Compositions and methods comprising a defined microbiome and methods of use thereof

Patent metadata

Field	Value
Publication number	US-2016243175-A1
Application number	US-201615090609-A
Country	US
Kind code	A1
Filing date	Apr 4, 2016
Priority date	Oct 3, 2013
Publication date	Aug 25, 2016
Grant date	—

Abstract

The invention features the use of a defined microbial consortia for the replacement of a gut microbiome associated with disease. In particular, the invention provides for the treatment of hyperammonemia, Clostridium difficile colitis, hepatic encephalopathy associated with cirrhosis, and inflammatory bowel disease.

First claim

1 . A method for altering gut microbiota to reduce urease gene content or activity via reducing or eliminating urease producing bacteria from the gut in order to reduce ammonia production therefrom, in a subject in need thereof, the method comprising; administering to the subject a composition comprising a defined microbial consortia of bacteria having minimal urease activity or no urease gene content, under conditions wherein said bacteria colonize the gut, thereby reducing urease gene content, or activity or both in gut microbiota and ammonia production in the gut of the subject.

2 . The method of claim 1 , wherein said subject is a human and has a disease associated with an undesirable gut microbiome, said treatment alleviating symptoms associated with said undesirable gut microbiome,
wherein said administration of the defined microbial consortia is via a route selected from the group consisting of by endoscopy, by enteroscopy, by colonoscopy, a nasoduodenal catheter, an enema and orally in a consumable capsule or pill and the defined microbial consortia consists of Clostridium sp. Lactobacillus sp., Lactobacillus murinus, Mucispirillum schaedleri, Eubacterium plexicaudatum Firmicutes bacterium, Clostridium sp. and Parabacteroides sp.

3 . (canceled)

4 . The method of claim 2 , comprising administering to the subject an effective amount of one or more antibiotics sufficient to reduce the population of bacteria in the gut microbiota to a level suitable for repopulation of newly introduced bacteria prior to administration of said defined microbial consortia of bacteria, wherein one or more antibiotics is administered for at least about 48, 72, or 96 hours prior to the administration of the defined microbial consortia.

5 . The method of claim 2 , comprising administering an effective amount of a purgative agent to the subject, thereby purging the intestines of said subject prior to administration of said defined microbial consortia of bacteria.

6 . The method of claim 5 , wherein said subject is administered antibiotics and a purging agent prior to administration of said defined microbial consortia of bacteria, said antibiotic being one or both of neomycin and vancomycin, and said purging agent being administered for at least about 12-36 hours prior to the administration of the defined microbial consortia.

7 . The method of claim 5 , wherein said purgative agent is selected from the group consisting of polyethene glycol (PEG), magnesium citrate, sodium picosulphate plus magnesium citrate, PEG plus ascorbic acid, and sodium phosphate.

8 - 11 . (canceled)

12 . The method of claim 1 , wherein the defined microbial consortia comprises one or more bacteria belonging to a genus selected from the group consisting of Bifidobacterium, Bacteroides, Tannerella, Parabacteroides, Bacillus, Lactobacillus, Anaerostipes, Anaerostipes, Blautia, Coprococcus, Dorea, Clostridium XI, Collinsella , and Paraprevotella.

13 . The method of claim 1 , wherein the defined microbial consortia consists of Paraprevotella clara, Bifidobacterium longum, Collinsella aerofaciens, Coprococcus comes, Dorea longicatena, Bacteroides eggerthii str., and Bacteroides vulgates.

14 . (canceled)

15 . The method of claim 2 , wherein the disease is a metabolic disorder selected from the group consisting of Carbamyl phosphate synthetase deficiency, Ornithine transcarbamylase deficiency, Arginosuccinate synthetase deficiency, Arginosuccinate lyase deficiency, Arginase deficiency, or N-acetylglutamate synthetase deficiency, Propionic acidemia, Methylmalonic acidemia, Isovaleric acidemia, Fatty Acid Oxidation Disorder, Short chain acyl-coA dehydrogenase deficiency, Medium-chain acyl-coA dehydrogenase deficiency, Long-chain acyl-coA dehydrogenase deficiency, a disorder of Amino Acid Transport, Lysinuric protein intolerance, Hyperammonemia, hyperornithinemia, homocitrullinemia syndrome, Transient Hyperammonemia of the Newborn, hyperinsulinemia, or hypoglycemia syndrome.

