COMPOSITIONS AND METHODS FOR TREATING OBESITY AND RELATED DISORDERS BY CHARACTERIZING AND RESTORING MAMMALIAN BACTERIAL MICROBIOTA

• US 20120058094A1
• Filed: 08/19/2011
• Published: 03/08/2012
• Est. Priority Date: 08/20/2010
• Status: Active Grant

• Current Assignee: New York University
• Original Assignee: Dow Global Technologies LLC (Dow, Inc.), New York University
• Inventors: Blaser, Martin J., Cho, Ilseung, Nondorf, Laura, Waters, Bart
• Granted Patent: US 9,386,793 B2
• Time in Patent Office: Days
• US Class Current: 424/93.41
• CPC Class Codes: A23L 33/10 using additives addition of substantially indigestible substances A23L33/21
• CPC Class Codes: A23L 33/135 Bacteria or derivatives thereof, e.g. probiotics
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61K 9/0031 Rectum, anus
• CPC Class Codes: A61K 9/0053 Mouth and digestive tract, i.e. intraoral and peroral administration rectal administration A61K9/0031
• CPC Class Codes: A61P 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 3/04 Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 3/06 Antihyperlipidemics
• CPC Class Codes: A61P 3/08 for glucose homeostasis pancreatic hormones A61P5/48
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis

Abstract

The present invention relates to characterizing changes in mammalian intestinal microbiota associated with associated with high-fat and low-fat diets and with diets containing hydroxypropylmethylcellulose (HPMC) and related methods for diagnosing, preventing and treating obesity and related conditions such as metabolic syndrome and diabetes mellitus. Therapeutic methods of the invention involve the use of probiotics, and/or prebiotics, and/or narrow spectrum antibiotics/anti-bacterial agents that are capable of restoring healthy mammalian bacterial intestinal microbiota.

Claims

1. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal;

(b) measuring the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal are increased as compared to the healthy control.

77. The method of any one of claims 1-52 and 113-118, wherein the mammal is human.

78. The method of any one of claims 1-52 and 113-118, wherein the mammal is on a high fat diet.

79. The method of any one of claims 1, 7, 8, 19, 25-27, 33-35, 41, 47, and 113 wherein the populations of bacteria are determined by qPCR of bacterial 16S rRNA.

2. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal.

3. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal.

4. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal

5. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of the mammal.

6. A method of lowering populations of Firmicutes and/or Bacteroidetes in the ileal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

7. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal;

(b) measuring the populations of Firmicutes in the cecal and/or fecal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal are increased as compared to the healthy control.

8. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the ratio of the populations of Firmicutes to the populations of Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal;

(b) measuring the F/E ratio in the cecal and/or fecal microbiota of a healthy control;

(c) comparing the F/E ratios measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the F/E ratio is increased in the cecal and/or fecal microbiota of the mammal as compared to the healthy control.

9. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic compostion lowers the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal.

10. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal.

53. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition comprises at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS).

54. The method of claim 53, wherein said strain is a live bacterial strain or spores.

55. The method of claim 54, wherein said strain is a conditionally lethal bacterial strain.

56. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition further comprises a buffering agent.

57. The method of claim 56, wherein the buffering agent is selected from the group consisting of sodium bicarbonate, juice, milk, yogurt, and infant formula.

58. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered conjointly with a prebiotic composition which stimulates growth and/or metabolic activity of bacteria contained in the probiotic composition.

59. The method of claim 58, wherein the probiotic and prebiotic compositions are administered in one composition.

60. The method of claim 58, wherein the probiotic and prebiotic compositions are administered simultaneously as two separate compositions.

61. The method of claim 58, wherein the probiotic and prebiotic compositions are administered sequentially.

62. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition further comprises a compound selected from the group consisting of xylose, arabinose, ribose, galactose, rhamnose, cellobiose, fructose, lactose, salicin, sucrose, glucose, esculin, tween 80, trehalose, maltose, mannose, mellibiose, raffinose, fructooligosaccharides, galactooligosaccharides, amino acids, alcohols, and any combinations thereof.

63. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition further comprises a compound selected from the group consisting of trehalose, cellobiose, maltose, mannose, sucrose, fructose, galactose, lactose, salicin, melibiose, raffinose, and any combinations thereof.

64. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition further comprises a compound selected from the group consisting of water-soluble cellulose derivatives, water-insoluble cellulose derivatives, unprocessed oatmeal, metamucil, all-bran, and any combinations thereof.

