METHODS AND COMPOSITIONS RELATING TO MICROBIAL TREATMENT AND DIAGNOSIS OF DISORDERS

• US 20170020932A1
• Filed: 10/05/2016
• Published: 01/26/2017
• Est. Priority Date: 10/31/2014
• Status: Abandoned Application

• Current Assignee: Pendulum Therapeutics, Inc.
• Original Assignee: Whole Biome, Inc.
• Inventors: CUTCLIFFE, Colleen, EID, John S., BULLARD, James H., SCHICKLBERGER, Marcus F.
• Application Number:
  US15/286,218
• Publication Number:
  US 20170020932A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A23L 33/135 Bacteria or derivatives thereof, e.g. probiotics
• CPC Class Codes: A23V 2002/00 Food compositions, function of food ingredients or processes for food or foodstuffs
• CPC Class Codes: A23V 2200/3202 Prebiotics, ingredients fermented in the gastrointestinal tract by beneficial microflora
• CPC Class Codes: A23V 2200/3204 Probiotics, living bacteria to be ingested for action in the digestive tract
• CPC Class Codes: A23V 2200/328 having effect on glycaemic control and diabetes
• CPC Class Codes: A23V 2200/332 Promoters of weight control and weight loss
• CPC Class Codes: A61K 2035/115 Probiotics
• CPC Class Codes: A61K 2300/00 Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
• CPC Class Codes: A61K 31/00 Medicinal preparations containing organic active ingredients
• CPC Class Codes: A61K 31/733 Fructosans, e.g. inulin
• CPC Class Codes: A61K 35/74 Bacteria therapeutic use of a bacterial protein A61K38/00
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: A61K 35/742 Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
• CPC Class Codes: A61K 35/745 Bifidobacteria
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61K 9/0053 Mouth and digestive tract, i.e. intraoral and peroral administration rectal administration A61K9/0031
• CPC Class Codes: A61K 9/2846 Poly(meth)acrylates
• CPC Class Codes: A61K 9/48 Preparations in capsules, e.g. of gelatin, of chocolate A61K9/0004 takes precedence; bite capsules A61K9/0056
• CPC Class Codes: A61K 9/4816 Wall or shell material
• CPC Class Codes: A61K 9/4891 Coated capsules; Multilayered drug free capsule shells with drug coating for immediate release A61K9/4808; osmotic devices A61K9/0004
• 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 3/10 : for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: C12N 1/20 : Bacteria; Culture media therefor
• CPC Class Codes: C12Q 1/689 : for bacteria
• CPC Class Codes: G01N 2333/605 : Glucagons
• CPC Class Codes: G01N 2800/04 : Endocrine or metabolic disorders
• CPC Class Codes: G01N 33/66 : involving blood sugars, e.g. galactose

Abstract

The present disclosure provides methods, systems, compositions, and kits to address the need for microbiome-related treatment of health conditions and disease. The present disclosure provides for treatment of metabolic conditions using microbial compositions.

Claims

1-20. -20. (canceled)

21. A method of treating a disorder, the method comprising:

administering to a subject in need thereof a pharmaceutical composition comprising a pharmaceutically-acceptable carrier and a therapeutically-effective amount of a population of isolated and purified microbes, wherein at least one of said microbes comprises a gene that encodes for an enzyme selected from the group consisting of;

butyrate kinase and butyryl Coenzyme A;

acetoacetate Coenzyme A transferase.

22. The method of claim 21, wherein the disorder is selected from the group consisting of:

metabolic disorder, obesity, diabetes, skin disorder, inflammation, gut permeability disorder, and neurological disorder.

23. The method of claim 21, wherein said population of isolated and purified microbes comprises a microbe with a rRNA sequence comprising at least about 85% sequence identity to a rRNA sequence of a microbe selected from the group consisting of:

Akkermansia muciniphila, Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Butyrivibrio fibrisolvens, Clostridium acetobutylicum, Clostridium aminophilum, Clostridium beijerinckii, Clostridium butyricum, Clostridium colinum, Clostridium indolis, Clostridium orbiscindens, Enterococcus faecium, Eubacterium hallii, Eubacterium rectale, Faecalibacterium prausnitzii, Fibrobacter succinogenes, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus caucasicus, Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus lactis, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Oscillospira guilliermondii, Roseburia cecicola, Roseburia inulinivorans, Ruminococcus flavefaciens, Ruminococcus gnavus, Ruminococcus obeum, Streptococcus cremoris, Streptococcus faecium, Streptococcus infantis, Streptococcus mutans, Streptococcus thermophilus, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus colihominis, Clostridium sporogenes, Clostridium tetani, Coprococcus, Coprococcus eutactus, Eubacterium cylindroides, Eubacterium dolichum, Eubacterium ventriosum, Roseburia faeccis, Roseburia hominis, Roseburia intestinalis, and any combination thereof.