16 . The method of claim 2 , wherein the disease is Clostridium difficile colitis, inflammatory bowel disease, atherosclerosis, obesity, metabolic syndrome, diabetes, colon cancer, cirrhosis, or hepatic encephalopathy.

17 . The method of claim 2 , wherein treatment efficacy is monitored by assessing a parameter selected from the group consisting of 16S rRNA copy number, 16S rRNA gene sequencing, fecal urease levels, fecal or circulating amino acids, biogenic amines, fecal ammonia levels, and circulating ammonia levels, said 16S rRNA copy number optionally being reduced by at least about 2-4 logs prior to administration of said altered gut microbiota.

18 . (canceled)

19 . A composition comprising an effective amount of a defined microbial consortia comprising a combination of one or more bacteria selected from the group consisting of Bifidobacterium, Collinsella, Bacteroides, Petrimonas, Tannerella, Parabacteroides, Bacillus, Isobaculum, Enterococcus, Lactobacillus, Anaerostipes, Blautia, Coprococcus, Dorea, Oribacterium, Syntrophococcus, Clostridium XI, Catenibacterium, Mitsuokella, Escherichia/Shigella , and Parapervotella , said consortia being effective to reduce urease levels in gut microbiota, said composition being present in a biological carrier suitable for administration to, and colonization, of the gut.

20 . (canceled)

21 . The composition of claim 19 , wherein said defined microbial consortia consists of Paraprevotella clara, Bifidobacterium longum, Collinsella aerofaciens, Coprococcus comes, Dorea longicatena, Bacteroides eggerthii str., and Bacteroides vulgates.

22 . A process for preparing a defined microbial consortia composition for decreasing urease levels in the gut, said process comprising;
a) preparing a liquid culture of bacteria cells comprising said defined microbial consortia of claim 19 , b) harvesting said cells after a suitable period of growth; c) resuspending said cells in lyophilization medium, said medium optionally comprising cyroprotectorants, biological or chemical oxygen scavengers; d) transferring said resuspended cells into a lyophilizer under anaerobic conditions and lyophilizing said cells; e) packaging said lyophilized cells into a capsule or pill under oxygen free conditions; and f) optionally packaging said capsules or pill into glass ampoules to maintain anaerobic conditions during shipment and storage.

23 . A capsule comprising the defined microbial consortia produced by the method of claim 22 .

24 . A method for altering gut microbiota to reduce urease gene content or activity via reducing or eliminating urease producing bacteria from the gut in order to reduce ammonia production therefrom, in a subject in need thereof, the method comprising; administering to the subject a composition comprising a single bacteria species lacking urease gene content or activity, under conditions wherein said bacteria colonizes the gut, thereby reducing urease gene content, or activity or both in gut microbiota and ammonia production in the gut of the subject.

25 . The method of claim 24 , comprising administering to the human subject an effective amount of one or more antibiotics sufficient to reduce the population of bacteria in the gut microbiota to a level suitable for repopulation of newly introduced bacteria prior to administration of said single bacterial species, said method optionally comprising administering an effective amount of a purgative agent to the subject, thereby purging the i

Assignees

• Univ Pennsylvania

Inventors

• Bushman Frederic
• Wu Gary
• Lewis James
• Goulian Mark

Classifications

• A61K35/744

  Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs · CPC title

• C12N1/20

  Bacteria; Culture media therefor · CPC title

• A61K35/747 Primary

  Lactobacilli, e.g. L. acidophilus or L. brevis · CPC title

• A61K9/48

  Preparations in capsules, e.g. of gelatin, of chocolate {(A61K9/0004 takes precedence; bite capsules A61K9/0056)} · CPC title

• A61K35/74

  Bacteria (therapeutic use of a bacterial protein A61K38/00) · CPC title