ruminant administration.
 
Embodiment 50. A method for increasing milk production or improving milk compositional characteristics in a ruminant, the method comprising orally administering to a ruminant an effective amount of a ruminant supplement comprising:
   a)  Ruminococcus bovis  comprising one or more mutations selected from the group consisting of;
           i) a G→T substitution at position 297 of SEQ ID NO: 2109;   ii) a CC→TA substitution at positions 301-302 of SEQ ID NO: 2111;   iii) a T→G substitution at position 307 of SEQ ID NO: 2111;   iv) a −A deletion at position 300 of SEQ ID NO: 2113;   v) a CCA→TTC substitution at positions 116-118 of SEQ ID NO: 2115,   vi) a +T insertion between positions 105-106 of SEQ ID NO: 2117;   vii) a C→T substitution at position 298 of SEQ ID NO: 2119;   viii) a C→A substitution at position 298 of SEQ ID NO: 2121; and   ix) a +AC insertion between positions 43-44 of SEQ ID NO: 2123; and   
           b) a carrier suitable for oral ruminant administration.
 
Embodiment 51. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits an increase in milk production that leads to a measured increase in milk yield.
 
Embodiment 52. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits an increase in milk production and improved milk compositional characteristics that leads to a measured increase in energy-corrected milk.
 
Embodiment 53. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits an improved milk compositional characteristic selected from the group consisting of: an increase in milk fat(s), an increase in milk protein(s), an increase of carbohydrates in milk, an increase of vitamins in milk, an increase of minerals in milk, or combinations thereof.
 
Embodiment 54. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits at least a 1% increase in the average production of: milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof.
 
Embodiment 55. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits at least a 100/% increase in the average production of: milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof.
 
Embodiment 56. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement exhibits at least a 20% increase in the average production of: milk fat(s), milk protein(s), energy-corrected milk, or combinations thereof.
 
Embodiment 57. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits at least one improved phenotypic trait, selected from the group consisting of: an improved efficiency in feed utilization, improved digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in manure production, improved dry matter intake, an improved efficiency of nitrogen utilization, or combinations thereof.
 
Embodiment 58. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits a shift in the microbiome of the rumen.
 
Embodiment 59. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits a shift in the microbiome of the rumen, wherein a population of microbes present in the rumen before administration of the ruminant supplement increase in abundance after administration of the ruminant supplement.
 
Embodiment 60. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits: a shift in the microbiome of the rumen, wherein a population of microbes present in the rumen before administration of the ruminant supplement decrease in abundance after administration of the ruminant supplement.
 
Embodiment 61. The method according to any one of embodiments 46-50, wherein the ruminant administered the effective amount of the ruminant supplement, further exhibits: a shift in the microbiome of the rumen,
       

     wherein a first population of microbes present in the rumen before administration of the ruminant supplement increase in abundance after administration of the ruminant supplement, and 
     wherein a second population of microbes present in the rumen before administration of the ruminant supplement decrease in abundance after administration of the ruminant supplement. 
     Embodiment 62. A composition comprising:
         a) a  Ruminococcus bovis  with a deposit accession number of PTA-125917, NRRL B-67764, TSD-225 or NCTC 14479;   b) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   c) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   d) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.
 
Embodiment 63. A composition that performs the same or better than recombinant bovine growth hormone for increasing milk production or improving milk compositional characteristics in a ruminant, wherein the composition comprises:
   a) a  Ruminococcus bovis ; and   b) a carrier suitable for ruminant administration.
 
Embodiment 64. A composition that performs the same or better than recombinant bovine growth hormone for increasing milk production or improving milk compositional characteristics in a ruminant, wherein the composition comprises:
   a)  Ruminococcus bovis  comprising a 16S nucleic acid sequence of SEQ ID NO: 2108; and   b) a carrier suitable for ruminant administration.
 
Embodiment 65. The composition of embodiment 63 or 64, wherein the composition comprises:
   a) one or more bacteria comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-30 and 2045-2103; and/or   b) one or more fungi comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 31-60 and 2104-2107.
 
Embodiment 66. The composition of embodiment 65, wherein the composition comprises:
   a) a  Clostridium  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 28;   b) a  Pichia  sp. comprising an ITS nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 32; and/or   c) a  Butyrivibrio  sp. comprising a 16S nucleic acid sequence sharing at least about 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 2067.
 
Embodiment 67. The composition of embodiment 66, wherein the composition comprises:
   a) a  Clostridium  sp. with a deposit accession number of NRRL B-67248;   b) a  Pichia  sp. with a deposit accession number of NRRL Y-67249; and/or   c) a  Butyrivibrio  sp. with a deposit accession number of NRRL B-67347.