24. The method of claim 23, wherein said population of isolated and purified microbes comprises at least two different microbial strains, wherein the microbial strain comprises at least about 85% sequence identity to a rRNA sequence of a microbe selected from the group consisting of:

Akkermansia muciniphila, Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Butyrivibrio fibrisolvens, Clostridium acetobutylicum, Clostridium aminophilum, Clostridium beijerinckii, Clostridium butyricum, Clostridium colinum, Clostridium indolis, Clostridium orbiscindens, Enterococcus faecium, Eubacterium hallii, Eubacterium rectale, Faecalibacterium prausnitzii, Fibrobacter succinogenes, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus caucasicus, Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus lactis, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Oscillospira guilliermondii, Roseburia cecicola, Roseburia inulinivorans, Ruminococcus flavefaciens, Ruminococcus gnavus, Ruminococcus obeum, Streptococcus cremoris, Streptococcus faecium, Streptococcus infantis, Streptococcus mutans, Streptococcus thermophilus, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus colihominis, Clostridium sporogenes, Clostridium tetani, Coprococcus, Coprococcus eutactus, Eubacterium cylindroides, Eubacterium dolichum, Eubacterium ventriosum, Roseburia faeccis, Roseburia hominis, Roseburia intestinalis, and any combination thereof.

25. The method of claim 21, wherein the administration is oral.

26. The method of claim 21, wherein the pharmaceutical composition comprises an enteric-coating that dissolves at a pH greater than about pH 6.5.

27. The method of claim 21, wherein the pharmaceutical composition is delivered to a small intestine, an ileum, a large intestine, or a combination thereof of a human subject.

28. The method of claim 21, wherein the pharmaceutical composition further comprises a prebiotic.

29. The method of claim 28, wherein the prebiotic is selected from the group consisting of:

complex carbohydrate, complex sugar, resistant dextrin, resistant starch, amino acid, peptide, nutritional compound, biotin, polydextrose, fructooligosaccharide (FOS), galactooligosaccharide (GOS), inulin, starch, lignin, psyllium, chitin, chitosan, gum, guar gum, high amylose cornstarch (HAS), cellulose, β

-glucan, hemi-cellulose, lactulose, mannooligosaccharide, mannan oligosaccharide (MOS), oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, pectin, resistant starch, xylooligosaccharide (XOS), carrageenan, and any combination thereof.

30. The method of claim 21, wherein the pharmaceutical composition is administered before food intake, with food intake, or both to the subject.

31. The method of claim 21, wherein the therapeutically-effective amount of the purified and isolated microbes in the pharmaceutical composition is at least about 10⁵ colony forming units (CFU).

32. The method of claim 21, wherein the pharmaceutical composition is administered after completion of an antibiotic regimen by the subject.

33. The method of claim 21, wherein the population of isolated and purified microbes comprises a first microbe and a second microbe, wherein the first microbe produces an intermediate compound of a butyrate pathway, wherein the second microbe converts the intermediate compound to butyrate.

34. The method of claim 33, wherein the intermediate compound is lactate or acetate.

35. The method of claim 21, wherein the population of isolated and purified microbes comprise a synergistic effect in the pharmaceutical composition as compared to any of the microbes individually.

36. The method of claim 21, wherein the pharmaceutical composition modulates gut permeability in the subject.

37. The method of claim 21, wherein the population of isolated and purified microbes produce butyrate in the subject.

38. The method of claim 21, further comprising determining a composition of a microbiome of the subject.

39. The method of claim 38, wherein the determining the composition of the microbiome comprises long-read sequencing.

40. The method of claim 21, wherein said treating results in an altered microbiome of the subject.