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WO2024163529A2 - Utilisation de compositions bactériennes synthétiques pour un traitement infectieux - Google Patents

Utilisation de compositions bactériennes synthétiques pour un traitement infectieux Download PDF

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Publication number
WO2024163529A2
WO2024163529A2 PCT/US2024/013624 US2024013624W WO2024163529A2 WO 2024163529 A2 WO2024163529 A2 WO 2024163529A2 US 2024013624 W US2024013624 W US 2024013624W WO 2024163529 A2 WO2024163529 A2 WO 2024163529A2
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seq
set forth
sequence set
rdna sequence
rdna
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WO2024163529A9 (fr
WO2024163529A3 (fr
Inventor
Elizabeth HALVORSEN
Nathaniel ENNIS
Jenna WURSTER
Edward O’BRIEN
Kelsey BARRASSO
Nicholas BEAUCHEMIN
Marin VULIĆ
Melissa MAYOL
Luo JIA
Kankana BARDHAN
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Seres Therapeutics Inc
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Seres Therapeutics Inc
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Priority to CN202480023173.7A priority Critical patent/CN121057584A/zh
Priority to AU2024215611A priority patent/AU2024215611A1/en
Publication of WO2024163529A2 publication Critical patent/WO2024163529A2/fr
Publication of WO2024163529A9 publication Critical patent/WO2024163529A9/fr
Publication of WO2024163529A3 publication Critical patent/WO2024163529A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C12N1/205—Bacterial isolates
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K2035/11—Medicinal preparations comprising living procariotic cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00—Microorganisms ; Processes using microorganisms
    • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales

Definitions

  • the present disclosure relates to bacterial compositions that are useful for the treatment of infection complications due to a wide-range of diseases or disorders (e.g., chronic liver disease, cancer neutropenia, and solid organ transplantation) in a subject (e.g., human subject). More specifically, the bacterial compositions provided herein have been designed to exhibit certain properties that are useful in reducing or preventing the risk of infection from certain microbial pathogens within the subject. As further described herein, through the treatment of such pathogens, the bacterial compositions provided herein can be useful in treating the wide-range of diseases or disorders described herein.
  • diseases or disorders e.g., chronic liver disease, cancer neutropenia, and solid organ transplantation
  • a subject e.g., human subject.
  • the bacterial compositions provided herein have been designed to exhibit certain properties that are useful in reducing or preventing the risk of infection from certain microbial pathogens within the subject.
  • the bacterial compositions provided herein can be useful in treating the wide-range of diseases or disorders described
  • Chronic liver disease is one of the frequent and leading causes of death, especially in the developing world.
  • CLD chronic liver disease
  • Many CLD patients are highly susceptible to bacterial infections, and many of the CLD-related deaths are directly associated with such bacterial infections.
  • SBP spontaneous bacterial peritonitis
  • BI bloodstream infection
  • Carriage of potentially pathogenic gastrointestinal micobes combines with increased intestinal permeability can result in translocation of these potential pathogens, leading to SBP and BSI.
  • This same phenomenon can drive bacterial infections in subjects suffering from other diseases and disorders associated with compromised immune function and/or febrile neutropenia ([e.g., solid-organ transplantation, chemotherapy for solid and hematological malignancy) and other conditions requiring acute care or prolonged care in the setting of the intensive care unit (see, e.g., Ford et al., Lancet 2(10): e438-44 (Oct. 2015); and Freedberg DE et al., Intensive Care Med 44(8) : 1203-1211 (Aug. 2018)).
  • compromised immune function and/or febrile neutropenia [e.g., solid-organ transplantation, chemotherapy for solid and hematological malignancy) and other conditions requiring acute care or prolonged care in the setting of the intensive care unit (see, e.g., Ford et al
  • a chronic liver disease for example, a chronic liver disease, a disease or disorder associated with a solid organ transplantation, or a neutropenia.
  • bacterial compositions are also provided.
  • the methods of treating a chronic liver disease in a subject in need thereof comprise administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cor
  • treating a chronic liver disease comprises (i) reducing or preventing an incidence of an infection in the subject, (ii) reducing or preventing a symptom of the chronic liver disease in the subject, or (iii) both (i) and (ii).
  • the chronic liver disease is caused by and/or associated with a toxin (e.g., prolonged alcohol and/or drug abuse), an infection, a metabolic disorder, an autoimmune disease, a genetic abnormality, or combinations thereof.
  • a toxin e.g., prolonged alcohol and/or drug abuse
  • the chronic liver disease is idiopathic.
  • the chronic liver disease comprises a cirrhosis, liver fibrosis, alcoholic liver disease, non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), hepatitis (including viral and alcoholic hepatitis), primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC), alpha-1 antitrypsin deficiency, hereditary hemochromatosis, Wilson's disease, autoimmune hepatitis (AIH), Budd-Chiari syndrome, and combinations thereof.
  • NAFLD non-alcoholic fatty liver disease
  • NASH non-alcoholic steatohepatitis
  • hepatitis including viral and alcoholic hepatitis
  • PBC primary biliary cirrhosis
  • PSC primary sclerosing cholangitis
  • alpha-1 antitrypsin deficiency hereditary hemochromatosis
  • Wilson's disease autoimmune hepatit
  • the chronic liver disease comprises fluid buildup in the belly (ascites), vomiting, gallstones, itching, jaundice, kidney failure, muscle loss, loss of appetite, bruising, spider-like veins in the skin, fatigue, weight loss, confusion, swelling in the legs (e.g., ankles), portal hypertension, hepatic encephalopathy, and combinations thereof.
  • the chronic liver disease comprises hepatic encephalopathy.
  • a method of treating a neutropenia in a subject in need thereof comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from Anaerotruncus colihominis. Blautia coccoides. Blautia hominis. Blautia obeum. Blautia w exlerae. Butyricicoccus sp2, Clostridium aldenense. Clostridium bolleae. Clostridium innocuum.
  • Clostridium scindens Clostridium symbiosum. Dorea longicalena. Eisenbergiella tayi, Emergencia limonensis. Erysipelatoclostridium ramosum. Eubacterium callanderi. Faecalicatena corlorla. Faecalicatena orolica. Flavonifractor plautii. Hungatella effluvii. Intestinimonas butyr iciproducens. Intestinimonas massiliensis. Lactonifactor longoviformis. Lawsonibacter sp7. Massilimaliae limonensis. Murimonas inteslini. Niameybacter sp1, Ruminococcaceae NG13 sp6, or Turicibacter sanguinis.
  • treating a neutropenia comprises (i) reducing or preventing an incidence of an infection in the subject, (ii) reducing or preventing a symptom of the neutropenia in the subject, or (iii) both (i) and (ii).
  • the neutropenia comprises a cancer neutropenia.
  • a method of treating a disease or disorder associated with a solid organ transplantation in a subject in need thereof comprising administering to the subject a composition comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum.
  • Blautia wexlerae, Butyricicoccus sp2 Clostridium aldenense, Clostridium bolleae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia limonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi. Faecalicatena corlorla, Faecalicatena orolica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyr iciproducens, Intestinimonas massiliensis.
  • Lactonifactor longoviformis Lawsonibacter sp7,Massilimaliae limonensis.
  • treating a disease or disorder associated with a solid organ transplantation comprises (i) reducing or preventing an incidence of an infection in the subject, (ii) reducing or preventing a symptom of the disease or disorder associated with a solid organ transplantation in the subject, or (iii) both (i) and (ii).
  • the solid organ transplantation comprises a liver transplantation.
  • the first species and/or the second species is selected from Clostridium innocuum, Clostridium bolleae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Emergencia timonensis. In some aspects, the plurality of bacteria further comprises Intestinimonas butyriciproducens. In some aspects, the plurality of bacteria further comprises Clostridium symbiosum. In some aspects, the plurality of bacteria further comprises Clostridium scindens. In some aspects, the plurality of bacteria further comprises Faecalicatena cortorta. In some aspects, the plurality of bacteria further comprises Lactonifactor longoviformis. In some aspects, the plurality of bacteria further comprises Massilimaliae timonensis. In some aspects, the plurality of bacteria further comprises Hungatella effluvii.
  • the plurality of bacteria further comprises Butyricicoccus sp2. In some aspects, the plurality of bacteria further comprises Intestinimonas massiliensis. In some aspects, the plurality of bacteria further comprises Niameybacter spl. In some aspects, the plurality of bacteria further comprises Turicibacter sanguinis. In some aspects, the plurality of bacteria further comprises RuminococcaceaeNG13 sp6. In some aspects, the plurality of bacteria further comprises Dorea longicatena. In some aspects, the plurality of bacteria further comprises Blautia obeum. In some aspects, the plurality of bacteria further comprises Lawsonibacter sp 7. In some aspects, the plurality of bacteria further comprises Blautia hominis. In some aspects, the plurality of bacteria further comprises Blautia wexlerae. In some aspects, the plurality of bacteria further comprises Eubacterium callanderi.
  • the plurality of bacteria comprises, consists essentially of, or consists of the following species of bacteria: (a) (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyriciprodiicens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens: (b) (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5)
  • the Anaerotruncus colihominis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;
  • the Blautia coccoides comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;
  • the Blautia hominis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at
  • the Anaerotruncus colihominis comprises the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81;
  • the Blautia coccoides comprises the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78;
  • the Blautia hominis comprises the 16S rDNA sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37;
  • the Blautia obeum comprises the 16S rDNA sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160
  • a method of treating a chronic liver disease in a subject in need thereof comprising administering to the subject a composition comprising a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species independently comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ
  • a method of treating a neutropenia in a subject in need thereof comprising administering to the subject a composition comprising a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species independently comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 158, SEQ ID NO:
  • a method of treating a disease or disorder associated with a solid organ transplantation in a subject in need thereof comprising administering to the subject a composition comprising a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species independently comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, S
  • a method of treating a disease or disorder associated with a solid organ transplantation in a subject in need thereof comprising administering to the subject a composition comprising a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species independently comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, S
  • the first species and/or the second species comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 5, SEQ ID NO:
  • the plurality of bacteria comprises each of the following: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105. In some aspects, the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in 17.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in 28. In some aspects, the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133. In some aspects, the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.
  • the plurality of bacteria comprises, consists essentially of, or consists of: (a) (1) the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65, (2) the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) the 16S
  • SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70 (3) the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, (6) the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, (7) the 16S rDNA sequence set forth in SEQ ID NO
  • a colonization of a pathogenic microorganism is reduced or prevented within the gastrointestinal tract of the subject.
  • an abundance of a pathogenic microorganism is reduced within the gastrointestinal tract of the subject.
  • the pathogenic microorganism comprises Enterococcus faecium (e.g., vancomycin-resistant), Enterococcus spp., Klebsiella pneumonia (e.g., carbapenem-resistant), E.
  • the plurality of bacteria further comprises an additional species of bacteria which has one or more features selected from:
  • a B vitamin e.g., thiamin (Bl) and/or pyridoxamine (B6)
  • coli pathogen carriage capable of reducing expression of claudin-2, (22) capable of being associated with the healthy human gut microbiota, (23) capable of not being associated with toxin and hemolysin genes associated with Clostridial pathogens and no significant cytopathic effects in vitro, (24) susceptible to multiple clinically relevant antibiotics, (25) capable of not being associated with genes that are both likely responsible for the observed antibiotic resistances and transmissible, (26) capable of inhibiting epithelial cell apoptosis, (27) capable of down-modulating one or more genes induced in IFN- ⁇ treated colonic organoids (e.g., those associated with inflammatory chemokine signaling, NF- ⁇ B signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th17 cell differentiation, Th1 differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation
  • each of the plurality of bacteria are capable of forming a spore. In some aspects, each of the plurality of bacteria are in a spore form. In some aspects, each of the plurality of bacteria are not vegetative cells.
  • the composition further comprises a pharmaceutically acceptable excipient. In some aspects, the composition is administered to the subject orally. In some aspects, the method further comprises administering an additional agent to the subject. In some aspects, the additional agent is administered concurrently or sequentially with the composition. In some aspects, the additional agent comprises a standard of care. In some aspects, the standard of care comprises lactulose, rifaximin, or both.
  • compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from Anaerotruncus colihominis, Blautia coccoides. Blautia hominis. Blautia obeum. Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolleae, Clostridium innocuum.
  • Clostridium scindens Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia limonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi. Faecalicatena corlorla, Faecalicatena orolica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyr iciproducens, Intestinimonas massiliensis. Lactonifactor longoviformis, Lawsonibacter sp7,Massilimaliae limonensis. Murimonas inleslini, Niameybacter spl, Ruminococcaceae NG13 sp6, or Turicibacter sanguinis.
  • compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are not the same, and wherein the first species and the second species are independently selected from Clostridium innocuum, Clostridium bolleae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, ox Eisenbergiella tayi.
  • the plurality of bacteria further comprises Emergencia timonensis.
  • the plurality of bacteria further comprises Intestinimonas butyr iciproducens, Clostridium symbiosum, Clostridium scindens, and/or Emergencia timonensis.
  • the plurality of bacteria further comprises Faecalicatena cortorta and/or Lactonifactor longoviformis .
  • the plurality of bacteria further comprises Massilimaliae limonensis. Hungatella effluvii. and/or Butyricicoccus sp2.
  • the plurality of bacteria further comprises Intestinimonas massiliensis. Niameybacter spi, and/or Turicibacter sanguinis. In some aspects, the plurality of bacteria further comprises Ruminococcaceae NG 13 sp6. In some aspects, the plurality of bacteria further comprises Dorea longicatena. In some aspects, the plurality of bacteria further comprises Blautia obeum. In some aspects, the plurality of bacteria further comprises Lawsonibacter sp7. In some aspects, the plurality of bacteria further comprises Blautia hominis. In some aspects, the plurality of bacteria further comprises Blautia wexlerae. In some aspects, the plurality of bacteria further comprises Eubacterium callanderi.
  • compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are not the same, and wherein the first species and the second species independently comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ
  • compositions comprising a plurality of bacteria, wherein the plurality of bacteria comprises a first species of bacteria and a second species of bacteria, wherein the first species and the second species are not the same, and wherein the first species and the second species are not the same, and wherein the first species and/or the second species comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 71, SEQ ID NO: 72,
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99.
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110, (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, and/or (d) a 16S rDNA sequence that has
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, and/or (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165.
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131, and/or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO:
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134, and/or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131, and/or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO:
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134, and/or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163.
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164.
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37; (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in any one of SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO:
  • the plurality of bacteria further comprises an additional species of bacteria which has one or more features selected from: (1) capable of engrafting (long-term and/or transient) when administered to a subject, (2) capable of having anti-inflammatory activity (e.g., inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro, ability to down-modulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)), (3) not capable of inducing pro-inflammatory activity, (4) capable of producing a secondary bile acid (e.g., 7 ⁇ -dehydroxylase and bile salt hydrolase activity), (5) capable of producing a tryptophan metabolite (e.g., indole, 3-methyl indole, indolepropionic acid), (6) capable of restoring and/or maintaining epithelial integrity (e.g., as determined by a primary epit
  • coli pathogen carriage capable of reducing expression of claudin-2, (22) capable of being associated with the healthy human gut microbiota, (23) capable of not being associated with toxin and hemolysin genes associated with Clostridial pathogens and no significant cytopathic effects in vitro, (24) susceptible to multiple clinically relevant antibiotics, (25) capable of not being associated with genes that are both likely responsible for the observed antibiotic resistances and transmissible, (26) capable of inhibiting epithelial cell apoptosis, (27) capable of down-modulating one or more genes induced in IFN- ⁇ treated colonic organoids (e.g., those associated with inflammatory chemokine signaling, NF-KB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th 17 cell differentiation, Thl differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation,
  • each of the plurality of bacteria are capable of forming a spore. In some aspects, each of the plurality of bacteria are in a spore form. In some aspects, the composition further comprises a pharmaceutically acceptable excipient.
