Synergistic bacterial compositions and methods of production and use thereof

Patent metadata

Field	Value
Publication number	US-12409197-B2
Application number	US-202418424354-A
Country	US
Kind code	B2
Filing date	Jan 26, 2024
Priority date	Nov 25, 2013
Publication date	Sep 9, 2025
Grant date	Sep 9, 2025

Abstract

Provided are therapeutic compositions containing microbial populations for prevention, treatment and reduction of symptoms associated with a dysbiosis of a mammalian subject such as a human.

First claim

What is claimed is:

1. A method of functionally populating the gastrointestinal tract of a human subject in need thereof, comprising administering to the subject a composition comprising: (a) a first species of an isolated bacterium capable of forming a spore, (b) a second species of isolated bacterium capable of forming a spore, and (c) a third species of isolated bacterium capable of forming a spore, and (d) a capsule;
wherein the capsule encapsulates the first species, the second species, and third species; wherein the first species, the second species, and the third species are not identical;
wherein the first species is Clostridium orbiscindens , the second species is Clostridium bolteae , and the third species is Lachnospiraceae bacterium 5_1_57FAA,
wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to a 16S rDNA the sequence set forth in SEQ ID NO: 609; and
wherein a combination of the first species, the second species, and the third species is capable of decreasing and/or inhibiting the growth and/or colonization of at least one type of pathogenic bacteria.

2. The method of claim 1 , wherein the combination of the first species, the second species, and the third species is capable of synergistically inhibiting the growth and/or colonization of the at least one type of pathogenic bacteria in a CivSim assay with a confidence interval of >99% (++++).

3. The method of claim 1 , wherein one or more of the first species, the second species, and the third species are in the form of spores.

4. The method of claim 3 , wherein the first species, the second species, and the third species are in the form of spores.

5. The method of claim 1 , wherein the composition further comprises a capsule, which encapsulates one or more of the first species, the second species, and the third species.

6. The method of claim 5 , wherein the capsule is enterically coated.

7. The method of claim 5 , wherein the capsule encapsulates the first species, the second species, and the third species.

8. The method of claim 1 , wherein the composition further comprises glycerol.

9. The method of claim 7 , wherein the composition further comprises glycerol.

10. The method of claim 1 , wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 98% identical to the sequence set forth in SEQ ID NO: 609.

11. The method of claim 1 , wherein the Clostridium bolteae comprises a 16S rDNA sequence that is at least 97% identical to the sequence set forth in SEQ ID NO: 559.

12. The method of claim 1 , wherein the Lachnospiraceae bacterium 5_1_57FAA comprises a 16S rDNA sequence that is at least 97% identical to the sequence set forth in SEQ ID NO: 1054.

13. The method of claim 1 , wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 99% identical to the sequence set forth in SEQ ID NO: 609.

14. The method of claim 1 , wherein the Clostridium orbiscindens comprises the 16S rDNA sequence set forth in SEQ ID NO: 609.

15. The method of claim 1 , wherein the Clostridium bolteae comprises a 16S rDNA sequence that is at least 98% identical to the sequence set forth in SEQ ID NO: 559.

16. The method of claim 1 , wherein the Clostridium bolteae comprises a 16S rDNA sequence that is at least 99% identical to the sequence set forth in SEQ ID NO: 559.

17. The method of claim 1 , wherein the Clostridium bolteae comprises the 16S rDNA sequence set forth in SEQ ID NO: 559.

18. The method of claim 1 , wherein the Lachnospiraceae bacterium 5_1_57FAA comprises a 16S rDNA sequence that is at least 98% identical to the sequence set forth in SEQ ID NO: 1054.

19. The method of claim 1 , wherein the Lachnospiraceae bacterium 5_1_57FAA comprises a 16S rDNA sequence that is at least 99% identical to the sequence set forth in SEQ ID NO: 1054.

20. The method of claim 1 , wherein the Lachnospiraceae bacterium 5_1_57FAA comprises the 16S rDNA sequence set forth in SEQ ID NO: 1054.

Assignees

• Seres Therapeutics Inc

Inventors

• Henn Matthew R
• Litcofsky Kevin Daniel
• D'Onofrio Anthony Mario
• Ohsumi Toshiro K
• Mckenzie Mary-Jane Lombardo
• Von Maltzahn Geoffrey
• Cook David N
• Berry David Arthur
• Afeyan Noubar B
• Aunins John Grant

Classifications

• A61K45/06

  Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca · CPC title

• Y02A50/30

  Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change · CPC title

• A23L33/135 Primary

  Bacteria or derivatives thereof, e.g. probiotics · CPC title

• C12N1/20

  Bacteria; Culture media therefor · CPC title

• A61K2035/115

  Probiotics · CPC title