65. The method of claim 64, wherein the water-soluble cellulose derivative is selected from the group consisting of methylcellulose, methyl ethyl cellulose, hydroxyethyl cellulose, ethyl hydroxyethyl cellulose, cationic hydroxyethyl cellulose, hydroxypropyl cellulose, hydroxyethyl methylcellulose, hydroxypropyl methylcellulose, and carboxymethyl cellulose.

66. The method of claim 64, wherein the water-insoluble cellulose derivative is ethyl cellulose.

67. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered orally.

68. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered in a form of a capsule.

69. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered rectally.

70. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered in a form of a suppository.

71. The method of any one of claims 2, 3, 9, 10, 14, 15, 20, 21, 36, 37, 42, 43, 48, 49, 114, and 115, wherein the probiotic composition is administered by a method selected from the group consisting of esophagogastroduodenoscopy, colonoscopy, nasogastric tube, and orogastric tube.

11. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal.

72. The method of any one of claims 4, 5, 6, 11-13, 16-18, 22-24, 32, 38-40, 44-46, 50-52, and 116-118, wherein the prebiotic composition comprises a compound selected from the group consisting of trehalose, cellobiose, maltose, mannose, sucrose, fructose, galactose, lactose, melibiose, raffinose, and any combinations thereof

73. The method of any one of claims 4, 5, 6, 11-13, 16-18, 22-24, 32, 38-40, 44-46, 50-52, and 116-118, wherein the prebiotic composition comprises a compound selected from the group consisting of xylose, arabinose, ribose, galactose, rhamnose, cellobiose, fructose, lactose, salicin, sucrose, glucose, esculin, tween 80, trehalose, maltose, mannose, mellibiose, raffinose, fructooligosaccharides, galactooligosaccharides, amino acids, alcohols, water-soluble cellulose derivatives, water-insoluble cellulose derivatives, unprocessed oatmeal, metamucil, all-bran, and any combinations thereof.

74. The method of claim 73, wherein the water-soluble cellulose derivative is selected from the group consisting of methylcellulose, methyl ethyl cellulose, hydroxyethyl cellulose, ethyl hydroxyethyl cellulose, cationic hydroxyethyl cellulose, hydroxypropyl cellulose, hydroxyethyl methylcellulose, hydroxypropyl methylcellulose, and carboxymethyl cellulose.

75. The method of claim 73, wherein the water-insoluble cellulose derivative is ethyl cellulose.

76. The method of any one of claims 4, 5, 6, 11-13, 16-18, 22-24, 32, 38-40, 44-46, 50-52, and 116-118, wherein the prebiotic composition is administered orally or rectally.

12. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the populations of Firmicutes in the cecal and/or fecal microbiota of the mammal.

13. A method of lowering the populations of Firmicutes in the cecal and/or fecal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

14. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the ratio of the populations of Firmicutes to Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal.

15. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the ratio of the populations of Firmicutes to Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal.

16. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the ratio of the populations of Firmicutes to Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal.

17. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the ratio of the populations of Firmicutes to Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal.

18. A method of lowering the ratio of the populations of Firmicutes to Eubacteria (F/E ratio) in the cecal and/or fecal microbiota of the mammal comprising administering to the mammal a prebiotic composition.

19. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal;

(b) measuring the populations of the same genus in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal are decreased as compared to the healthy control.

20. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition stimulates growth or metabolic activity of at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal.

25. A method for determining whether weight loss can be achieved in a mammal by the method of claim 20 or 22 comprising

(a) measuring the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal;

(b) measuring the populations of the same genus in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that weight loss can be achieved in the mammal by the method of claim 20 or 22 if the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal is decreased as compared to the healthy control.

21. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition stimulates growth or metabolic activity of at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal.

26. A method for determining whether a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis can be prevented or treated by the method of claim 21 or 23 comprising

(a) measuring the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal;

(b) measuring the populations of the same genus in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the disease in the mammal can be prevented or treated by the method of claim 21 or 23 if the populations of at least one genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal is decreased as compared to the healthy control.

22. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition stimulates growth or metabolic activity of at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal.

23. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition stimulates growth or metabolic activity of at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of the mammal.

24. A method of stimulating growth or metabolic activity of at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS) in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

27. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal;

(b) measuring the populations of the same taxon in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the populations of at least one taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal is increased as compared to the healthy control.

28. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a composition or a compound, wherein said composition or compound inhibits growth or metabolic activity of at least one strain from the taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal.