  • FIG. 1 provides a table listing exemplary designed bacterial compositions described herein. SEQ ID NOs for the 16S sequences of the bacterial species present in the different designed bacterial compositions are provided. "0" indicates that the bacterial species is not included; “ 1” indicates that the bacterial species is included in the given bacterial composition. Bacterial species that are part of the strain core and R groups are also indicated.
  • FIGs. 2A-2I show the ability of different bacterial compositions to decolonize or reduce the abundance of vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Enterobacteriaceae (CRE) in a mouse model.
  • FIG. 2A provides a schematic of the experimental design. As shown, the animals were infected with either VRE or CRE and then treated with one of the following: (1) PBS, (2) DEI, (3) DE2, (4) DE3, (5) DE4, (6) DE5.1, (7) DE6, and (8) fecal microbial transplant (FMT). Naive animals (ie., no pathogen infection and no treatment) were used as control.
  • FIG. 1 vancomycin-resistant Enterococcus
  • CRE carbapenem-resistant Enterobacteriaceae
  • FIG. 2B provides a comparison of VRE titer over a course of 21 days post VRE challenge.
  • FIG. 2C provides a comparison of CRE titer over a course of 21 days post CRE challenge.
  • VRE titer and CRE titer are shown as colony-forming units (CFU)/g feces.
  • LOD refers to the limit of detection.
  • FIGs. 2D-2F show engraftment of different bacterial species present in DE2 (FIG. 2D), DE3 (FIG. 2E), and DE5.1 (FIG. 2F) after administration into mice infected with CRE.
  • FIGs. 2G-2I show engraftment of different bacterial species present in DE2 (FIG. 2G), DE3 (FIG. 2H), and DE5.1 (FIG. 21) after administration into mice infected with VRE.
  • FIGs. 3A-3C show the ability of different bacterial compositions to decolonize or reduce the abundance of three pathogens (i.e. , carbapenem-resistant Klebsiella pneumoniae, extended spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model.
  • pathogens i.e. , carbapenem-resistant Klebsiella pneumoniae, extended spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus
  • FIG. 3A provides a comparison of CRE titer over a course of 21 days post CRE challenge.
  • FIG. 3B provides a comparison of ESBL + E.
  • FIG. 3C provides a comparison of VRE titer over a course of 21 days post VRE challenge.
  • Pathogen titer is shown as colony-forming units (CFU)/g.
  • FIGs. 4A-4C show the ability of different bacterial compositions to decolonize or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coli) in an in vitro gut ecology model (iGEM).
  • Cr-Kpn (FIG. 4A), VRE (FIG. 4B), or Cr-E. coli (FIG. 4C) were added prior (day 4) to vancomycin pretreatment and Cr-Kpn (FIG. 4A) or VRE (FIG. 4B) were added (day 6) again during vancomycin pretreatment.
  • Test bacterial compositions (i.e., DE3, DE5.1, DE7, DE9, DE 10, DE2 or FMTFMT) were added over 7 days starting one day after the end of vancomycin treatment (day 10-16) (microbiome intervention). Pathogen load was measured by scoring CFUs (colony forming units) on pathogen-selective plates.
  • FIGs. 5A-5G5G show the ability of the DE2 bacterial composition to decolonize or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, vancomycin-resistant Enterococcus, and carbapenem-resistant Escherichia coll) in an in vitro gut ecology model (iGEM).
  • Cr-Kpn (FIG. 5A), VRE (FIG. 5B5B), or Cr-E. coli (FIG. 5C) were added prior (day 4) to vancomycin pretreatment and VRE (FIG. 5B5B) was added (day 6) again during vancomycin pretreatment.
  • Bacterial compositions DE2 was added over 5 days starting one day after the end of vancomycin treatment (day 10-14). Pathogen load was measured by scoring CFUs (colony forming units) on pathogen-selective plates.
  • FIG. 5G shows the ability of DE3 and DE5.2 bacterial compositions to reduce the abundance of Cr-E. coli compared to spore preparation and FMT in iGEM. Cr-E. coli was added prior (day 4) to vancomycin pretreatment. Bacterial compositions, spore preparation, and FMT were added over 5 days starting one day after the end of vancomycin treatment (day 10-14). Pathogen load was measured by scoring CFUs (colony forming units) on pathogen-selective plates.
  • FIGs. 6A-6B providesprovides the average concentration of secondary bile acid produced in culture for DE2, DE3, DE8, DE 10, DE9, DE7, and FCMA.BA.
  • FIG. 6A provides the average concentrations for the following bile acids: 12-ketolithocholic acid, 3 -oxocholic acid, cholic acid, deoxycholic acid, glycocholic acid, ketodeoxychlic acid like, taurocholic acid, and ursocholic acid.
  • FIG. 6B provides the average concentrations for the following bile acids: 3- oxochenodeoxycholic acid, chenodeoxycholic acid, glycochendeoxycholic acid, isolithocholic acid, lithocholic acid, taurochendeoxycjolic acid, ursodeoxycholic acid, and z-ketolithocholic acid- like 3.
  • FIGs. 7A-7B show the effects of DE5.2 (FIG. 7A) and DE11 (FIG. 7B) on carbapenem-resistant Klebsiella pneumonia (Cr-Kpn) decolonization in a mouse model.
  • Cr-Kpn carbapenem-resistant Klebsiella pneumonia
  • FIGs. 8A-8B show the effects of DE5.2 (FIG. 8A) and DE11 (FIG. 8B) on vancomycin-resistant Enterococcus (VRE) decolonization.
  • VRE vancomycin-resistant Enterococcus
  • FIG. 9 shows a schematic of and in vitro IFN-y induced epithelial barrier damage assay using ALTIS REPLIGUT® System.
  • FIGs. 10A-10B show thethe effect of the following bacterial compositions to protect against IFN- ⁇ induced barrier damage: DE3, DE5.2 , DE9, DE10, and DE2.
  • Relative fluorescent units (RFU) were measured. The effect is shown as relative fluorescent units (RFU) of lucifer yellow fluorescence for IFN-y alone compared to the DE culture supernatants tested.
  • FIGs. 11A-11 show the ability of bacterial spore preparation to decolonize or reduce the abundance of three pathogens (i.e., carbapenem-resistant Klebsiella pneumoniae, extended spectrum beta-lactamase+ Escherichia coli, and vancomycin-resistant Enterococcus) in a mouse model. After pathogen challenge, the mice were treated with one of the following: (1) PBS, (2) bacterial spore preparation.
  • FIG. 11A provides a comparison of CRE titer over a course of 21 days post CRE challenge.
  • FIG. 11B provides a comparison of ESBL + E. coli (EC) titer over a course of 21 days post EC challenge.
  • FIG. 11C provides a comparison of VRE titer over a course of 21 days post VRE challenge.
  • Pathogen titer is shown as colony-forming units (CFU)/g feces
  • a disease or disorder e.g., treating an infection complication due to chronic liver disease, cancer neutropenia, and/or a disease or disorder associated with solid organ transplantation
  • a bacterial composition that have been specifically designed to comprise certain plurality of commensal bacteria.
  • the plurality of commensal bacteria exhibit certain properties (e.g., those disclosed herein) that are useful in reducing or preventing the colonization (i.e. , promoting decolonization) and/or reducing the abundance of certain microbial pathogens within the gastrointestinal tract of the subject. Additional aspects are provided throughout the present disclosure.
  • a or “an” entity refers to one or more of that entity; for example, "a bacterial composition,” is understood to represent one or more bacterial compositions.
  • a bacterial composition is understood to represent one or more bacterial compositions.
  • the terms “a” (or “an”), “one or more,” and “at least one” can be used interchangeably herein.
  • the term "at least" prior to a number or series of numbers is understood to include the number adjacent to the term “at least,” and all subsequent numbers or integers that could logically be included, as clear from context.
  • the number of nucleotides in a nucleic acid molecule must be an integer.
  • "at least 18 nucleotides of a 21-nucleotide nucleic acid molecule” means that 18, 19, 20, or 21 nucleotides have the indicated property.
  • At least is present before a series of numbers or a range, it is understood that “at least” can modify each of the numbers in the series or range.
  • “At least” is also not limited to integers (e.g., "at least 5%” includes 5.0%, 5.1%, 5.18% without consideration of the number of significant figures.
  • the term “approximately” or “about” is applied herein to a particular value, the value without the term “approximately” or “about is also disclosed herein.
  • any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
  • treating refers to any type of intervention or process performed on, or administering an active agent (e.g., any of the bacterial compositions provided herein) to a subject with the objective of reversing, alleviating, ameliorating, inhibiting, preventing, or slowing down the progression, development, severity or recurrence of a symptom, complication, condition or biochemical indicia associated with a disease or condition described herein (e.g., chronic liver disease, neutropenia, and/or disease or disorder associated with a solid organ transplantation).
  • an active agent e.g., any of the bacterial compositions provided herein
  • treating comprises reducing or preventing an incidence of an infection in a subject suffering from the disease or disorder.
  • any of the bacterial compositions provided herein can help prevent the incidence of an infection in a subject suffering from a disease or disorder provided herein.
  • a bacterial composition provided herein can help treat the disease or disorder in the subject.
  • microbiota refers to the ecological community of microorganisms that occur (sustainably or transiently) in and on an animal subject, typically a mammal such as a human, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses ie., phage).
  • microbiome refers to the genetic content of the communities of microbes that live in and on the human body, both sustainably and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e. , phage)), wherein "genetic content” includes genomic DNA, RNA such as ribosomal RNA, the epigenome, plasmids, and all other types of genetic information.
  • ecological niche refers to the ecological space in which an organism or group of organisms occupies.
  • Niche describes how an organism or population or organisms responds to the distribution of resources, physical parameters (e.g., host tissue space) and competitors (e.g., by growing when resources are abundant, and when predators, parasites and pathogens are scarce) and how it in turn alters those same factors (e.g., limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey).
  • the term "dysbiosis” refers to a state of the microbiota of the GI tract or other body area in a subject, including mucosal or skin surfaces in which the normal diversity and/or function of the ecological network is disrupted. This unhealthy state can be due to a decrease in diversity, the overgrowth of one or more pathogens or pathobionts, symbiotic organisms able to cause disease only when certain genetic and/or environmental conditions are present in a subject, or the shift to an ecological microbial network that no longer provides an essential function to the host subject, and therefore no longer promotes health.
  • a disease or disorder that can be treated with the present disclosure can be associated with a dysbiosis.
  • the term "operational taxonomic units" or "OTU” refers to a terminal leaf in a phylogenetic tree and is defined by a nucleic acid sequence, e.g., the entire genome, or a specific genetic sequence, and all sequences that share sequence identity to this nucleic acid sequence at the level of species.
  • the specific genetic sequence can be the 16S rDNA sequence or a portion of the 16S rDNA sequence.
  • the entire genomes of two entities are sequenced and compared.
  • select regions such as multilocus sequence tags (MLST), specific genes, or sets of genes can be genetically compared.
  • OTUs are frequently defined by comparing sequences between organisms. Generally, sequences with less than 95% sequence identity are not considered to form part of the same OTU.
  • an OTU is characterized by a combination of nucleotide markers, genes, and/or single nucleotide variants (SNVs).
  • the referenced genes are highly conserved genes (e.g., "house-keeping" genes).
  • the features defining an OTU can be a combination of the foregoing. Such characterization employs, e.g., WGS data or a whole genome sequence. Where the OTUs are the same, the OTUs will generally share common functial features.
  • phylogenetic tree refers to a graphical representation of the evolutionary relationships of one genetic sequence to another that is generated using a defined set of phylogenetic reconstruction algorithms (e.g., parsimony, maximum likelihood, or Bayesian). Nodes in the tree represent distinct ancestral sequences and the confidence of any node is provided by a bootstrap or Bayesian posterior probability, which measures branch uncertainty.
  • phylogenetic reconstruction algorithms e.g., parsimony, maximum likelihood, or Bayesian
  • the terms "subject,” “individual,” and “patient” can be used interchangeably and refer to any animal subject including humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs, turkeys, and chickens), and household pets (e.g., dogs, cats, and rodents).
  • laboratory animals e.g., primates, rats, mice
  • livestock e.g., cows, sheep, goats, pigs, turkeys, and chickens
  • household pets e.g., dogs, cats, and rodents.
  • the "colonization" of a host organism includes the non-transitory residence of a bacterium or other microscopic organism.
  • the host is generally referred to herein as a "subject", typically a human or other mammal.
  • "reducing colonization” or “inhibiting colonization” of a host subject's gastrointestinal tract (or any other microbiotal niche) by a pathogenic bacterium includes a reduction in the residence time of the pathogen in the gastrointestinal tract as well as a reduction in the number (or concentration) of the pathogen in the gastrointestinal tract or adhered to the luminal surface of the gastrointestinal tract. Measuring reductions of adherent pathogens can be demonstrated, e.g., by a biopsy sample, or reductions can be measured indirectly, e.g., by measuring the pathogenic burden in the stool of a mammalian host.
  • inhibitor comprises both complete inhibition and partial inhibition.
  • the term "plurality of bacteria” refer to a combination of two or more bacteria.
  • a “combination" of two or more bacteria includes the physical co-existence of the two bacteria, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the two bacteria.
  • nucleic acids the term “substantial homology” indicates that two nucleic acids, or designated sequences thereof, when optimally aligned and compared, are identical, with appropriate nucleotide insertions or deletions, in at least about 80% of the nucleotides, at least about 90% to 95%, or at least about 98% to 99.5% of the nucleotides.
  • two nucleic acids e.g., 16S rDNA sequences
  • two nucleic acids share substantial homology if they have a sequence identity of at least about 95%, at least about 95.5%, at least about 96%, at least about 96.5%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, or at least about 99.9%.
  • bacteria which share substantial homology in their 16S rDNA sequence can be considered to be the same species.
  • bacteria that are the same species share one or more functional properties (e.g., described herein).
  • substantial homology exists when the segments will hybridize under selective hybridization conditions, to the complement of the strand.
  • substantial homology indicates that two polypeptides, or designated sequences thereof, when optimally aligned and compared, are identical, with appropriate amino acid insertions or deletions, in at least about 80% of the amino acids, at least about 90% to 95%, or at least about 98% to 99.5% of the amino acids.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm, as described in the non-limiting examples below.
  • the percent identity between two nucleotide sequences can be determined using the GAP program in the GCG software package (available at worldwideweb.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide or amino acid sequences can also be determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4: 11-17 (1989)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • the percent identity between two amino acid sequences can be determined using the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at worldwideweb.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • nucleic acid and protein sequences described herein can further be used as a "query sequence" to perform a search against public databases to, for example, identify related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
  • Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402.
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • XBLAST and NBLAST can be used. See worldwideweb.ncbi.nlm.nih.gov. Other methods of determining identity that are known in the art can be used.
  • compositions comprising a plurality of bacteria (“bacterial compositions”), including one or more OTUs or species of bacteria, that are useful for treating and/or preventing a wide-range of diseases and disorders (e.g., those described herein).
  • the plurality of bacteria can comprise any suitable bacteria that are useful for treating and/or preventing the diseases and disorders described herein.
  • the plurality of bacteria comprises bacteria directly derived from feces of healthy humans or bacteria fermented from culture (“cultured bacteria”), including a biologically pure culture.
  • cultured bacteria bacteria directly derived from feces
  • bacteria or equivalent thereof of a healthy human subject refers to bacteria that have not been cultured.
  • a bacterial composition provided herein comprises a plurality of bacteria, wherein each of the plurality of bacteria is directly derived from human feces (e.g., of a healthy human subject).
  • a bacterial composition provided herein comprises a plurality of bacteria, wherein each of the plurality of bacteria has been cultured.
