Microbiome-based informed method to formulate live biotherapeutics

Patent metadata

Field	Value
Publication number	US-11464813-B2
Application number	US-202117223754-A
Country	US
Kind code	B2
Filing date	Apr 6, 2021
Priority date	Oct 16, 2019
Publication date	Oct 11, 2022
Grant date	Oct 11, 2022

Abstract

Methods of formulating live biotherapeutics are disclosed in which a deficiency or excess of a specific bacterial strain in a person's microbiome is identified by comparing a gene-specific characterization of the person's microbiome against a comprehensive, non-redundant reference gene catalog, and the biotherapeutic is formulated by selecting bacteria to address the deficiency or excess. Embodiments include the formulation of live biotherapeutics for improving the health of a person's vaginal microbiome, i.e. using a vaginal reference gene catalog, and may be suitable for ameliorating, treating, or preventing a malignancy such as a cancer of the female genitourinary system.

First claim

The invention claimed is:

1. A live biotherapeutic formulation adapted for administration to a vaginal environment of a female human subject, comprising a selected strain or consortium of strains, wherein the selected strain or consortium of strains consists essentially of any combination of:
(i) Lactobacillus crispatus bacteria configured to express at least one of the asparagine synthase B (asnB) gene of SEQ ID NO: 2 and the asparagine synthase B (asnB) gene of SEQ ID NO: 3;
(ii) Lactobacillus crispatus bacteria containing an asparagine synthase B (asnB) gene encoding at least one of a polypeptide of SEQ ID NO: 5 and a polypeptide of SEQ ID NO: 6; and
(iii) a preselected strain or consortium of strains of Lactobacillus crispatus, comprising at least one strain selected from the group consisting of LUCA111 (ATCC Accession Deposit No. PTA-127219), LUCA011 (ATCC Accession Deposit No. PTA-127214), LUCA015 (ATCC Accession Deposit No. PTA-127215) LUCA009 (ATCC Accession Deposit No. PTA-127213), LUCA102 (ATCC Accession Deposit No. PTA-127217), LUCA006 (ATCC Accession Deposit No. PTA-127211), LUCA059 (ATCC Accession Deposit No. PTA-127216), LUCA103 (ATCC Accession Deposit No. PTA-127218), and LUCA008 (ATCC Accession Deposit No PTA-127212).

2. The live biotherapeutic formulation of claim 1 , wherein the live biotherapeutic formulation further comprises a pH buffer configured to maintain a healthy pH of the vaginal environment and a redox potential control agent.

3. The live biotherapeutic formulation of claim 1 , further comprising a pharmaceutically acceptable carrier.

4. The live biotherapeutic formulation of claim 1 , further comprising an agent adapted to reduce or remove free ammonia from the vaginal environment.

5. The live biotherapeutic formulation of claim 1 , comprising Lactobacillus crispatus bacteria configured to express the asparagine synthase B (asnB) gene of SEQ ID NO: 2.

6. The live biotherapeutic formulation of claim 1 , comprising Lactobacillus crispatus bacteria configured to express the asparagine synthase B (asnB) gene of SEQ ID NO: 3.

7. The live biotherapeutic formulation of claim 1 , comprising Lactobacillus crispatus bacteria containing an asparagine synthase B (asnB) gene encoding the polypeptide of SEQ ID NO: 5.

8. The live biotherapeutic formulation of claim 1 , comprising Lactobacillus crispatus bacteria containing an asparagine synthase B (asnB) gene encoding the polypeptide of SEQ ID NO: 6.

9. The live biotherapeutic formulation of claim 1 , further comprising a redox potential control agent.

10. The live biotherapeutic formulation of claim 1 , further comprising a pH buffer configured to maintain a healthy pH of the vaginal environment.

11. The live biotherapeutic formulation of claim 1 , further comprising an antimicrobial agent.

12. The live biotherapeutic formulation of claim 1 , further comprising a growth promoter.

13. A live biotherapeutic formulation adapted for administration to a vaginal environment of a female human subject, comprising a selected strain or consortium of strains, wherein the selected strain or consortium of strains consists essentially of any combination of:
(i) Lactobacillus crispatus bacteria configured to express at least one of the asparagine synthase B (asnB) gene of SEQ ID NO: 2 and the asparagine synthase B (asnB) gene of SEQ ID NO: 3; and
(ii) Lactobacillus crispatus bacteria containing an asparagine synthase B (asnB) gene encoding at least one of a polypeptide of SEQ ID NO: 5 and a polypeptide of SEQ ID NO: 6; and
wherein the live biotherapeutic formulation further comprises at least one of an antimicrobial agent, a redox potential control agent and a pH buffer configured to maintain a healthy pH of the vaginal environment.

14. The live biotherapeutic formulation of claim 13 , further comprising a growth promoter.

15. The live biotherapeutic formulation of claim 13 , wherein the live biotherapeutic formulation further comprises a redox potential control agent.

16. The live biotherapeutic formulation of claim 13 , wherein the live biotherapeutic formulation further comprises a pH buffer configured to maintain a healthy pH of the vaginal environment.

17. A live biotherapeutic formulation adapted for administration to a vaginal environment of a female human subject, comprising bacteria adapted to remedy a deficiency or excess of at least one bacterial strain in the subject's vaginal microbial community, wherein the bacteria comprise a selected strain or consortium of strains comprises at least one of:
(i) Lactobacillus crispatus bacteria configured to express at least one of the asparagine synthase B (asnB) gene of SEQ ID NO: 2 and the asparagine synthase B (asnB) gene of SEQ ID NO: 3; and
(ii) Lactobacillus crispatus bacteria containing an asparagine synthase B (asnB) gene encoding at least one of a polypeptide of SEQ ID NO: 5 and a polypeptide of SEQ ID NO: 6,
wherein the live biotherapeutic formulation further comprises at least one of an antimicrobial agent and a pH buffer configured to maintain a healthy pH of the vaginal environment.

18. The live biotherapeutic formulation of claim 17 , further comprising an agent adapted to reduce or remove free ammonia from the vaginal environment.

19. The live biotherapeutic formulation of claim 17 , wherein the live biotherapeutic formulation further comprises an antimicrobial agent.

20. The live biotherapeutic formulation of claim 17 , further comprising a growth promoter.

Assignees

• Univ Maryland

Inventors

• Ravel Jacques
• France Michael
• Rutt Lindsay
• Ma Bing

Classifications

• C12N1/20

  Bacteria; Culture media therefor · CPC title

• A61K35/742 Primary

  Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes · CPC title

• A61K35/74

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

• A61K35/747 Primary

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

• A61P15/02

  for disorders of the vagina · CPC title