30. The method of claim 28 or 29, wherein the compound is a narrow spectrum antibiotic.

31. The method of claim 28 or 29, wherein the composition is a probiotic composition comprising at least one strain from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS).

33. A method for determining whether weight loss can be achieved in a mammal by the method of claim 28 comprising

(a) measuring the populations of at least one taxon selected from Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal;

(b) measuring the populations of the same taxon in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that weight loss can be achieved in the mammal by the method of claim 28 if the populations of at least one taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal is increased as compared to the healthy control.

29. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a composition or a compound, wherein said composition or compound inhibits growth or activity of at least one strain from the taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal.

34. A method for determining whether a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis can be prevented or treated by the method of claim 29 comprising

(a) measuring the populations of at least one taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal;

(b) measuring the populations of the same taxon in the intestinal microbiota of a healthy control;

(c) comparing the populations measured in steps (a) and (b), and

(d) determining that the disease in the mammal can be prevented or treated by the method of claim 29 if the populations of at least one taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of the mammal is increased as compared to the healthy control.

32. A method of inhibiting growth or metabolic activity of at least one strain from the taxon selected from the group consisting of Johnsonella, Oscillibacter, Lachnospiraceae, Ruminococcaceae, and Clostridiales in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

35. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one genus selected from the group consisting of Coprobacillus (C), Sporacetigenium (S), and Holdemania (H), in the intestinal microbiota of the mammal;

(b) measuring the populations of at least one genus selected from Johnsonella (J) and Oscillibacter (O) in the intestinal microbiota of the mammal;

(c) determining a ratio of one of C+S+H, C+H, C+S, S+H, C, S, or H as measured in step (a) to one of J+O, J, or O as measured in step (b), and

(d) determining that the mammal has a predisposition to the disease if the ratio in step (c) is below 1, or determining that the mammal has no predisposition to the disease if the ratio in step (c) is above 3.

36. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), C+H, C+S, S+H, or C+S+H to populations of one of (b) Johnsonella (J), Oscillibacter (O), or J+O to above 3 in the intestinal microbiota of the mammal.

37. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), C+H, C+S, S+H, or C+S+H to populations of one of (b) Johnsonella (J), Oscillibacter (O), or J+O to above 3 in the intestinal microbiota of the mammal.

38. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), C+H, C+S, S+H, or C+S+H to populations of one of (b) Johnsonella (J), Oscillibacter (O), or J+O to above 3 in the intestinal microbiota of the mammal.

39. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), C+H, C+S, S+H, or C+S+H to populations of one of (b) Johnsonella (J), Oscillibacter (O), or J+O to above 3 in the intestinal microbiota of the mammal.

40. A method of increasing the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), C+H, C+S, S+H, or C+S+H to populations of one of (b) Johnsonella (J), Oscillibacter (O), or J+O in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

41. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one genus selected from the group consisting of Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), and Clostridium cocleatum (Cc) in the intestinal microbiota of the mammal;

(b) measuring the populations of Firmicutes (F) in the intestinal microbiota of the mammal;

(c) determining a ratio of one of C+S+H, C+H, C+S, S+H, C, S, H, EIS, PIS, or Cc as measured in step (a) to F as measured in step (b), and

(d) determining that the mammal has a predisposition to the disease if the ratio in step (c) is below 0.1, or determining that the mammal has no predisposition to the disease if the ratio in step (c) is above 0.1.

42. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), C+H, C+S, S+H, or C+S+H to populations of (b) Firmicutes (F) to above 0.1 in the intestinal microbiota of the mammal.

43. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), C+H, C+S, S+H, or C+S+H to populations of (b) Firmicutes (F) to above 0.1 in the intestinal microbiota of the mammal.

44. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), C+H, C+S, S+H, or C+S+H to populations of (b) Firmicutes (F) to above 0.1 in the intestinal microbiota of the mammal.

45. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), C+H, C+S, S+H, or C+S+H to populations of (b) Firmicutes (F) to above 0.1 in the intestinal microbiota of the mammal.

46. A method of increasing the ratio of populations of one of (a) Coprobacillus (C), Sporacetigenium (S), Holdemania (H), Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), C+H, C+S, S+H, or C+S+H to populations of (b) Firmicutes (F) in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

47. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one family selected from Erysipelotrichaceae and Peptostreptococcacea, in the intestinal microbiota of the mammal;

(b) measuring the populations of at least one family selected from Lachnospiraceae and Ruminococcaceae in the intestinal microbiota of the mammal;

(c) determining a ratio of one of Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea as measured in step (a) to one of Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae as measured in step (b), and

(d) determining that the mammal has a predisposition to the disease if the ratio in step (c) is below 0.1, or determining that the mammal has no predisposition to the disease if the ratio in step (c) is above 0.1.

48. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea to populations of one of (b) Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae to above 0.1 in the intestinal microbiota of the mammal

49. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea to populations of one of (b) Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae to above 0.1 in the intestinal microbiota of the mammal.

50. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea to populations of one of (b) Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae to above 0.1 in the intestinal microbiota of the mammal.

51. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea to populations of one of (b) Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae to above 0.1 in the intestinal microbiota of the mammal.

52. A method of increasing the ratio of populations of one of (a) Erysipelotrichaceae+Peptostreptococcacea, Erysipelotrichaceae, or Peptostreptococcacea to populations of one of (b) Lachnospiraceae+Ruminococcaceae, Lachnospiraceae, or Ruminococcaceae in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

80. A probiotic composition comprising one or more strains from the genus selected from the group consisting of Coprobacillus, Sporacetigenium, Holdemania, Dorea, Blautia, Enterococcus, Erysipelotrichaceae Incertae Sedis (EIS), Clostridium cocleatum, and Peptosteptococcaceae IS (PIS).

81. The composition of claim 80, wherein said strain is a live bacterial strain or spores.

82. The composition of claim 80, wherein said strain is a conditionally lethal bacterial strain.

83. The composition of claim 80 which further comprises a buffering agent.

84. The composition of claim 83, wherein the buffering agent is selected from the group consisting of sodium bicarbonate, juice, milk, yogurt, and infant formula.

85. The composition of claim 80, which further comprises a compound selected from the group consisting of xylose, arabinose, ribose, galactose, rhamnose, cellobiose, fructose, lactose, salicin, sucrose, glucose, esculin, tween 80, trehalose, maltose, and mannose, and any combinations thereof.

86. The composition of claim 80, which further comprises a compound selected from the group consisting of trehalose, cellobiose, maltose, mannose, sucrose, fructose, galactose, lactose, salicin, melibiose, raffinose, and any combinations thereof.

87. The composition of claim 80, which further comprises a compound selected from the group consisting of water-soluble cellulose derivatives, water-insoluble cellulose derivatives, unprocessed oatmeal, metamucil, all-bran, and any combinations thereof.

88. The composition of claim 87, wherein the water-soluble cellulose derivative is selected from the group consisting of methylcellulose, methyl ethyl cellulose, hydroxyethyl cellulose, ethyl hydroxyethyl cellulose, cationic hydroxyethyl cellulose, hydroxypropyl cellulose, hydroxyethyl methylcellulose, hydroxypropyl methylcellulose, and carboxymethyl cellulose.

89. The composition of claim 87, wherein the water-insoluble cellulose derivative is ethyl cellulose.

90. The composition of any one of claims 80-89 which is orally administrable.

91. The composition of any one of claims 80-89 which is in a form of a capsule.

92. The composition of any one of claims 80-83 and 85-89 which is in a form of a suppository.

93. A probiotic composition comprising one or more strains from the genus Holdemania and one or more compounds selected from the group consisting of Tween 80, esculin, fructose, glucose, lactose, maltose, salicin, and sucrose.94. A probiotic composition comprising one or more strains from the genus Sporoacetigenicum and one or more compounds selected from the group consisting of arabinose, fructose, glucose, maltose, and xylose.

95. A probiotic composition comprising one or more strains from the genus Coprobacillus and one or more compounds selected from the group consisting of mannose, fructose, sucrose, maltose, cellobiose, trehalose, salicin, lactose, glucose, and galactose.

96. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the total number of Butyryl CoA transferase (BCoAT)-encoding genes in the intestinal microbiota of the mammal;

(b) measuring the total number of BCoAT-encoding genes in the intestinal microbiota of a healthy control;

(c) comparing the total number of BCoAT-encoding genes measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the total number of BCoAT-encoding genes in the intestinal microbiota of the mammal is increased as compared to the healthy control.