  • the plurality of bacteria comprises a mixture of bacteria directly derived from feces of a healthy human subject and cultured bacteria.
  • a plurality of bacteria useful for the present disclosure comprises spores, vegetative cells, or both.
  • a bacterial composition provided herein comprises a plurality of bacteria, wherein one or more of the plurality of bacteria are in a spore form.
  • a bacterial composition provided herein comprises a plurality of bacteria, wherein each of the plurality of bacteria are in a spore form. In some aspects, such a bacterial composition does not comprise any vegetative cells.
  • a bacterial composition provided herein comprises a pluraity of bacteria, wherein one or more of the plurality of bacteria are in a vegetative form.
  • a bacterial composition provided comprises a plurality of bacteria, wherein one or more of the plurality of bacteria are in a spore form and one or more of the plurality of bacteria are in a vegetative form.
  • Non-limiting examples of bacteria that are useful for the present disclosure include those that exhibit one or more of the following features: one or more features selected from: (1) capable of engrafting (long-term and/or transient) when administered to a subject, (2) capable of having anti-inflammatory activity (e.g., inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro, ability to down-modulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1)), (3) not capable of inducing pro-inflammatory activity, (4) capable of producing a secondary bile acid (e.g., 7a-dehydroxylase and bile salt hydrolase activity), (5) capable of producing a tryptophan metabolite (e.g., indole, 3-methyl indole, indolepropionic acid), (6) capable of restoring and/or maintaining epithelial integrity (e.g., as determined by a primary epithelial cell
  • coli pathogen carriage capable of reducing expression of claudin-2, (22) capable of being associated with the healthy human gut microbiota, (23) capable of not being associated with toxin and hemolysin genes associated with Clostridial pathogens and no significant cytopathic effects in vitro, (24) susceptible to multiple clinically relevant antibiotics, (25) capable of not being associated with genes that are both likely responsible for the observed antibiotic resistances and transmissible, (26) capable of inhibiting epithelial cell apoptosis, (27) capable of down-modulating one or more genes induced in IFN- ⁇ treated colonic organoids (e.g., those associated with inflammatory chemokine signaling, NF-KB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th 17 cell differentiation, Thl differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation,
  • a bacterial composition provided herein comprises a pluralilty of bacteria which exhibit one, two, three, four, five, six, seven, eight, nine, 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, or all of the features described above.
  • the plurality of bacteria exhibits one of the features provided above. In some aspects, the plurality of bacteria exhibits two of the features provided above. In some aspects, the plurality of bacteria exhibits three of the features provided above. In some aspects, the plurality of bacteria exhibits three of the features provided above. In some aspects, the plurality of bacteria exhibits four of the features provided above. In some aspects, the plurality of bacteria exhibits five of the features provided above. In some aspects, the plurality of bacteria exhibits six of the features provided above. In some aspects, the plurality of bacteria exhibits seven of the features provided above. In some aspects, the plurality of bacteria exhibits eight of the features provided above. In some aspects, the plurality of bacteria exhibits nine of the features provided above.
  • the plurality of bacteria exhibits 10 of the features provided above. In some aspects, the plurality of bacteria exhibits 11 of the features provided above. In some aspects, the plurality of bacteria exhibits 12 of the features provided above. In some aspects, the plurality of bacteria exhibits 13 of the features provided above. In some aspects, the plurality of bacteria exhibits 14 of the features provided above. In some aspects, the plurality of bacteria exhibits 15 of the features provided above. In some aspects, the plurality of bacteria exhibits 16 of the features provided above. In some aspects, the plurality of bacteria exhibits 17 of the features provided above. In some aspects, the plurality of bacteria exhibits 18 of the features provided above. In some aspects, the plurality of bacteria exhibits 19 of the features provided above.
  • the plurality of bacteria exhibits 20 of the features provided above. In some aspects, the plurality of bacteria exhibits 21 of the features provided above. In some aspects, the plurality of bacteria exhibits 22 of the features provided above. In some aspects, the plurality of bacteria exhibits 23 of the features provided above. In some aspects, the plurality of bacteria exhibits 24 of the features provided above. In some aspects, the plurality of bacteria exhibits 25 of the features provided above. In some aspects, the plurality of bacteria exhibits 26 of the features provided above. In some aspects, the plurality of bacteria exhibits 27 of the features provided above. In some aspects, the plurality of bacteria exhibits 28 of the features provided above. In some aspects, the plurality of bacteria exhibits 29 of the features provided above.
  • the plurality of bacteria exhibits 30 of the features provided above. In some aspects, the plurality of bacteria exhibits 31 of the features provided above. In some aspects, the plurality of bacteria exhibits 32 of the features provided above. In some aspects, the plurality of bacteria exhibits 33 of the features provided above. In some aspects, the plurality of bacteria exhibits 34 of the features provided above. In some aspects, the plurality of bacteria exhibits 35 of the features provided above. In some aspects, the plurality of bacteria exhibits 36 of the features provided above. In some aspects, the plurality of bacteria exhibits 37 of the features provided above. In some aspects, the plurality of bacteria exhibits 38 of the features provided above. In some aspects, the plurality of bacteria exhibits 39 of the features provided above.
  • the plurality of bacteria exhibits 40 of the features provided above. In some aspects, the plurality of bacteria exhibits 41 of the features provided above. In some aspects, the plurality of bacteria exhibits 42 of the features provided above. In some aspects, the plurality of bacteria exhibits 43 of the features provided above. In some aspects, the plurality of bacteria exhibits 44 of the features provided above. In some aspects, the plurality of bacteria exhibits 45 of the features provided above. In some aspects, the plurality of bacteria exhibits 46 of the features provided above. In some aspects, the plurality of bacteria exhibits 47 of the features provided above. In some aspects, the plurality of bacteria exhibits 48 of the features provided above. In some aspects, the plurality of bacteria exhibits 49 of the features provided above.
  • the plurality of bacteria exhibits 50 of the features provided above. In some aspects, the plurality of bacteria exhibits all of the features provided above.
  • Bacterial compositions that have been constructed to specifically exhibit one or more of the features described above are also referred to herein as "designed composition" (DE) (or variants thereof).
  • designed compositions are provided in FIG. 1. Compositions were designed with a set of core strains (i.e., strain core) and R-group supplements to optimize functions.
  • the plurality of bacteria were derived from cultivated consortia. In some aspects, the plurality of bacteria were dervied donor-derived spore-preparations.
  • the plurality of bacteria comprises a species of bacteria (also referred to herein as "bacterial species") that is capable of engrafting when administered to a subject.
  • the plurality of bacteria comprises a bacterial species that is capable of long-term engraftment when administered to a subject ("long-term engrafter”).
  • the plurality of bacteria comprises a bacterial species that is capable of transient engraftment when administered to a subject ("transient engrafter”).
  • the plurality of bacteria comprises both a long-term engrafter and a transient engrafter.
  • the plurality of bacteria comprises a species of bacteria that is capable of having an anti-inflammatory activity.
  • anti-inflammatory activities include: (a) inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro, (b) ability to down-modulate expression of inflammatory genes (e.g., CXCL1, CXCL2, CXCL3, CXCL11, ICAM1), or (c) both (a) and (b).
  • the plurality of bacteria comprises a bacterial species that is capable of inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro.
  • the plurality of bacteria comprises a bacterial species that is capable of down-modulating the expression of one or more inflammatory genes. In some aspects, the plurality of bacteria comprises both a bacterial species that is capable of inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro and a bacterial species that is capable of down-modulating the expression of one or more inflammatory genes. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of both inhibiting TNF- ⁇ -driven IL-8 secretion in epithelial cells in vitro and down-modulating the expression of one or more inflammatory genes. In some aspects, the plurality of bacteria comprises a bacterial species that is not capable of inducing pro- inflammatory activity.
  • the plurality of bacteria comprises a species of bacteria that is capable of producing a metabolite that is useful in treating a disease or disorder described herein.
  • the plurality of bacteria comprises a bacterial species that is capable of producing a secondary bile acid.
  • secondary bile acids include 7a- dehydroxylase and bile salt hydrolase activity.
  • the plurality of bacteria comprises a bacterial species that is capable of producing a tryptophan metabolite.
  • tryptophan metabolites include: indole, 3-methyl indole, and indolepropionic acid.
  • the plurality of bacteria comprises a bacterial species that is capable of producing a short-chain fatty acid.
  • short-chain fatty acids include butyrate and propionate.
  • the plurality of bacteria comprises a bacterial species that is capable of producing a medium-chain fatty acid.
  • medium-chain fatty acids include valerate and hexanoate.
  • the plurality of bacteria comprises a bacterial species is capable of producing a B vitamin.
  • B vitamins include: thiamin (Bl) and pyridoxamine (B6).
  • a bacterial composition useful for the present disclosure comprises a plurality of bacteria, wherein the plurality of bacteria comprises one or more species of bacteria that are capable of producing: (a) a secondary bile acid, (b) a tryptophan metabolite, (c) a short-chain fatty acid, (d) a medium-chain fatty acid, (e) a B vitamin, or (f) any combination of (a) to (e).
  • the plurality of bacteria comprises a bacterial species that is capable of restoring and/or maintaining epithelial integrity, e.g., as determined by a primary epithelial cell monolayer barrier integrity assay. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of inhibiting a HDAC activity. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of expressing catalase activity. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of having alpha- fucosidase activity. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of reducing fecal calprotectin level.
  • the plurality of bacteria comprises a bacterial species that is not capable of activating a toll-like receptor pathway (e.g., TLR4 or TLR5). In some aspects, the plurality of bacteria comprises a bacterial species that is capable of activating a toll-like receptor pathway (e.g., TLR2). In some aspects, the plurality of bacteria comprises a bacterial species that is capable of restoring colonization resistance. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of a broad range of carbon source utilization. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of reducing VRE pathogen carriage.
  • the plurality of bacteria comprises a bacterial species that is capable of reducing CRE (e.g., carbapenem-resistant Klebsiella pneumonia) pathogen carriage.
  • the plurality of bacteria comprises a bacteria species that is capable of reducing E. coli (e.g., carbapenem-resistant Escherichia coli) pathogen clearance.
  • the plurality of bacteria comprises a bacterial species that is capable of reducing expression of claudin-2.
  • the plurality of bacteria comprises a bacterial species that is capable of being associated with the healthy human gut microbiota.
  • the plurality of bacteria comprises a bacterial species that is associated with reduced abundance in patients with a liver disease (e.g., cirrhosis). In some aspects, the plurality of bacteria comprises a bacterial species that is capable of not being associated with toxin and hemolysin genes associated with Clostridial pathogens and no significant cytopathic effects in vitro. In some aspects, the plurality of bacteria comprises a bacterial species that is susceptible to multiple clinically relevant antibiotics. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of not being associated with genes that are both likely responsible for the observed antibiotic resistances and transmissible.
  • a liver disease e.g., cirrhosis
  • the plurality of bacteria comprises a bacterial species that is capable of not being associated with toxin and hemolysin genes associated with Clostridial pathogens and no significant cytopathic effects in vitro. In some aspects, the plurality of bacteria comprises a bacterial species that is susceptible to multiple clinically relevant antibiotics. In some aspects
  • the plurality of bacteria comprises a bacterial species that is capable of inhibiting epithelial cell apoptosis. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of down-modulating one or more genes induced in IFN- ⁇ treated colonic organoids.
  • Non-limiting examples of such genes include: those associated with inflammatory chemokine signaling, NF-KB signaling, TNF family signaling, type I interferon signaling, type II interferon signaling, TLR signaling, lymphocyte trafficking, Th 17 cell differentiation, Thl differentiation, Th2 differentiation, apoptosis, inflammasomes, autophagy, oxidative stress, MHC class I and II antigen presentation, complement, mTor, nod-like receptor signaling, PI3K signaling, or combinations thereof.
  • the plurality of bacteria comprises a bacterial species that is capable of reducing the expression of one or more inhibitory receptors on CD8+ T cells.
  • Non-limiting examples of inhibitor receptors include: TIGIT, TIM-3, and LAG-3.
  • the plurality of bacteria comprises a bacterial species that is capable of increasing expression of one or more genes/proteins associated with CD8+ T cell activation and/or function.
  • genes include: CD45RO, CD69, IL-24, TNF- ⁇ , perforin, and IFN- ⁇ .
  • the plurality of bacteria are capable of enhacing and/or improving the tolerance of chemotherapeutic agents (e.g., such as those that can cause and/or be associated with neutropenia).
  • chemotherapeutic agents e.g., such as those that can cause and/or be associated with neutropenia.
  • the plurality of bacteria comprises a bacterial species that is capable of inducing an anti-inflammatory IL-10-skewed IL-10/IL-6 cytokine ratio in macrophages. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of inducing less inflammatory responses but similar pathogen defense responses in macrophages than a donor-derived spore-based composition (i.e., a spore-based composition). In some aspects, the plurality of bacteria comprises a bacterial species that is capable of increasing the amount of anti-inflammatory mediators. Non-limiting examples of such anti- inflammatory mediators include: IL-1 receptor antagonists (IL-IRA), IL-4, IL-10, IL-11, IL-13, and TGF-p.
  • IL-1 receptor antagonists IL-IRA
  • IL-4 IL-4
  • IL-10 IL-11
  • IL-13 TGF-p.
  • the plurality of bacteria comprises a bacterial species that is capable of reducing colonic inflammation. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of treating and/or preventing a disease or disorder, such as those associated with dysbiosis of a gastrointestinal tract. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of increasing the diversity of the gastrointestinal microbiome in a subject. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of improving mucosal and/or epithelial barrier integrity in a subject compared to a reference control (e.g., untreated patients or the subject prior to treatment).
  • a reference control e.g., untreated patients or the subject prior to treatment.
  • the plurality of bacteria comprises a bacterial species that is capable of promoting mucosal healing. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of reducing incidence of infection. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of reducing the need for antibiotics in a subject. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of reducing the abundance of a biomarker of infection in the stool of a subject. In some aspects, the plurality of bacteria comprises a bacterial species that is capable of increasing the abundance of a biomarker of an administered species in the stool of a subject.
  • the plurality of bacteria comprises a bacterial species that is capable of targeted delivery of most (e.g., 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% of the administered species relative to the number of colony forming units administered) or all of the administered species to the intestines of the subject.
  • the plurality of bacteria comprises a bacterial species that is capable of a therapeutic benefit following a single administration of a composition or pharmaceutical composition described herein to a subject.
  • the plurality of bacteria comprises a bacterial species that is capable of coadministration with an additional agent described herein, without substantially decreasing the therapeutic benefit of the administered species.
  • the plurality of bacteria comprises a bacterial species that is capable of coadministration with a carrier or excipient described herein, without substantially decreasing the therapeutic benefit of the administered species.
  • the plurality of bacteria comprises a bacterial species that is capable of lactulose utilization.
  • the plurality of bacteria comprises a bacterial species that comprise a lantibiotic operon. It will be apparent to those skilled in the arts that a bacterial species that comprises a lantibiotic operton could be capable of producing lantibiotic. Accordingly, in some aspects, the plurality of bacteria comprises a bacterial species that is capable of producing lantibiotic.
  • a bacterial composition useful for the present disclosure comprises a plurality of bacteria, wherein the plurality of bacteria comprise a first species of bacteria and a second species of bacteria, and wherein the first species and the second species are not the same.
  • the first species of bacteria is selected from the following bacterial species: Anaerotruncus colihominis, Blautia coccoides (also referred to herein as “Blautia pseudococcoides”), Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2 (also referred to herein as "Intestinibacillus massiliensis”), Clostridium aldenense (also referred to herein as "Enterocloster aldenensis”), Clostridium bolteae (also referred to herein as " Enter ocloster bolteae”).
