IP Library › Granted Patent US 12,409,197
Granted Patent B2
US 12,409,197 · App. 18/424,354 · Granted Sep 9, 2025

Synergistic bacterial compositions and methods of production and use thereof

Inventors: Matthew R. Henn (Somerville, MA); Kevin Daniel Litcofsky (Boston, MA); Anthony Mario D'Onofrio (Northborough, MA); Toshiro K. Ohsumi (Cambridge, MA); Mary-Jane Lombardo Mckenzie (Arlington, MA); Geoffrey Von Maltzahn (Boston, MA); David N. Cook (Brooklyn, NY); David Arthur Berry (Brookline, MA); Noubar B. Afeyan (Lexington, MA); John Grant Aunins (Doylestown, PA)
Assignee: Seres Therapeutics, Inc.
A61K35/742A23L33/135A61K35/74A61K45/06C12N1/20A61K2035/11A61K2035/115Y02A50/30
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Quick Facts
Patent No.
US 12,409,197
App. No.
18/424,354
Granted
Sep 9, 2025
Kind
B2
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.

Claims (24)

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.

Assignments (6)
CROSS-LICENSE AGREEMENT Recorded Mar 30, 2026
From: SERES THERAPEUTICS, INC.
To: SOCIÉTÉ DES PRODUITS NESTLÉ S.A.
Reel/Frame 075314/0554 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Aug 4, 2025
From: 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
To: SERES HEALTH, INC.
Reel/Frame 071924/0799 →
SECURITY INTEREST Recorded Aug 4, 2025
From: SERES THERAPEUTICS, INC.
To: OAKTREE FUND ADMINISTRATION, LLC
Reel/Frame 071925/0410 →
RELEASE OF SECURITY INTEREST Recorded Aug 4, 2025
From: OAKTREE FUND ADMINISTRATION, LLC
To: SERES THERAPEUTICS, INC.
Reel/Frame 071926/0236 →
CHANGE OF NAME Recorded Aug 4, 2025
From: SERES HEALTH, INC.
To: SERES THERAPEUTICS, INC.
Reel/Frame 072345/0841 →
SECURITY INTEREST Recorded Mar 11, 2024
From: SERES THERAPEUTICS, INC.
To: OAKTREE FUND ADMINISTRATION, LLC
Reel/Frame 066718/0331 →
Continuity (7)
Division 17588122 · Jan 28, 2022
Division 16230807 · Dec 21, 2018
Division 15039007
Provisional Application 61908702 · Nov 25, 2013
Provisional Application 61908698 · Nov 25, 2013
Provisional Application 62004187 · May 28, 2014
Related Publication 20240325464A1 · Oct 3, 2024
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