97. The method of claim 96, wherein the total number of BCoAT-encoding genes is measured by qPCR.

98. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring a ratio of the total number of Butyryl CoA transferase (BCoAT)-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal;

(b) measuring a ratio of the total number of BCoAT-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of a healthy control;

(c) comparing the ratios of the total number of BCoAT-encoding genes to copies of Bacteroidetes 16S rRNA measured in steps (a) and (b), and

(d) determining that the mammal has a predisposition to the disease if the ratio of the total number of BCoAT-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal is increased as compared to the healthy control.

99. The method of claim 98, wherein the ratio of the total number of BCoAT-encoding genes to copies of Bacteroidetes 16S rRNA is measured by qPCR.

100. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the levels of Butyryl CoA transferase (BCoAT) enzyme and/or the levels of butyrate in the intestinal microbiota of the mammal.

105. The method of any one of claims 100-104, wherein the levels of Butyryl CoA transferase (BCoAT) enzyme are measured by determining the total number of BCoAT-encoding genes or by BCoAT enzyme functional assay.

106. The method of any one of claims 100-104, wherein the levels of butyrate are measured using chromatographic methods.

101. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the levels of Butyryl CoA transferase (BCoAT) enzyme and/or the levels of butyrate in the intestinal microbiota of the mammal.

102. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the levels of Butyryl CoA transferase (BCoAT) enzyme and/or the levels of butyrate in the intestinal microbiota of the mammal.

103. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the levels of Butyryl CoA transferase (BCoAT) enzyme and/or the levels of butyrate in the intestinal microbiota of the mammal

104. A method of lowering the levels of Butyryl CoA Transferase (BcoAT) enzyme and/or the levels of butyrate in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

107. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the ratio of the total number of Butyryl CoA transferase (BCoAT)-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal.

112. The method of any one of claims 107-111, wherein the ratio of the total number of BCoAT-encoding genes to copies of Bacteroidetes 16S rRNA is measured by qPCR.

108. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition lowers the ratio of the total number of Butyryl CoA transferase (BCoAT)-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal.

109. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the ratio of the total number of Butyryl CoA transferase (BCoAT)-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal.

110. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition lowers the ratio of the total number of Butyryl CoA transferase (BCoAT)-encoding genes to copies of Bacteroidetes 16S rRNA in the intestinal microbiota of the mammal.

111. A method of lowering the ratio of the total number of Butyryl CoA Transferase (BcoAT)- encoding genes to copies of bacteroidetes 16S rRNA in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

113. A method for diagnosing predisposition to a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising

(a) measuring the populations of at least one genus selected from the group consisting of Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), and Clostridium cocleatum (Cc) in the intestinal microbiota of the mammal;

(b) measuring the populations of Johnsonella (J) in the intestinal microbiota of the mammal;

(c) determining a ratio of one of EIS, PIS, EIS+PIS, or Cc as measured in step (a) to J as measured in step (b), and

(d) determining that the mammal has a predisposition to the disease if the ratio in step (c) is below 1, or determining that the mammal has no predisposition to the disease if the ratio in step (c) is above 1.

114. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), or EIS+PIS to populations of (b) Johnsonella (J) to above 1 in the intestinal microbiota of the mammal

115. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a probiotic composition, wherein said probiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), or EIS+PIS to populations of (b) Johnsonella (J) to above 1 in the intestinal microbiota of the mammal.

116. A method for promoting weight loss in a mammal comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), or EIS+PIS to populations of (b) Johnsonella (J) to above 1 in the intestinal microbiota of the mammal.

117. A method for preventing or treating a disease in a mammal selected from the group consisting of obesity, metabolic syndrome, diabetes mellitus, insulin-deficiency related disorders, insulin-resistance related disorders, glucose intolerance, non-alcoholic fatty liver, abnormal lipid metabolism, and atherosclerosis, said method comprising administering to the mammal a therapeutically effective amount of a prebiotic composition, wherein said prebiotic composition increases the ratio of populations of one of (a) Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), or EIS+PIS to populations of (b) Johnsonella (J) to above 1 in the intestinal microbiota of the mammal.

118. A method of increasing the ratio of populations of one of (a) Erysipelotrichaceae Incertae Sedis (EIS), Peptostreptococcaceae Incertae Sedis (PIS), Clostridium cocleatum (Cc), or EIS+PIS to populations of (b) Johnsonella (J) in the intestinal microbiota of a mammal comprising administering to the mammal a prebiotic composition.

119. A probiotic composition comprising one or more strains from the genus Clostridium cocleatum and one or more compounds selected from the group consisting of cellobiose, fructose, galactose, glucose, inulin, lactose, maltose, mannose, mellibiose, raffinose, and sucrose.