  • the second species of bacteria is selected from the following bacterial species: Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyr iciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis,
  • both the first species and the second species are selected from: Anaerotruncus colihominis, Blautia coccoides, Blautia hominis, Blautia obeum, Blautia wexlerae, Butyricicoccus sp2, Clostridium aldenense, Clostridium bolteae, Clostridium innocuum, Clostridium scindens, Clostridium symbiosum, Dorea longicatena, Eisenbergiella tayi, Emergencia timonensis, Erysipelatoclostridium ramosum, Eubacterium callanderi, Faecalicatena cortorta, Faecalicatena orotica, Flavonifractor plautii, Hungatella effluvii, Intestinimonas butyr iciproducens, Intestinimonas massiliensis, Lactonifactor longoviformis, Lawson
  • a bacterial composition provided herein comprises a plurality of bacteria, wherein the plurality of bacteria comprises one or more of the following: Clostridium innocuum, Clostridium bolleae. Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas inleslini. Erysipelatoclostridium ramosum, Faecalicatena orolica. Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Emergencia timonensis.
  • a bacterial composition useful for the present disclosure comprises a plurality of bacteria, which comprise Emergencia timonensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Emergencia timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Intestinimonas butyr iciproducens, Clostridium symbiosum, Clostridium scindens, or Emergencia timonensis.
  • the plurality of bacteria comprises Intestinimonas butyr iciproducens, Clostridium symbiosum, Clostridium scindens, or Emergencia timonensis and one or more of the following: Intestinimonas butyr iciproducens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, ox Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Intestinimonas butyr iciproducens, Clostridium symbiosum, Clostridium scindens, Emergencia timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi .
  • a bacterial composition comprises a plurality of bacteria, which comprises Intestinimonas butyriciproducens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Intestinimonas butyriciproducens, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Clostridium symbiosum.
  • the plurality of bacteria comprises Clostridium symbiosum and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Clostridium symbiosum, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Clostridium scindens.
  • the plurality of bacteria comprises Clostridium scindens and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, o Eisenbergiella tayi.
  • the plurality of bacteria comprise each of the following: Clostridium scindens, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi
  • the plurality of bacteria further comprises Faecalicatena cortortaox Lactonifactor longoviformis.
  • the plurality of bacteria comprises Faecalicatena cortorta or Lactonifactor longoviformis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifr actor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Faecalicatena cortorta, Lactonifactor longoviformis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Faecalicatena cortorta.
  • the plurality of bacteria can comprise Faecalicatena cortorta and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Faecalicatena cortorta, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Lactonifactor longoviformis.
  • the plurality of bacteria comprises Lactonifactor longoviformis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Lactonifactor longoviformis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria further comprises Massilimaliae timonensis, Hungatella effluvii, or Butyricicoccus sp2.
  • the plurality of bacteria comprises Massilimaliae timonensis, Hungatella effluvii, or Butyricicoccus sp2 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, ox Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Massilimaliae timonensis, Hungatella effluvii, Butyricicoccus sp2, Clostridium innocuum, Clostridium bolteae, Flavonifr actor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria further comprises Massilimaliae timonensis.
  • the plurality of bacteria comprises Massilimaliae timonensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Massilimaliae timonensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Hungatella effluvii.
  • the plurality of bacteria comprises Hungatella effluvii and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Hungatella effluvii, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, o Eisenbergiella tayi.
  • the plurality of bacteria further comprises Butyricicoccus sp2.
  • the plurality of bacteria comprises Butyricicoccus sp2 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Butyricicoccus sp2, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi. [0101] In some aspects, the plurality of bacteria further comprises Intestinimonas massiliensis, Niameybacter spl, or Turicibacter sanguinis.
  • the plurality of bacteria comprises Intestinimonas massiliensis, Niameybacter spl, or Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifr actor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Intestinimonas massiliensis, Niameybacter spl, Turicibacter sanguinis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Intestinimonas massiliensis.
  • the plurality of bacteria comprises Intestinimonas massiliensis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Intestinimonas massiliensis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Niameybacter spl.
  • the plurality of bacteria comprises Niameybacter spl and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Niameybacter spl, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Turicibacter sanguinis.
  • the plurality of bacteria comprises Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Turicibacter sanguinis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Ruminococcaceae NG 13 sp6.
  • the plurality of bacteria comprises Ruminococcaceae NG13 sp6 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Ruminococcaceae NG 13 sp6, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Dorea longicatena.
  • the plurality of bacteria comprises Dorea longicatena and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Dorea longicatena, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Blautia obeum.
  • the plurality of bacteria comprises Blautia obeum and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Blautia obeum, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Lawsonibacter sp7.
  • the plurality of bacteria comprises Lawsonibacter sp7 and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifr actor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Lawsonibacter sp7, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Blautia hominis.
  • the plurality of bacteria comprises Blautia hominis and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Blautia hominis, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Blautia wexlerae.
  • the plurality of bacteria comprises Blautia wexlerae and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Blautia wexlerae, Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria further comprises Eubacterium callanderi.
  • the plurality of bacteria comprises Eubacterium callanderi and one or more of the following: Clostridium innocuum, Clostridium bolteae, Flavonifractor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, or Eisenbergiella tayi.
  • the plurality of bacteria comprises each of the following: Eubacterium callanderi.
  • Clostridium innocuum Clostridium bolteae, Flavonifr actor plautii, Blautia coccoides, Anaerotruncus colihominis, Murimonas intestini, Erysipelatoclostridium ramosum, Faecalicatena orotica, Clostridium aldenense, and Eisenbergiella tayi.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyr iciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyr iciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Intestinimonas butyr iciproducens, (12) Eisenbergiella tayi, (13) Clostridium symbiosum, and (14) Clostridium scindens.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolleae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas inleslini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas bulyriciprodiicens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, and (14) Emergencia timonensis.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolleae. (3) Flavonifr actor plautii. (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 sp6.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG13 sp6.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, and (17) Ruminococcaceae NG 13 sp6.
  • the plurality of bacteria comprises (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, and (19) Butyricicoccus sp2.
  • the plurality of bacteria consists essentially of (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orolica, (9) Clostridium aldenense, (10) Intestinimonas butyr iciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia limonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae limonensis. (18) Hungatella effluvii, and (19) Butyricicoccus sp2.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2, (20
  • Flavonifractor plautii (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Massilimaliae timonensis, (18) Hungatella effluvii, (19) Butyricicoccus sp2 , (20) Intestinimonas massiliensis. (21) Niamey bacler spl, and (22) Turicibacter
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolleae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas inleslini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolleae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Dorea longicatena, and (13) Blautia obeum.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter sp7.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter sp7.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium sym biosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Blautia obeum, and (16) Lawsonibacter sp7.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifr actor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG 13 sp6, (18) Blautia obeum, and (19) Lawsonibacter sp7.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyr iciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter sp
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyr iciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Ruminococcaceae NG13 sp6, (18) Blautia obeum, and (19) Lawsonibacter sp7.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyr iciproducens. (11) Eisenbergiella tayi, (12) Clostridium symbiosum, and (13) Emergencia timonensis.
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter spl, and (19) Turicibacter sanguinis.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter spl, and (19) Turicibacter sanguinis.
  • the plurality of bacteria consists of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia coccoides, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Clostridium aldenense, (10) Intestinimonas butyriciproducens, (11) Eisenbergiella tayi, (12) Clostridium symbiosum, (13) Clostridium scindens, (14) Emergencia timonensis, (15) Faecalicatena cortorta, (16) Lactonifactor longoviformis, (17) Intestinimonas massiliensis, (18) Niameybacter spl, and (19) Turicibacter sanguinis .
  • the plurality of bacteria comprises: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orotica, (9) Emergencia timonensis, (10) Clostridium aldenense, (11) Eisenbergiella tayi, (12) Clostridium scindens, (13) Dorea longicatena, ( 14) Blautia obeum, (15) Blautia wexlerae, and (16) Eubacterium callanderi.
  • the plurality of bacteria consists essentially of: (1) Clostridium innocuum, (2) Clostridium bolteae, (3) Flavonifractor plautii, (A) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas intestini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orolica, (9) Emergencia limonensis, (10) Clostridium aldenense.
  • the plurality of bacteria consists of: (1) Clostridium innocuum. (2) Clostridium bolleae, (3) Flavonifractor plautii, (4) Blautia hominis, (5) Anaerotruncus colihominis, (6) Murimonas inleslini, (7) Erysipelatoclostridium ramosum, (8) Faecalicatena orolica. (9) Emergencia limonensis.
  • the Anaerotruncus colihominis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81.
  • the Anaerotruncus colihominis comprises the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81.
  • the Blautia coccoides comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,.
  • the Blautia coccoides comprises the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78.
  • the Blautia hominis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37.
  • the Blautia hominis comprises the 16S rDNA sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37.
  • the Blautia obeum comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163.
  • the Blautia obeum comprises the 16S rDNA sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163.
  • the Blautia wexlerae comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172.
  • the Blautiawexlerae comprises the 16S rDNA sequence set forth in SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172.
  • the Butyricicoccus sp2 comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132. In some aspects, the Butyricicoccus sp2 comprises the 16S rDNA sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132.
  • the Clostridium aldenense comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104.
  • the Clostridium aldenense comprises the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104.
  • the Clostridium bolteae comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70.
  • the Clostridium bolteae comprises the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70.
  • the Clostridium innocuum comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65.
  • the Clostridium innocuum comprises the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65.
  • the Clostridium scindens comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114.
  • the Clostridium scindens comprises the 16S rDNA sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114.
  • the Clostridium symbiosum comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110. In some aspects, the Clostridium symbiosum comprises the 16S rDNA sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110.
  • the Dorea longicatena comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the Dorea longicatena comprises the 16S rDNA sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the Eisenbergiella tayi comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the Eisenbergiella tayi comprises the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the Emergencia timonensis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116.
  • the Emergencia timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116.
  • the Erysipelatoclostridium ramosum comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91.
  • the Erysipelatoclostridium ramosum comprises the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91.
  • the Eubacterium callanderi comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.
  • the Eubacterium callanderi comprises the 16S rDNA sequence set forth in SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.
  • the Faecalicatena cortorta comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120.
  • the Faecalicatena cortorta comprises the 16S rDNA sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120.
  • the Faecalicatena orotica comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96.
  • the Faecalicatena orotica comprises the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96.
  • the Flavonifractor plautii comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 3. In some aspects, the Flavonifractor plautii comprises the 16S rDNA sequence set forth in SEQ ID NO: 3.
  • the Hungatella effluvia comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131.
  • the Hungatella effluvia comprises the 16S rDNA sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131.
  • the Intestinimonas butyriciproducens comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105.
  • the Intestinimonas butyriciproducens comprises the 16S rDNA sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105.
  • the Intestinimonas massiliensis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133.
  • the Intestinimonas massiliensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133.
  • the Lactonifactor longoviformis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 28, or SEQ ID NO: 165.
  • the Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO: 17, SEQ ID NO: 28, or SEQ ID NO: 165.
  • the Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124.
  • the Lactonifactor longoviformis comprises the 16S rDNA sequence set forth in SEQ ID NO: 28 or SEQ ID NO: 165.
  • the Lawsonibacter sp7 comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164.
  • the Lawsonibacter sp7 comprises the 16S rDNA sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164.
  • the Massilimaliae timonensis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125.
  • the Massilimaliae timonensis comprises the 16S rDNA sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125.
  • Muri monas intestini comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86.
  • the Murimonas intestini comprises the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86.
  • the Niameybacter spl comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134. In some aspects, the Niameybacter spl comprises the 16S rDNA sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134.
  • the Ruminococcaceae NG 13 sp6 comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO:
  • the Ruminococcaceae NG13 sp6 comprises the 16S rDNA sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO:
  • the Turicibacter sanguinis comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO:
  • SEQ ID NO: 142 SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ
  • the Turicibacter sanguinis comprises the 16S rDNA sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO:
  • SEQ ID NO: 143 SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148.
  • a bacterial composition useful for the present disclosure comprises a plurality of bacteria, wherein the plurality of bacteria comprise a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, S
  • the plurality of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99 and a second
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 9, SEQ ID NO: 97, SEQ ID NO: 98, or SEQ ID NO: 99;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105; (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110; (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114, or (d) a 16S rDNA sequence that
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 11 or SEQ ID NO: 105 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 1, SEQ ID NO: 61,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • the bacterial composition comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 13 or SEQ ID NO: 110 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO:
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • (e) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78 comprising a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • the bacterial composition comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 14, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, or SEQ ID NO: 114 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, S
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, [0173] (e) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • the bacterial composition comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 15, SEQ ID NO: 115, or SEQ ID NO: 116 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120, or (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 28, or SEQ ID NO: 165.
  • the pluraity of bacteria further comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 16, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, or SEQ ID NO: 120 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, S
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identify of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 17, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, or SEQ ID NO: 124 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, [0231] (8) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109 [0235]
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO:28.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 28 or SEQ ID NO: 165 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, S
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plaurality of bacteria provided herein further comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131, or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 125 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, or SEQ ID NO: 131 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 129,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 20 or SEQ ID NO: 132 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, [0293] (4) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, [0308] (7) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises: (a) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133, (b) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134, or (c) a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 21 or SEQ ID NO: 133 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 134 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, [0338] (8) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 23, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148, and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or
  • the plurality of bacteria comprises each of the following:
  • SEQ ID NO: 23 SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, or SEQ ID NO: 148;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, [0349] (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 24, SEQ ID NO: 149, SEQ ID NO: 150, or SEQ ID NO: 151, and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68,
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, [0376] (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 25 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 50 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 51 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 52 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 53 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 54 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 55 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 56 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 57 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 58 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 59 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157, and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO
  • the plurality of bacteria comprises each of the following:
  • SEQ ID NO: 25 SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, or SEQ ID NO: 157;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86, [0392] (8) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 26, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163, and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO:
  • the plurality of bacteria comprises each of the following:
  • SEQ ID NO: 26 SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, or SEQ ID NO: 163;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, or SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • [0401] (4) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, [0403] (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 27 or SEQ ID NO: 164 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, S
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 65,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 29 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 32 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 33 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 34 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 35 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 36 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 37 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO:
  • SEQ ID NO: 70 SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 10, SEQ ID NO
  • the plurality of bacteria comprises each of the following:
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO:
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 30, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 30 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO:
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 38 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 39 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 39 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 40 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 41 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 42 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 43 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 44 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises each of the following:
  • SEQ ID NO: 30 SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, or SEQ ID NO: 172;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, or SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, or SEQ ID NO: 109.
  • the plurality of bacteria comprises a 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 31, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177.
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 31 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 10072, SEQ ID NO: 101,73, SEQ ID NO: 102, SEQ ID NO
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 45 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 46 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 47 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 48 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises a first 16S rDNA sequence that has a sequence identity of at least 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% to the sequence set forth in SEQ ID NO: 49 and a second 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75,
  • the plurality of bacteria comprises each of the following:
  • SEQ ID NO: 31 SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, or SEQ ID NO: 177;
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78,
  • (6) a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 5, SEQ ID NO: 79, SEQ ID NO: 80, or SEQ ID NO: 81,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 6, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, or SEQ ID NO: 86,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 7, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, or SEQ ID NO: 91,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 8, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, or SEQ ID NO: 96,
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 10, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, and
  • a 16S rDNA sequence that has a sequence identity of at least about 95%, at least about 96%, at least about 97%, at least about 97.5%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or about 100% to the 16S rDNA sequence set forth in SEQ ID NO: 12.
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • SEQ ID NO: 95 or SEQ ID NO: 96, (9) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 10, (10) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 11, (11) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 12, (12) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 14 (14) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 15, (15) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 16, (16) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 17, (17) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 18, (18) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 19, (19) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 20, (20) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 21, (21) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 22, and (22) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 23.
