Microbiome-based informed method to formulate live biotherapeutics
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.
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.