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises, consists essentially of, or consists of the following: (1) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 1, (2) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 2, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, or SEQ ID NO: 70, (3) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 3, SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73, (4) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 4, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, or SEQ ID NO: 78, (5) a bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO:
  • a bacterial composition provided herein comprises any of the designed compositions provided in FIG. 1.
  • a bacterial composition comprises, consists essentially of, or consists of the the designed bacterial composition referred to herein as "DEI.”
  • a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE2.”
  • a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE3.”
  • a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE4.”
  • a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE5.” As further described elsewhere in the present application, DE5 comprises DE5.1 and DE5.2.
  • DE5.1 is identical to DE5.2 except that the bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 28 has been replaced with the bacterial species comprising the 16S rDNA sequence set forth in SEQ ID NO: 17.
  • DE5 refers to both DE5.1 and DE5.2.
  • a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE6.” In some aspects, a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE7.” In some aspects, a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE8.” In some aspects, a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE9.” In some aspects, a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE10.” In some aspects, a bacterial composition comprises, consists essentially of, or consists of the designed bacterial composition referred to herein as "DE11."
  • any of the bacterial compositions described herein can be administered to a subject (e.g., suffering from a chronic liver disease, a neutropenia, and/or a disease or disorder associated with a solid organ transplantation) as a formulation. Accordingly, unless indicated otherwise, any disclosure provided herein relating to a bacterial composition can equally apply to formulations comprising such a bacterial composition.
  • a bacterial composition as described herein is combined with additional active and/or inactive materials to produce a formulation.
  • a bacterial composition is formulated in a unit dosage form, each dosage form containing, e.g., from about 10 2 to about 10 9 CFUs, for example, about 10 4 to about 10 8 CFUs.
  • all the bacteria of a composition described herein can be formulated as spores.
  • the spores can be formulated as lyophilized spores.
  • the spores can be suspended in a cryoprotectant, for example glycerol.
  • all the bacteria of a composition described herein can be vegetative cells.
  • a bacterial composition described herein can comprise a mixture of spores and vegetative bacteria.
  • bacterial spores and vegetative bacteria can be formulated at the same dosage.
  • bacterial spores and vegetative bacteria can be formulated at different dosages.
  • the vegetative bacteria can be formulated at a higher dose compared to the bacterial spores.
  • the bacterial spores are formulated at a higher dose compared to the vegetative bacteria.
  • a bacterial composition is formulated in a multi-dose format. Formulations and methods of formulating that can be used with the bacterial compositions described herein are described in US20220017853 Al, which is incorporated by reference herein in its entirety.
  • formulations disclosed herein can be effective over a wide dosage range and is generally administered at an effective amount (e.g., therapeutically effective amount).
  • an effective amount or “effective dosage” is defined as an amount sufficient to achieve or at least partially achieve a desired effect.
  • a “therapeutically effective amount” or “therapeutically effective dosage” of a drug or therapeutic agent is any amount of the drug that, when used alone or in combination with another therapeutic agent, promotes disease regression evidenced by a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction.
  • a therapeutically effective amount or dosage of a drug includes a "prophylactically effective amount” or a “prophylactically effective dosage”, which is any amount of the drug that, when administered alone or in combination with another therapeutic agent to a subject at risk of developing a disease or of suffering a recurrence of disease, inhibits the development or recurrence of the disease.
  • a therapeutic agent to promote disease regression or inhibit the development or recurrence of the disease can be evaluated using a variety of methods known to the skilled practitioner, such as in human subjects during clinical trials, in animal model systems predictive of efficacy in humans, or by assaying the activity of the agent in in vitro assays.
  • the term “amount,” “dose,” and “dosage” can be used interchangeably and refer to the total number of colony forming units (CFUs) of each individual species or strain; or can refer to the total number of microorganisms in the dose. It is understood in the art that determining the number of organisms in a dosage is not exact and can depend on the method used to determine the number of organisms present. If the composition includes spores, for example, the number of spores in a composition can be determined using any suitable methods known in the art, e.g., a dipicolinic acid assay (Fichtel et al.
  • Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • unit dosage forms or “dosage unit forms” refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active component calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
  • a unit dosage form can be in the form of a solid (e.g., capsules, tablets, caplets, pills, troches, lozenges, powders, and granules).
  • a unit dosage form can be in the form of a liquid (e.g., liquid suspension).
  • more than one unit dosage form constitutes a dose.
  • a single dose can be one unit dosage form, two dosage unit forms, three dosage unit forms, four unit dosage forms, five unit dosage forms, or more.
  • the number of unit dosage forms constituting a single dose is about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 20, about 25, or about 30 unit dosage forms.
  • a single dose can be, e.g., about 10 3 to about 10 9 CFUs, for example, about 10 4 to about 10 8 CFUs.
  • a dose is about 1, about 2, about 3, or about 4 capsules containing a total of between about 10 2 and about 10 8 CFUs in the dose.
  • the dosage forms are generally delivered within a prescribed period, e.g., within about 1 hour, about 2 hours, about 5 hours, about 10 hours, about 15 hours, or about 24 hours.
  • a formulation described herein comprises at least one carbohydrate.
  • a “carbohydrate” refers to a sugar or polymer of sugars.
  • saccharide The terms “saccharide,” “polysaccharide,” “carbohydrate,” and “oligosaccharide” can be used interchangeably.
  • Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule.
  • Carbohydrates generally have the molecular formula CnEEnOn.
  • a carbohydrate can be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide.
  • the most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose.
  • Disaccharides are two joined monosaccharides. Exemplary disaccharides include sucrose, maltose, cellobiose, and lactose.
  • an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, stachyose), and polysaccharides include six or more monosaccharide units.
  • Exemplary polysaccharides include starch, glycogen, and cellulose.
  • Carbohydrates can contain modified saccharide units such as 2 '-deoxyribose wherein a hydroxyl group is removed, 2'-fluororibose wherein a hydroxyl group is replaced with a fluorine, or N-acetylglucosamine, a nitrogencontaining form of glucose (e.g., 2'-fluororibose, deoxyribose, and hexose).
  • Carbohydrates can exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.
  • a formulation described herein comprises at least one lipid.
  • a "lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans).
  • the lipid comprises at least one fatty acid selected from lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16: 1), margaric acid (17:0), heptadecenoic acid (17: 1), stearic acid (18:0), oleic acid (18: 1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid (20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoic acid (22: 1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6) (DHA), and t
  • a formulation described herein comprises at least one supplemental mineral or mineral source.
  • minerals include, without limitation: chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium.
  • Suitable forms of any of the foregoing minerals include soluble mineral salts, slightly soluble mineral salts, insoluble mineral salts, chelated minerals, mineral complexes, non-reactive minerals such as carbonyl minerals, and reduced minerals, and combinations thereof.
  • a formulation described herein comprises a vitamin.
  • the vitamin comprises fat-soluble vitamin, water-soluble vitamin, or both.
  • Non-limiting examples of suitable vitamins include vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin.
  • suitable forms of any of the foregoing are salts of the vitamin, derivatives of the vitamin, compounds having the same or similar activity of the vitamin, and metabolites of the vitamin.
  • a formulation described herein comprises an excipient.
  • suitable excipients include a buffering agent, a diluent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, a coloring agent, a glidant, and an anti-adherent.
  • the excipient is a buffering agent.
  • suitable buffering agents include sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate.
  • the excipient serves as a diluent.
  • the excipient can be a solid, semi-solid, or liquid material that acts as a vehicle, carrier, or medium for the active component (e.g., bacteria of the formulation disclosed herein).
  • a formulation can be in the form of, e.g., a tablet, pill, powder, lozenge, sachet, cachet, elixir, suspension, emulsion, solution, syrup, aerosol (as a solid or in a liquid medium), ointment containing, for example, up to 10% by weight of the active component, soft capsule, hard capsule, gel-cap, tablet, suppository, solution, or packaged powder.
  • maximizing delivery of viable bacteria is enhanced by including gastro-resistant polymers, adhesion enhancers, or controlled release enhancers in a formulation.
  • the excipient comprises a preservative.
  • suitable preservatives include antioxidants, such as alpha-tocopherol and ascorbate, and antimicrobials, such as parabens, chlorobutanol, and phenol.
  • a formulation described herein comprises a binder as an excipient.
  • suitable binders include starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C12-C18 fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, and combinations thereof.
  • a formulation described herein comprises a lubricant as an excipient.
  • suitable lubricants include magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and light mineral oil.
  • a formulation described herein comprises a dispersion enhancer as an excipient.
  • Non-limiting examples of suitable dispersants include starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and microcrystalline cellulose as high HLB emulsifier surfactants.
  • a formulation described herein comprises a disintegrant as an excipient.
  • the disintegrant is a non-effervescent disintegrant.
  • suitable non-effervescent disintegrants include starches such as com starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, microcrystalline cellulose, alginates, sodium starch glycolate, gums such as agar, guar, locust bean, karaya, pectin, and tragacanth.
  • the disintegrant is an effervescent disintegrant.
  • suitable effervescent disintegrants include sodium bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid.
  • the excipient comprises a flavoring agent.
  • Flavoring agents can be chosen from synthetic flavor oils and flavoring aromatics; natural oils; extracts from plants, leaves, flowers, and fruits; and combinations thereof.
  • the flavoring agent is selected from cinnamon oils; oil of wintergreen; peppermint oils; clover oil; hay oil; anise oil; eucalyptus; vanilla; citrus oil such as lemon oil, orange oil, grape and grapefruit oil; and fruit essences including apple, peach, pear, strawberry, raspberry, cherry, plum, pineapple, and apricot.
  • the excipient comprises a sweetener.
  • suitable sweeteners include glucose (com syrup), dextrose, invert sugar, fructose, and mixtures thereof (when not used as a carrier); saccharin and its various salts such as the sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia Rebaudiana (Stevioside); chloro derivatives of sucrose such as sucralose; and sugar alcohols such as sorbitol, mannitol, sylitol, and the like.
  • hydrogenated starch hydrolysates and the synthetic sweetener 3,6-dihydro-6-methyl-l,2,3-oxathiazin-4-one-2,2-dioxide particularly the potassium salt (acesulfame-K), and sodium and calcium salts thereof.
  • a formulation described herein comprises a coloring agent.
  • suitable color agents include food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), and external drug and cosmetic colors (Ext. D&C).
  • the coloring agents can be used as dyes or their corresponding lakes.
  • Additional suitable excipients include, for example, saline, phosphate buffered saline (PBS), cocoa butter, polyethylene glycol, polyalcohols (e.g., glycerol, sorbitol, or mannitol) and prebiotic oligosaccharides such as inulin, Crystalean® starch, or dextrin.
  • Excipients can also be selected to account, at least in part, for the ability of the bacterial species in a particular composition to withstand gastric pH (if being delivered orally or directly to the GI tract) and/or bile acids, or other conditions encountered by the formulation upon delivery to a subject.
  • the weight fraction of the excipient or combination of excipients in the formulation is about 99% or less, such as about 95% or less, about 90% or less, about 85% or less, about 80% or less, about 75% or less, about 70% or less, about 65% or less, about 60% or less, about 55% or less, 50% or less, about 45% or less, about 40% or less, about 35% or less, about 30% or less, about 25% or less, about 20% or less, about 15% or less, about 10% or less, about 5% or less, about 2% or less, or about 1% or less of the total weight of the formulation.
  • a formulation of the present disclosure can be milled to provide the appropriate particle size prior to combining with the other ingredients, e.g., those described herein.
  • a bacterial composition is formulated so as to provide quick, sustained, or delayed release of the active component after administration to a subject, for example, for release in the colon, by employing methods and forms known in the art.
  • the bacterial compositions disclosed herein can be formulated into a variety of forms and administered by a number of different means.
  • a bacterial composition can be administered orally, rectally, topically (e.g., ear instillation), nasally, intravaginally, or parenterally, in formulations containing conventionally acceptable carriers, adjuvants, and vehicles as desired.
  • parenteral as used herein includes subcutaneous, intravenous, intramuscular, or intrasternal injection and infusion techniques.
  • a bacterial composition provided herein is formulated for oral administration.
  • Solid dosage forms for oral administration include capsules, tablets, caplets, pills, troches, lozenges, powders, and granules.
  • a capsule typically comprises a core material comprising a bacterial composition (e.g., that which has been formulated as described herein) and a shell wall that encapsulates the core material.
  • the core material comprises at least one of a solid, a liquid, and an emulsion.
  • the shell wall material comprises at least one of a soft gelatin, a hard gelatin, and a polymer.
  • Suitable polymers include, but are not limited to: cellulosic polymers such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose (HPMC), methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and copolymers, such as those formed from acrylic acid, methacrylic acid, methyl acrylate, ammonio methylacrylate, ethyl acrylate, methyl methacrylate and/or ethyl methacrylate (e.g., those copolymers sold under the trade name "Eudragit”); vinyl polymers and copolymers such as polyvinyl pyrrolidone, polyvinyl acetate, polyvinylacetate phthalate, vinylacetate crotonic acid copoly
  • Tablets, pills, and the like can be compressed, multiply compressed, multiply layered, and/or coated.
  • the coating can be single or multiple.
  • the coating material comprises at least one of a saccharide, a polysaccharide, and glycoproteins extracted from at least one of a plant, a fungus, and a microbe.
  • Non-limiting examples include com starch, wheat starch, potato starch, tapioca starch, cellulose, hemicellulose, dextrans, maltodextrin, cyclodextrins, inulins, pectin, mannans, gum arabic, locust bean gum, mesquite gum, guar gum, gum karaya, gum ghatti, tragacanth gum, funori, carrageenans, agar, alginates, chitosans, or gellan gum.
  • the coating material comprises a protein.
  • the coating material comprises at least one of a fat and an oil.
  • the at least one of a fat and an oil is high temperature melting.
  • the at least one of a fat and an oil is hydrogenated or partially hydrogenated. In some aspects, the at least one of a fat and an oil is derived from a plant. In some embodiments the at least one of a fat and an oil comprises at least one of glycerides, free fatty acids, and fatty acid esters. In some aspects, the coating material comprises at least one edible wax.
  • the edible wax can be derived from animals, insects, or plants. Non-limiting examples include beeswax, lanolin, bayberry wax, carnauba wax, and rice bran wax.
  • a tablet or pill comprises an inner component surrounding the composition (e.g., which can be formulated as described herein) and an outer component, the latter serving as an envelope over the former.
  • the two components can be separated by an enteric coating layer that can resist disintegration in the stomach and permits the inner component to pass intact into the duodenum or to be delayed in release.
  • powders or granules embodying a bacterial composition can be incorporated into a food product.
  • the food product is a drink for oral administration.
  • suitable drink include fruit juice, a fruit drink, an artificially flavored drink, an artificially sweetened drink, a carbonated beverage, a sports drink, a liquid diary product, a shake, an alcoholic beverage, a caffeinated beverage, infant formula and so forth.
  • suitable means for oral administration include aqueous and nonaqueous solutions, emulsions, suspensions and solutions and/or suspensions reconstituted from non-effervescent granules, containing at least one of suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, coloring agents, and flavoring agents.
  • the food product is a solid foodstuff.
  • a solid foodstuff include without limitation a food bar, a snack bar, a cookie, a brownie, a muffin, a cracker, an ice cream bar, a frozen yogurt bar, and the like.
  • a bacterial composition disclosed herein (e.g., which can be formulated as described herein) is incorporated into a therapeutic food.
  • the therapeutic food is a ready -to-use food that optionally contains some or all essential macronutrients and micronutrients.
  • a bacterial composition disclosed herein (e.g., which can be formulated as described herein) is incorporated into a supplementary food that is designed to be blended into an existing meal.
  • the supplemental food contains some or all essential macronutrients and micronutrients.
  • a bacterial composition disclosed herein is blended with or added to an existing food to fortify the food's protein nutrition.
  • examples include food staples (grain, salt, sugar, cooking oil, margarine), beverages (coffee, tea, soda, beer, liquor, sports drinks), snacks, sweets and other foods.
  • the formulations are filled into gelatin capsules for oral administration.
  • An example of an appropriate capsule is a 250 mg gelatin capsule containing from 10 (up to 100 mg) of lyophilized powder (10 8 to 10 11 bacteria), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate.
  • from about 10 5 to about 10 12 bacteria can be used, about 10 5 to about 10 7 , about 10 6 to about 10 7 , or about 10 8 to about 10 10 , with attendant adjustments of the excipients if necessary.
  • an enteric-coated capsule or tablet or with a buffering or protective composition can be used.
  • enteric polymers such as those used to coat a capsule or tablet described herein
  • the enteric polymers allow for more efficient delivery of the bacterial compositions disclosed herein to a subject's gastrointestinal tract.
  • the enteric-coated capsule or tablet release their contents (i.e., bacteria or combinations of bacteria disclosed herein) when the pH becomes alkaline after the enteric-coated capsule or tablet passes through the stomach.
  • a pH sensitive composition e.g., enteric polymers
  • the pH sensitive composition is a polymer whose pH threshold of the decomposition of the composition is about 6.8 to about 7.5.
  • the pH threshold range can be lower, e.g., about 5.5 or about 6.0, or higher, e.g., about 7.0 or about 8.0.
  • Such a numeric value range is a range where the pH shifts toward the alkaline side at a distal portion of the stomach, and hence is a suitable range for use in the delivery to the colon.
  • the pH threshold range can be about 5.0 to about 8.0, about 5.5 to about 8.0, about 6.0 to about 8.0, about 6.5 to about 8.0, about 5.0 to about 7.5, about 5.5 to about 7.5, about 6.0 to about 7.5, about 6.5 to about 7.5, about 5.0 to about 7.0, about 5.5 to about 7.0, about 6.0 to about 7.0, about 6.5 to about 7.0, or a range between any two preceding values.
  • an approach to improving delivery of a bacterial composition disclosed herein (e.g., which can be formulated as described herein) to the colon specifically can include a composition which ensures the delivery to the gastrointestinal tract by delaying the release of the contents by approximately 3 to 5 hours, which corresponds to the small intestinal transit time.
  • the delayed release of the contents of the formulation is about 1 to about 8 hours, about 1 to about 7 hours, about 1 to about 6 hours, about 1 to about 5 hours, about 1 to about 4 hours, about 1 to about 3 hours, about 1 to about 2 hours, about 2 to 8 hours, about 2 to about 7 hours, about 2 to about 6 hours, about 2 to about 5 hours, about 2 to about 4 hours, about 2 to about 3 hours, about 3 to 8 hours, about 3 to about 7 hours, about 3 to 6 hours, about 3 to about 5 hours, about 3 to about 4 hours, about 4 to about 8 hours, about 4 to about 7 hours, about 4 to about 6 hours, about 4 to about 5 hours, about 5 to about 6 hours, about 6 to about 8 hours, about 6 to about 7 hours, about 7 to about 8 hours, or a range between any two preceding values.
  • a hydrogel is used as a shell.
  • the hydrogel is hydrated and swells upon contact with gastrointestinal fluid, so that the contents are effectively released.
  • the delayed release dosage units include drug-containing compositions having a material which coats or selectively coats a drug.
  • a selective coating material include in vivo degradable polymers, gradually hydrolyzable polymers, gradually water- soluble polymers, and/or enzyme degradable polymers. Additional non-limiting examples include cellulose-based polymers such as hydroxypropyl cellulose, acrylic acid polymers and copolymers such as methacrylic acid polymers and copolymers, and vinyl polymers and copolymers such as polyvinylpyrrolidone.
  • compositions that target delivery to the colon include bioadhesive compositions which specifically adhere to the colonic mucosal membrane (for example, a polymer described in the specification of U.S. Pat. No. 6,368,586), and compositions into which a protease inhibitor is incorporated for protecting particularly a bacterial composition disclosed herein (e.g., which can be formulated as described herein) in the gastrointestinal tracts from decomposition due to an activity of a protease.
  • An additional colon-delivery mechanism is via pressure change, such that the contents are released from the colon by generation of gas in bacterial fermentation at a distal portion of the stomach.
  • pressure-change is not particularly limited, and a more specific example thereof is a capsule which has contents dispersed in a suppository base and which is coated with a hydrophobic polymer (for example, ethyl cellulose).
  • a further composition for delivery to the colon includes, for example, a bacterial composition disclosed herein (e.g., which can be formulated as described herein) comprising a component that is sensitive to an enzyme (for example, a carbohydrate hydrolase or a carbohydrate reductase) present in the colon.
  • a bacterial composition disclosed herein e.g., which can be formulated as described herein
  • an enzyme for example, a carbohydrate hydrolase or a carbohydrate reductase
  • Such a composition is not particularly limited, and more specific examples thereof include compositions that use food components such as non-starch polysaccharides, amylose, xanthan gum, and azopolymers.
  • a bacterial composition disclosed herein is formulated with a germinant to enhance engraftment or efficacy. In some aspects, a bacterial composition is formulated or administered with a prebiotic substance to enhance engraftment or efficacy.
  • the number of bacteria of each type can be present in the same level or amount or in different levels or amounts.
  • a bacterial composition e.g., which can be formulated as described herein
  • the bacteria can be present in from about a 1 : 10,000 ratio to about a 1 :1 ratio, from about a 1 : 10,000 ratio to about a 1 : 1,000 ratio, from about a 1 : 1,000 ratio to about a 1 : 100 ratio, from about a 1 : 100 ratio to about a 1 :50 ratio, from about a 1 :50 ratio to about a 1 :20 ratio, from about a 1 :20 ratio to about a 1 : 10 ratio, from about a 1 : 10 ratio to about a 1 : 1 ratio, or a range between any two preceding values.
  • the ratio of type of bacteria can be chosen pairwise from ratios for bacterial compositions with two types of bacteria.
  • a bacterial composition e.g., which can be formulated as described herein
  • at least one of the ratio between bacteria A and B, the ratio between bacteria B and C, and the ratio between bacteria A and C can be chosen, independently, from the pairwise combinations above.
  • any of the bacterial compositions can be used to treat various medical ailments.
  • Non-limiting examples include: a chronic liver disease, neutropenia, a disease or disorder associated with a solid organ transplantation, a disease or disorder associated with compromised immune function, and/or a disease or disorder associated impaired gastrointestinal barrier function.
  • the present disclosure relates to a method of treating a chronic liver disease in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • treating a chronic liver disease is not particularly limiting and comprises any intervention that helps reverse, alleviate, ameliorate, inhibit, prevent, or slow down the progression, development, severity or recurrence of a symptom, complication, condition or biochemical indicia associated with a chronic liver disease.
  • "treating a chronic liver disease” comprises treating, reducing, or preventing an incidence of an infection in the subject suffering from a chronic liver disease.
  • chronic liver disease refers to a disease process of the liver that involves destruction and regeneration of the liver parenchyma leading to fibrosis and cirrhosis, which results in progressive deterioration of liver functions for more than 6 months.
  • liver functions include: production of clotting factors and other proteins, detoxification of harmful products of metabolism, and excretion of bile. Accordingly, in some aspects, administering a bacterial composition described herein to a subject suffering from a chronic liver disease can improve one or more liver functions in the subject.
  • the bacterial compositions described herein can be used to treat any chronic liver diseases.
  • the classification of the sources of chronic liver diseases fall into five groupings: (i) viral causes, such as hepatitis B and C or cytomegalovirus or Epstein Banvirus, (ii) metabolic causes, such as hemochromatosis, nonalcoholic fatty liver disease or Wilson's disease, (iii) autoimmune response causes, such as autoimmune chronic hepatitis, primary biliary cirrhosis or primary sclerosing cholangitis, (iv) toxin-related causes, such as prolonged alcohol and/or drug (e.g., nitrofurantoin, amiodarone, isoniazid, phenytoin, or methotrexate) abuse, and (v) other miscellaneous causes, such as right heart failure.
  • viral causes such as hepatitis B and C or cytomegalovirus or Epstein Banvirus
  • metabolic causes such as hemochromatosis, nonalcoholic fatty liver
  • a chronic liver disease that can be treated with the present disclosure can be caused by any of such sources.
  • Non-limiting examples of chronic liver diseases that can be treated with the present disclosure include: cirrhosis, liver fibrosis, alcoholic liver disease, non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), hepatitis (including viral and alcoholic hepatitis), primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC), alpha-1 antitrypsin deficiency, hereditary hemochromatosis, Wilson's disease, autoimmune hepatitis (AIH), Budd-Chiari syndrome, and combinations thereof.
  • the chronic liver disease comprises a cirrhosis.
  • "cirrhosis” refers the final stage of chronic liver disease that results in disruption of liver architecture, the formation of widespread nodules, vascular reorganization, neo-angiogenesis, and deposition of an extracellular matrix. Acute states of decompensation in cirrhotic patients ultimately lead to liver failure and subsequent need of liver transplant. Accordingly, some aspects of the present disclosure relates to a method of treating a cirrhosis in a subject in need thereof, comprising administering to the subject any of the bacteria compositions provided herein. In some aspects, the cirrhosis comprises decompensated cirrhosis.
  • treating a chronic liver disease comprises reducing, preventing, and/or alleviating one or more symptoms of a chronic liver disease.
  • symptoms include: fluid buildup in the belly (ascites), vomiting, gallstones, itching, jaundice, kidney failure, muscle loss, loss of appetite, bruising, spider-like veins in the skin, fatigue, weight loss, confusion, swelling in the legs (e.g., ankles), portal hypertension, hepatic encephalopathy, and combinations thereof.
  • provided herein is a method of reducing, preventing, and/or alleviating one or more symptoms of a chronic liver disease in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein, wherein after the administration, one or more symptoms of the chronic liver disease is reduced, prevented, and/or alleviated in the subject.
  • treating a chronic liver disease comprises reducing and/or preventing an incidence of an infection in the subject suffering from a chronic liver disease.
  • bacterial infections are a frequent and severe complication in many chronic liver disease patients, which can ultimately result in the death of the patients. Dionigi, E., et al. , Am J Gastroenterol 112(4): 588-596 (Apr. 2017); Fernandez, J., et aL, Hepatology 55(5): 1551-61 (May 2012); Tandon, P., et al., Clin Gastroenterol Heptatol 10(11): 1291-8 (Nov.
  • the incidence of an infection can be reduced and/or prevented in the subject suffering from a chronic liver disease, which can in turn help treat the chronic liver disease.
  • some aspects of the present disclosure relates to a method of reducing and/or preventing an incidence of an infection in a subject suffering from a chronic liver disease, comprising administering to the subject any of the bacterial compositions provided herein.
  • Non-limiting examples of infections are provided elsewhere in the present disclosure.
  • Some aspects of the present disclosure relates to a method of treating a neutropenia in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • “treating a neutropenia” e.g., febrile neutropenia
  • "treating a neutropenia” comprises treating, reducing, or preventing an incidence of an infection in the subject suffering from a neutropenia.
  • neutrophils refers to a disorder characterized by an abnormally low number of neutrophils.
  • a subject suffering from a neutropenia has an absolute neutrophil count (ANC) less than about 1,500 cells/pL of blood.
  • a subject suffering from a neutropenia has an ANC less than about 1,400 cells/ pL of blood, less than about 1,300 cells/pL of blood, less than about 1,200 cells/pL of blood, less than about 1,100 cells/pL of blood, less than about 1,000 cells/pL of blood, less than about 900 cells/pL of blood, less than about 800 cells/pL of blood, less than about 700 cells/pL of blood, less than about 600 cells/pL of blood, or less than about 500 cells/pL of blood.
  • any neutropenia can be treated with any of the bacterial compositions described herein.
  • the neutropenia is caused by and/or associated with any of the following radiation, chemotherapy, alcoholism, drugs, allergic disorders, aplastic anemia, autoimmune disease, T-y lymphoproliferative disease LPD), myelodysplasia, myelofibrosis, dysgammaglobulinemia, paroxysmal nocturnal hemoglobinuria, cancer, vitamin B12 deficiency, folate deficiency, viral infection, bacterial infection and sepsis, spleen disorder, hemodialysis, or transplantation, leukemia, myeloma, lymphoma, metastatic solid tumors which infiltrate and replace the bone marrow, toxins, bone marrow failure, Schwachman-Diamond syndrome, cartilage-hair hypoplasia, dyskeratosis congenita, glycogen storage disease type IB, splenomegaly
  • Nonlimiting examples of neutropenia include: cancer neutropenia, febrile neutropenia, primary neutropenia, acute neutropenia, severe chronic neutropenia (SCN), severe congenital neutropenia (Kostmann's syndrome), severe infantile genetic agranulocytosis, benign neutropenia, cyclic neutropenia, chronic idiopathic neutropenia, secondary neutropenia, syndrome associated neutropenia, immune-mediated neutropenia, and combinations thereof.
  • a neutropenia that can be treated with the present disclosure is a cancer neutropenia. Accordingly, some aspects of the present disclosure relates to a method of treating a cancer neutropenia in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • cancer neutropenia refers to a neutropenia caused by and/or associated with a cancer treatment.
  • the cancer treatment is a chemotherapy.
  • chemotherapeutic agents that can cause and/or be associated with a neutropenia include: alkylating agent, antimetabolite, antimicrotubular agent, antibiotic, and combinations thereof.
  • an alkylating agent used for chemotherapy comprises nitrogen mustard (e.g., bendamustine, cyclophosphamide, ifosfamide), nitrosoureas (e.g., carmustine, lomustine), platinum analog (e.g., carboplatin, cisplatin, oxaliplatin), triazene (e.g., dacarbazine, procarbazine, temozolamide), alkyl sulfonate (e.g., busulfan), ethyleneimine (e.g., thiotepa), or combinations thereof.
  • nitrogen mustard e.g., bendamustine, cyclophosphamide, ifosfamide
  • nitrosoureas e.g., carmustine, lomustine
  • platinum analog e.g., carboplatin, cisplatin, oxaliplatin
  • triazene e.g., dacarbazine,
  • an antimetabolite used for chemotherapy comprises cytidine analog (e.g., azacitidine, decitabine, cytarabine, gemcitabine), folate antagonist (e.g, methotrexate, pemetrexed), purine analog (e.g., cladribine, clofarabine, nelarabine), pyrimidine analog (e.g., fluorouracil (5-FU), capecitabine (prodrug of 5-FU)), or combinations thereof.
  • cytidine analog e.g., azacitidine, decitabine, cytarabine, gemcitabine
  • folate antagonist e.g, methotrexate, pemetrexed
  • purine analog e.g., cladribine, clofarabine, nelarabine
  • pyrimidine analog e.g., fluorouracil (5-FU), capecitabine (prodrug of 5-FU)
  • an antimicrotubular agent used for chemotherapy comprises a topoisomerase II inhibitor (e.g., anthracy cline, such as doxorubicin, daunorubicin, idarubicin, mitoxantrone), topoisomerase I inhibitor (e.g., irinotecan, topotecan), taxane (e.g., paclitaxel, docetaxel, cabazitaxel), vina alkaloid (e.g., vinblastine, vincristine, vinorelbine), or combinations thereof.
  • an antibiotic used for chemotherapy comprises actinomycin D, bleomycin, daunomycin, or combinations thereof.
  • Non-limiting examples of other agents used for chemotherapy include: hydroxyurea, tretinoin, arsenic trioxide, proteasome inhibitor, and combinations thereof.
  • the neutropenia is associated with a fever ("febrile neutropenia"). Accordingly, in some aspects, provided herein is a method of treating a febrile neutropenia in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • a neutropenia e.g., cancer neutropenia
  • administering any of the bacterial compositions described herein to a subject suffering from a neutropenia can be useful in reducing or preventing the incidence of such infections.
  • treating a neutropenia comprises reducing and/or preventing an incidence of an infection in the subject suffering from the neutropenia, which in turn can help treat the neutropenia.
  • the present disclosure relates to a method of reducing and/or preventing an incidence of an infection in a subject suffering from a neutropenia, comprising administering to the subject any of the bacterial compositions provided herein.
  • Non-limiting examples of infections are provided elsewhere in the present disclosure.
  • treating a neutropenia comprises reducing, preventing, and/or alleviating one or more symptoms of a neutropenia.
  • symptoms include: a fever (e.g., temperature of 100.5°F or higher), chills or sweating, sore throat, sores in the mouth, abdominal pain, pain and/or sores near the anus, pain or burning when urinating, urinating often, diarrhea, cough and/or shortness of breathing, unusual vaginal discharge or itching, or combinations thereof.
  • Some aspects of the present disclosure relates to a method of reducing, preventing, and/or alleviating one or more symptoms of a neutropenia (e.g., cancer neutropenia) in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein, wherein after the administration, one or more symptoms of the neutropenia is reduced, preventing, and/or alleviated in the subject.
  • a neutropenia e.g., cancer neutropenia
  • Some aspects of the present disclosure relates to a method of treating a disease or disorder associated with a solid organ transplantation in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • treating a disease or disorder associated with a solid organ transplantation is not particularly limiting and comprises any intervention that helps reverse, alleviate, ameliorate, inhibit, prevent, or slow down the progression, development, severity or recurrence of a symptom, complication, condition or biochemical indicia associated with solid organ transplantation.
  • treating a disease or disorder associated with a solid organ transplanation comprises treating, reducing, or preventing an incidence of an infection in the subject having undergone a solid organ transplanation. Accordingly, as described further below, in some aspects a "disease or disorder associated with a solid organ transplantation” comprises an infection resulting from having undergone a solid organ transplantation.
  • solid organ transplantation refers to the transplantation of any tissue or organ within a patient's body.
  • tissues or organs include: liver, heart, lungs, kidney, pancreas, or combinations thereof.
  • solid organ transplantation is regarded as a successful form of intervention following irreversible organ failure, with transplant success rates varying across organ types and age of recipients.
  • most solid organ transplantation patients have to undergo immunosuppressant therapy.
  • administering any of the bacterial compositions provided herein can be useful in reducing or preventing an incidence of an infection in the subject having undergone a solid organ transplantation.
  • a disease or disorder associated with a solid organ transplantation can be treated in the subject.
  • the present application relates to a method of reducing and/or preventing an incidence of an infection in a subject having undergone a solid organ transplantation, comprising administering to the subject any of the bacterial compositions provided herein.
  • infections are provided elsewhere in the present disclosure.
  • treating a disease or disorder associated with a solid organ transplantation comprises reducing, preventing, and/or alleviating one or more symptoms associated with the solid organ transplantation.
  • symptoms include: a fever (e.g., temperature of 100.5°F or higher), severe headache, diarrhea, vomiting, shortness of breath, new chest pain, fatigue, or combinations thereof.
  • Some aspects of the present disclosure relates to a method of reducing, preventing, and/or alleviating one or more symptoms of a solid organ transplantation in a subject in need thereof, comprising administering to the subject any of the bacterial compositions provided herein.
  • any of the bacterial compositions provided herein can treat a disease or disorder (e.g., chronic liver disease, neutropenia, and/or a disease or disorder associated with a solid organ transplantation) by reducing or preventing the incidence of an infection, including bloodstream infection (BSI) and sepsis, in the subject suffering from the disease or disorder.
  • a disease or disorder e.g., chronic liver disease, neutropenia, and/or a disease or disorder associated with a solid organ transplantation
  • the infection is spontaneous bacterial peritonitis (SBP).
  • SBP spontaneous bacterial peritonitis
  • SBP spontaneous bacterial peritonitis
  • SBP spontaneous bacterial peritonitis
  • reducing or preventing the incidence of an infection comprises reducing or preventing the colonization of a pathogenic microorganism within the gastrointestinal tract of the subject, wherein the pathogenic microorganism is associated with the infection.
  • some aspects of the present disclosure relates to a method of reducing or preventing the colonization of a pathogenic microorganism within the gastrointestinal tract of a subject suffering from a disease or disorder, comprising administering to the subject any of the bacterial compositions provided herein, wherein the disease or disorder comprises a chronic liver disease, neutropenia, or a disease or disorder associated with a solid organ transplantation.
  • pathogenic microorganisms include those belonging to the following families: Enterococcaceae.
  • Non- limiting examples of pathogenic microorganisms include: Enterococcus faecium (e.g., vancomycin-resistant), Enterococcus spp., Klebsiella pneumonia (e.g., carbapenem -resistant), E.
  • compositions and formulations disclosed herein can be used for the treatment and/or prevention of a disease or disorder, such as those associated with dysbiosis of a gastrointestinal tract (e.g., infection or GvHD following HSCT), e.g., by ameliorating one or more signs or symptoms of the disease.
  • a disease or disorder such as those associated with dysbiosis of a gastrointestinal tract (e.g., infection or GvHD following HSCT), e.g., by ameliorating one or more signs or symptoms of the disease.
  • the bacterial compositions disclosed herein can also be useful for the treatment of diseases or disorders, including but not limited to acute leukemia (ALL), acute myelogenous leukemia (AML), multiple myeloma and lymphomas [non-Hodgkin's lymphoma (NHL) and Hodgkin's disease (HD), myelodysplastic syndromes [MDS, combined with myeloproliferative neoplasms (MPNs)] and related cancers that require HSCT, mucositis, infections including but not limited to blood and tissue infection with ESKAPE pathogens (including: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) with Enterococcus species including but not limited to Enterococcus fae
  • ALL acute leukemia
  • AML acute myelog
  • CDI C. difficile infection
  • ICI immune check point inhibitor-induced colitis
  • viral infection and reactivation e.g., candidemia, etc.
  • fungal infection including gastrointestinal infection and systemic, e.g., candidemia, etc.
  • treatment with a bacterial composition described herein is associated with at least one of the following: (i) an increase in the diversity of the gastrointestinal (GI) microbiome in a subject, (ii) a reduction in GI inflammation in a subject, (iii) improvement in mucosal and/or epithelial barrier integrity in a subject compared to a reference control (e.g., untreated patients or the subject prior to treatment), (iv) promotion of mucosal healing, (v) reduction in incidence of infection, (vi) reduction in the use of antibiotics, (vii) increase in the probability of survival, and (viii) other improvements of at least one sign or symptom of a disease or disorder disclosed herein.
  • GI gastrointestinal
  • improvement associated with an increase in the diversity of the gastrointestinal (GI) microbiome in a subject includes improvement measured by species domination, including, for example, by pathobionts, drug resistant organisms, or MDROs, or as measured by an increase in diversity of species such as in the number of species (e.g., species richness) and/or species distribution (e.g., even skew of distribution).
  • Such improvements can also include, for example, improvements detected via biomarkers, such as a decrease or increase in the level of certain biological molecules (e.g., fecal calprotectin, secondary bile acids, tryptophan metabolites, or short-chain and/or medium-chain fatty acids) following treatment.
  • Bacterial compositions disclosed herein can be used to treat any disease or disorder associated with a dysbiosis of the gastrointestinal tract. Non-limiting examples of such diseases or disorders are provided further below.
  • Bacterial compositions provided herein are useful for administration to a subject, e.g., a mammal, such as a human in need of treatment, e.g., to prevent or treat a disease or disorder disclosed herein or a sign or symptom of a disease or disorder disclosed herein or to prevent recurrence of a disease or disorder disclosed herein.
  • the mammalian subject is a human subject.
  • the human subject e.g., patient
  • has one or more signs or symptoms of a disease or disorder such as those associated with infection (including, but not limited to, blood stream infection, sepsis, tissue infection, invasive infection, viral infection or reactivation, and gastrointestinal infection including but not limited to C. difficile).
  • a therapeutically effective treatment using any of the bacterial compositions provided herein can ameliorate one or more of such signs and symptoms of a disease or disorder disclosed herein.
  • Efficacy of a treatment can be determined by any suitable methods known in the art. For example, in some aspects, efficacy of a treatment can be determined by evaluating signs and/or symptoms and according to whether induction of improvement and/or maintenance of an improved condition is achieved, e.g., for at least about 1 week, at least about two weeks, at least about three weeks, at least about four weeks, at least about 8 weeks, or at least about 12 weeks.
  • indicators of efficacy include engraftment of at least one bacterial species or OTU identified in any of the bacterial compositions described, for example, at about 2 weeks, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9 weeks, about 10 weeks, about 11 weeks, about 12 weeks, or longer after initial dosing with the bacterial composition.
  • the indicators of efficacy include the reduced abundance of at least one species or OTU identified herein (e.g., ESKAPE pathogens including: Enterococcus fciecium.
  • the indicators of efficacy include the reduced abundance of at least one species or OTU identified herein (e.g., Enterococcus spp. and Enterobacteriaceae spp.
  • MDROs drug resistant or multi-drug resistant organisms
  • VRE vancomycin-resistant enterococci
  • CRE carbapenem-resistant Enterobacteriaceae
  • MRS A methicillin resistant Staphylococcus aureus
  • ESBL extended-spectrum beta-lactamase
  • administering any of the bacterial compositions disclosed herein to a subject can improve a dysbiosis, including, but not limited to, an improvement in the representation of one or more OTUs identified as reduced in a population of subjects suffering from a disease or disorder associated with dysbiosis.
  • treatment with a bacterial composition described herein can reduce the representation of one or more microbial species that are associated with a disease or disorder disclosed herein (also referred to herein as "pathogenic microorganism").
  • treatment with a bacterial composition disclosed herein can increase the representation of microbial species that are associated with an improvement of a disease or disorder disclosed herein.
  • the improvement of a disease or disorder can be improvement on overall survival (OS), the incidence and duration of survival endpoints including transplant-related mortality (TRM), relapse free survival (RFS), the frequency and length of hospitalizations and Intensive Care Unit (ICU) stays, or incidence and severity of the disease or disorder described herein.
  • OS overall survival
  • TRM transplant-related mortality
  • RFS relapse free survival
  • ICU Intensive Care Unit
  • subjects suffering from a disease or disorder described herein e.g., chronic liver disease, neutropenia, and/or a disese or disorder associated with a solid organ transplantation
  • any of the bacterial compositions described herein have i) an increased prevelance in their stool of one or more strains in the bacterial composition, ii) a reduced abundance in their stool of Enterococcus spp., Enterobacteriaceae spp., or both, iii) a decreased incidence of bloodstream infections and sepsis including but not limited to bacterial infections (VRE, CRE, or ESBL), fungal infections, or combinations thereof, iv) a decreased incidence of gastrointestinal infections including but not limited to Clostridiodes difficile, viral infections or reactivations (including but not limited to norovirus, adenovirus, or rotavirus), parasitic infections (including but not limited to Cryptosporidia), or combinations thereof, v) a decreased incidence of neutropeni
  • VRE bacterial infections
  • a subject that can be treated with the present disclosure receives a pretreatment protocol prior to administration of the bacterial composition wherein the pretreatment protocol prepares the gastrointestinal tract to receive the bacterial composition.
  • the pretreatment protocol comprises an oral antibiotic treatment, wherein the antibiotic treatment alters the bacteria in the subject.
  • the antibiotic is not absorbed through the gut or minimally bioavailable for systemic distribution.
  • the pretreatment protocol comprises a colonic cleansing (e.g., enema), wherein the colonic cleansing substantially empties the contents of the subject's colon.
  • substantially emptying the contents of the colon refers to removal of at least about 75%, at least about 80%, at least about 90%, at least about 95%, or about 100% of the contents of the ordinary volume of colon contents.
  • the subject receives more than one pretreatment protocol, e.g., an antibiotic treatment preceding a colon-cleansing protocol.
  • a subject that can be treated with the present disclosure does not receive a pretreatment protocol prior to administration of the bacterial composition.
  • the bacterial composition can be administered to reduce, alleviate, or prevent intestinal dysbioses associated with subsequent treatment of the subject for a disease or disorder requiring treatment (e.g., those described herein).
  • a subject receives a pretreatment protocol prior to administration of the bacterial composition described herein and the subject receives subsequent treatment for a disease or disorder requiring treatment (e.g., those described herein) following administration of the bacterial composition.
  • a pretreatment protocol is administered to a subject at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 10 days, or at least about 15 days prior to administration of a bacterial composition described herein.
  • subsequent treatment of the subject for a disease or disorder requiring treatment occurs at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 10 days, or at least about 15 days after administration of a bacterial composition provided herein.
  • the subject receives multiple doses of a bacterial composition provided herein. In some aspects, the subject receives multiple doses of a bacterial composition through a course of about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 8 days, about 9 days, about 10 days, about 11 days, about 12 days, about 13 days, about 14 days, about 15 days, about 16 days, about 17 days, about 18 days, about 19 days, or about 20 days. In some aspects, the subject receives at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, or at least about 10 courses of a treatment regimen provided herein.
  • the subject has at least one sign or symptom of a disease or disorder, such as those disclosed herein, prior to administration of the bacterial composition.
  • the subject does not exhibit a sign or symptom of a disease or disorder, such as those disclosed herein, prior to administration of the bacterial composition, e.g., the bacterial composition is administered prophylactically to reduce the risk of a sign or symptom of a disease or disorder, such as those disclosed herein.
  • a bacterial composition described herein is administered enterically (e.g., by a route of access to the gastrointestinal tract).
  • the bacterial composition is administered to the subject via oral administration, rectal administration (including enema, suppository, or colonoscopy), by an oral or nasal tube (nasogastric, nasojejunal, oral gastric, or oral jejunal), or any other method known in the art.
  • any of the bacterial compositions provided herein can be administered to the subject orally.
  • a bacterial composition is administered to at least one region of the gastrointestinal tract, including the mouth, esophagus, stomach, small intestine, large intestine, and rectum. In some aspects, a bacterial composition is administered to all regions of the gastrointestinal tract. In some aspects, a bacterial composition is administered orally in the form of medicaments such as powders, capsules, tablets, gels or liquids. The bacterial composition can also be administered in gel or liquid form by the oral route or through a nasogastric tube, or by the rectal route in a gel or liquid form, by enema or instillation through a colonoscope or by a suppository.
  • a bacterial composition is provided in a dosage form.
  • the dosage form is designed for administration of at least one OTU or combination thereof disclosed herein, wherein the total amount of bacterial composition administered is selected from about 0.1 ng to about 10 g, about 10 ng to about 1 g, about 100 ng to about 0.1 g, about 0.1 mg to about 500 mg, about 1 mg to about 1000 mg, from about 1000 to about 5000 mg, or more.
  • the bacterial composition is provided in a single dosage form comprising a capsule.
  • the bacteria compositions are provided in a single dosage form comprising at least about one capsule, at least about two capsules, at least about three capsules, at least about four capsules, at least about five capsules, at least about six capsules, at least about seven capsules, at least about eight capsules, at least about ninecapsules, or at least about ten capsules.
  • the capsule comprise a liquid formulation of bacterial spores from a bacterial species delivered at a target dose strength of about 1 x 10 6 to about 5 x 10 7 colony-forming units (CFUs) per dose.
  • the capsule comprise a liquid formulation of bacterial spores from about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or about 20 species of bacteria delivered at a target dose strength of about 1 x 10 6 to about 5 x 10 7 colony -forming units (CFUs) per dose.
  • the capsule comprise a dry powder formulation of bacterial spores from a bacterial species delivered at a target dose strength of about 1 x 10 6 to about 5 x 10 7 colonyforming units (CFUs) per dose.
  • the capsule comprise a dry powder formulation of bacterial spores from about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or about 20 strains delivered at a target dose strength of about 1 x 10 6 to about 5 x 10 7 colonyforming units (CFUs) per dose.
  • CFUs colonyforming units
  • the treatment period (i.e., period of time during which a bacterial composition described herein is administered to the subject) is at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 1 week, at least about 2 weeks, at least about 3 weeks, at least about 4 weeks, at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 5 months, at least about 6 months, or at least about 1 year.
  • the treatment period is from about 1 day to 1 week, from about 1 week to 4 weeks, from about 1 month, to 3 months, from about 3 months to 6 months, from about 6 months to 1 year, or for over a year.
  • a bacterial composition described herein is administered once, on a single occasion or on multiple occasions, such as once a day for several days or more than once a day on the day of administration (including twice daily, three times daily, or up to five times daily).
  • a bacterial composition is administered intermittently according to a set schedule, e.g. , once a day, once weekly, or once monthly, or when the patient relapses from clinical improvement of a disease or disorder, such as those disclosed herein, or exhibits a sign or symptoms of a disease or disorder, such as those disclosed herein.
  • a bacterial composition is administered on a long-term basis to individuals who are at risk for active disease or disorder, such as those disclosed herein or are diagnosed as being at risk for developing a disease or disorder (e.g., have a family history of the diseases or a history of isotretinoin use by the individual).
  • a bacterial composition of the present disclosure is administered with other agents as a combination therapy.
  • a bacterial composition described herein can be administered to a subject in combination with a standard of care treatment.
  • standard of care treatment refers to a treatment that is generally accepted by clinicians for subjects suffering from a disease or disorder (e.g., those described herein).
  • a standard of care treatment can comprise lactulose, rifaximin, or both.
  • a standard of care treatment can comprise a chemotherapy, immunotherapy, or both.
  • a skilled artisan will be aware of the appropriate standard of care treatment for the particular disease or disorder.
  • a bacterial composition of the present disclosure is administered without other agents.
  • a bacterial composition as described herein is administered with other agents, where the other agent (e.g., anti-microbial agents or prebiotics) is administered, for example, about one day, about two days, about three days, about four days, about five days, about six days, about seven days, or more than about seven days prior to the administration of the bacterial composition.
  • the bacterial composition is then administed over several days, for example, about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days, about ten days, or more.
  • the other agent e.g., anti-microbial agents or prebiotics
  • is administered for example, for about one day, about two days, about three days, about four days, about five days, about six days, about seven days, or more than about seven days, followed by administration of a bacterial composition as described herein over several days, for example, about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days, about ten days, or more.
  • the other agent that can be administered in combination with a bacterial composition described herein comprises anti-microbial agents, which include antibacterial agents, anti-fungal agents, anti-viral agents, anti-parasitic agents, or combinations thereof.
  • anti-bacterial agents include cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cefamandole, cefoxitin, cefprozil, and ceftobiprole); fluoroquinolone antibiotics (cipro, Levaquin, floxin, tequin, avelox, and norflox); tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); penicillin antibiotics (amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin);
  • anti-viral agents include Abacavir, Acyclovir, Adefovir, Amprenavir, Atazanavir, Cidofovir, Darunavir, Delavirdine, Didanosine, Docosanol, Efavirenz, Elvitegravir, Emtricitabine, Enfuvirtide, Etravirine, Famciclovir, Foscarnet, Fomivirsen, Ganciclovir, Indinavir, Idoxuridine, Lamivudine, Lopinavir Maraviroc, MK-2048, Nelfinavir, Nevirapine, Penciclovir, Raltegravir, Rilpivirine, Ritonavir, Saquinavir, Stavudine, Tenofovir Trifluridine, Valaciclovir, Valganciclovir, Vidarabine, Ibacitabine, Amantadine, Oseltamivir, Rimantidine, Tipranavir, Zal
  • Non-limiting examples of antifungal compounds include, but are not limited to polyene antifungals such as natamycin, rimocidin, fllipin, nystatin, amphotericin B, candicin, and hamycin; imidazole antifungals such as miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, and tioconazole; triazole antifungals such as fluconazole, itraconazole, isavuconazole, ravuconazole, posaconazole, voriconazole, terconazole, and albaconazole; thiazole antifungals such as abafungin; allylamine antifungals such as terbinafine, naftif
  • Other compounds that have antifungal properties include, but are not limited to polygodial, benzoic acid, ciclopirox, tolnaftate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprogin.
  • a prebiotic is a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon a treated subject's well-being and health.
  • Prebiotics can include complex carbohydrates, amino acids, peptides, or or other nutritional components that allow bacterial composition benefits such as better survival, fitness, enhanced engraftment, enhanced competition with resident bacteria or pathobionts or pathogens.
  • Prebiotics include, but are not limited to, amino acids, biotin, fructooligosaccharide, galactooligosaccharides, inulin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, and xylooligosaccharides.
  • signs or symptoms of an adverse event or disease recurrence are evaluated post-treatment ranging from, e.g., about 1 day to about 6 months after administration of a bacterial composition.
  • evaluation involves obtaining fecal material from the subject and assessment of microbes present in the gastrointestinal tract, e.g., using 16S rDNA or metagenomic shotgun sequencing analysis or other analyses known in the art.
  • Population of the gastrointestinal tract by bacterial species present in the formulation as well as augmentation by commensal microbes not present in the formulation can be used to indicate an improvement in the GI dysbiosis associated with e.g., a disease or disorder described herein, and therefore a decreased risk of an adverse event or a decrease in the severity of an adverse event.
  • Table 1 shows “STR” designations for strains described herein, SEQ ID NOs of 16S rDNA sequences encoding the 16S rRNA of each STR, and a reference to the species or strain name sharing high sequence identity with the 16S rDNA sequence for each SEQ ID NO.
  • Example 1 Identification of microbiome signatures of disease and in silico design strategy for candidate bacterial compositions
  • Bacterial compositions were designed with a set of core strains and R- group supplements to optimize functions related to engraftment, colonization resistance, restoration of epithelial barrier integrity, and reduction of inflammation (see FIG. l).
  • the different designed bacterial compositions were assessed for the following: safety and suitability, pharmacokinetic (PK), activity against pathogen targets, and impact on epithelial barrier.
  • PK pharmacokinetic
  • the design input included: human evidence of engraftment from Seres clinical trials, in human evidence of depletion in chronic liver disease (CLD) datasets; genomic profiling for strains with properties that support PK to restore colonization resistance; phenotypic for strains with properties that support safety, pharmacokinetic (PK), and key functional attributes [including data supporting efficacy against vancomycin-resistant Enterococcus (VRE)/ Carbapenem-resistant Klebsiella pneumoniae (Cr-Kpn), restoration of epithelial barrier integrity, and reduction of inflammation;] and bioprocessing profile supporting formulation as a spore .
  • VRE vancomycin-resistant Enterococcus
  • Cr-Kpn Carbapenem-resistant Klebsiella pneumoniae
  • Example 2 Effect of Designed Bacterial Compositions on Decolonization of Microbial Pathogens
  • mice On the fourth day of AVCM treatment (i.e., day 0), mice were challenged with VRE or CRE by oral gavage. Two days later, AVCM treatment was stopped. And, starting at day 2 post VRE or day 4 post CRE challenge, the animals were treated (daily for six days via oral gavage) with one of the following: (1) PBS, (2) DEI, (3) DE2, (4) DE3, (5) DE4, (6) DE5.1, (7) DE6, or (8) fecal microbial transplant (FMT). Naive animals (i.e., no pathogen challenge and no treatment) were used as control. Pathogen burden was quantified in fecal pellets by plating on selective media at various time points post VRE or CRE challenge. Statistical significance was determined by non-parametric Mann-Whitney U-test to compare pathogen colonization between DE intervention arms against the pathogen-only control group.
  • iGEM004 pathogens i.e., Cr-Kpn/CRE, VRE, and carbapenem-resistant Escherichia coli (Cr-E. coli) ⁇ were added into cultures of donor MCD4100 prior (day 4) to vancomycin pretreatment and CRE or VRE were added again (day 6) during vancomycin pretreatment.
  • test bacterial compositions i.e., DE 10, DE3, DE9, DE7, or DE8 were added over 7 days starting one day after the end of vancomycin treatment (day 10-16).
  • MCD4100 FMT was used as a positive control and no treatment was the negative control.
  • each of the bacterial compositions tested was associated with a significant reduction in pathogen titer, as compared to the no treatment group for each of the pathogens tested (i.e., CRE, VRE, and E. coli).
  • the statistical findings are summarized in Tables 8-10 (* P ⁇ 0.05, ** P ⁇ 0.01, *** P ⁇ 0.001, **** P ⁇ 0.0001).
  • All five DEs showed >5 Log reduction in Cr-Kpn titers in the in vitro iGEM experiment, and >1 Log reduction for three of the five DEs tested in vivo across multiple timepoints. Further, all five DEs show >1 Log reduction in Cr-E. coli titers in the in vitro iGEM experiment across multiple timepoints, while in vivo, three of the five DEs showed some reduction in ESBL+ E. coli titers at 1-2 timepoints, which was better than other DEs tested, but most timepoints were not statistically significant.
  • DE2 reduced CRE titer during DE dosing window and effect lead to CRE titer dropping below limit of detection.
  • DE2 also resulted in reduced VRE and E. coli titers, respectively, as compared to the no treatment group.
  • most (if not all) of the species present in DE2 successfully engrafted see FIGs. 5D-5F.
  • FIG. 5G a spore preparation results in reduced E. coli titers as compared to the no treatment group.
  • compositions provided herein were tested for their ability to produce different metabolites.
  • Exemplary methods used to assess production of different metabolites are provided below.
  • Bile acid metabolism Bacterial compositions were diluted (e.g., to a final concentration of 5xl0 6 CFU/mL) and inoculated as biological replicates in a synthetically derived fecal culture medium 4 (FCM4).
  • FCM4 is composed of complex carbohydrates and mucin in addition to other nutrients that support growth of numerous phylogenetically diverse anaerobic species found in the colon.
  • the medium was supplemented with conjugated bile acids (gCA, tCA, gCDCA and tCDCA) at a final concentration of 100 pM to allow for analysis of microbial bile acid metabolism.
  • HDAC-Glo I/II assay kit Promega
  • HeLa nuclear extract Promega
  • Assays were performed with 15 pL supernatant, 10 pL IM Tris pH 8, 75 pL of assay buffer containing diluted HeLa nuclear extract which were preincubated for 15 minutes prior to the addition of developing reagent. Luminescence was measured after 20 minutes.
  • Bile acid metabolism Bacterial cell-free supernatant was then extracted with an equal volume of acetonitrile and filtered through a 0.2 pm filter, generating samples for LC-MS analysis. Bile acids were separated using an Agilent 1260 HPLC equipped with a Microsolv bidentate Cl 8 column preceded by a 0.2 pm pre-column filter. Separation was achieved using a water and acetonitrile gradient with 0.1% formic acid at a flow rate of 0.4 ml/minute. Samples were injected at a volume of 5 pL.
  • the HPLC system was coupled to a Bruker CompassTM qTOF mass spectrometer calibrated to a mass range of 50 to 1700 m/z using the Agilent low-mass tuning mix. Each run was additionally calibrated to a reference mass solution injected at the beginning of each run. Bile acids were detected in negative mode and identified by unique m/z and retention times compared to known pure standards. Area under the peak was determined using Bruker data analysis software. Metabolites were quantified using calibration curves generated from pure standards, ranging in concentration from 0.001 pM to 100 pM.
  • DEs tested largely had similar profiles for HD AC inhibition, catalase activity, indole production, and anti-inflammatory activity.
  • secondary bile acid production specifically, compared to the other DEs tested, DE7 had reduced levels of secondary bile acids with corresponding increase in primary bile acids in culture. Without being bound to any one theory, such data suggests the importance of Clostridium scindens (STR00014) as DE7 lacked this bacterial species.
  • pH reduction DE5.2 and DE3 had the largest effect. Acidification paired with presence of SCFA has been shown to inhibit growth of relevant pathogens and could be a major factor in decolonization.
  • Bile acids profiles are also critical due to the fact that cirrhotic patients have impaired hepatic functions and can have highly altered bile acid profiles.
  • C. scindens was shown to be critical for secondary bile acid production, which is of critical importance to cirrhoitic populations due to lower liver function.
  • DE7 has a drop of the C. scindens strain with known secondary bile acid activity, which resulted in increased levels of primary bile acids in the culture compared to others [e.g., cholic acid (FIG. 6A) and chenodeoxy cholic acid (FIG. 6B)] .
  • DE5 and DE3 were designed to contain bacterial species that capture the following potentially therapeutic mechanisms of action (1) survival in NO 3 , O 2 , tetrathionate environment; (2) lactulose and rifaximin effects; (3) lantibiotic production to inhibit VRE; (4) short- chain fatty acid (SCFA) production and pH reduction to inhibit E. coli (5) nutrient competition; (6) 2 nd bile acid production; (7) butyrate production to switch colonycte metabolism; (8) anti-inflammatory activity; and/or (9) epithelial barrier protection.
  • Table 12 provides the functional profile for the bacterial species included in DE5 and DE3.
  • the bacterial species that make up DE5 and DE3 capture a spectrum of phenotypes relevant to engraftment (i.e,. 1-2), pathogen decolonization (i.e, . 3-6), and host interaction (i.e., 6-9).
  • DE treatment was administered on Days 4-10 and pathogen burden in stool was evaluated throughout the study DE5.2 also exhibited therapeutic efficacy (i.e., decolonization) when administered to both Cr-Kpn (FIGs. 7A- B and Table 13) and VRE (FIGs. 8A-B and Table 14) mouse models (see Examples 1 and 2 for methods used).
  • Example 6 In vitro and in vivo model development to target intestinal permeability, inflammation, and bacterial translocation
  • FIG. 9 provides a schematic of the experimental design. As shown in FIGs. 10A and 10B, the different designed compositions culture supernatant provided herein provide significant protection against IFN- ⁇ induced barrier damage.
  • Example 7 In vivo model of acute intestinal permeability using a hepatotoxin liver fibrosis model
  • Intestinal permeability, bacterial translocation, and local and systemic inflammation will be assessed in an in vivo rodent model of acute cirrhosis development.
  • Carbon tetrachloride (CC14) will be repeatedly administered to animals to induce recurring episodes of acute hepatotoxicity, causing hepatic decompensation and portal hypertension.
  • this model is highly reproducible to induce fibrosis and then cirrhosis with ascites in 8-12 and 12-24 weeks, respectively, of CC14 administration and is well established in the field for inducing liver injury and causing liver damage in a dose-dependent manner to evaluate the efficacy of potential hepatoprotective strategies and asses markers of liver injury.
  • Balb/c germ-free mice colonized with human fecal microbiome suspensions or one or more of the DEs described herein will be tested in this in vivo rodent model of acute cirrhosis development.

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Abstract

L'invention concerne des compositions bactériennes qui sont utiles pour traiter et/ou prévenir une maladie hépatique chronique, une neutropénie et/ou une maladie ou un trouble associé à une transplantation d'organe solide. Dans certains aspects, le traitement et/ou la prévention comprend le traitement d'une complication d'infection due à une maladie hépatique chronique, une neutropénie et/ou une transplantation d'organe solide. Les compositions bactériennes de l'invention sont conçues pour présenter une ou plusieurs caractéristiques fonctionnelles qui sont utiles pour le traitement de tels troubles et maladies.
PCT/US2024/013624 2023-01-30 2024-01-31 Utilisation de compositions bactériennes synthétiques pour un traitement infectieux Ceased WO2024163529A2 (fr)

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