Microbiome-based informed method to formulate live biotherapeutics

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.

1 - 20 . (canceled) 
     
     
         21 . A method for ameliorating, treating, or preventing human papillomavirus (HPV) infection of the female genitourinary system, comprising:
 administering a remedial live biotherapeutic formulation to a vaginal environment of a female human subject,   wherein the remedial live biotherapeutic formulation comprises bacteria adapted to remedy a deficiency or excess of at least one bacterial strain in the subject's vaginal microbial community, and   wherein the bacteria comprise a selected strain or consortium of strains comprising 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; 
 (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) at least one strain selected from the group consisting of LUCA111, LUCA011, LUCA015, LUCA009, LUCA102, LUCA006, LUCA059, LUCA103, and LUCA008. 
   
     
     
         22 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises a pharmaceutically acceptable carrier. 
     
     
         23 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises an agent adapted to reduce or remove free ammonia from the vaginal environment. 
     
     
         24 . The method of  claim 21 , wherein the  Lactobacillus  crispatus bacteria are configured to express the asparagine synthase B (asnB) gene of SEQ ID NO: 2. 
     
     
         25 . The method of  claim 21 , wherein the  Lactobacillus  crispatus bacteria are configured to express the asparagine synthase B (asnB) gene of SEQ ID NO: 3. 
     
     
         26 . The method of  claim 21 , wherein the  Lactobacillus  crispatus bacteria containing an asparagine synthase B (asnB) gene encode the polypeptide of SEQ ID NO: 5. 
     
     
         27 . The method of  claim 21 , wherein the  Lactobacillus  crispatus bacteria containing an asparagine synthase B (asnB) gene encode the polypeptide of SEQ ID NO: 6. 
     
     
         28 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises a redox potential control agent. 
     
     
         29 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises a pH buffer configured to maintain a healthy pH of the vaginal environment. 
     
     
         30 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises an antimicrobial agent. 
     
     
         31 . The method of  claim 21 , wherein the live biotherapeutic formulation further comprises a growth promoter. 
     
     
         32 . The method of  claim 21 , wherein the administering step achieves an improvement in the genitourinary health of the subject selected from the group consisting of decreasing ammonia in the vaginal environment of the subject, reducing inflammation in the subject, suppressing the growth or hampering the survival of at least one of  Gardnerella vaginalis  and  Prevotella bivia  in the vagina of the subject, and combinations thereof. 
     
     
         33 . A method for ameliorating, treating, or preventing a cancer of the female genitourinary system, comprising:
 administering a remedial live biotherapeutic formulation to a vaginal environment of a female human subject,   wherein the remedial live biotherapeutic formulation comprises bacteria adapted to remedy a deficiency or excess of at least one bacterial strain in the subject's vaginal microbial community, and   wherein the bacteria comprise a selected strain or consortium of strains comprising 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; 
 (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) at least one strain selected from the group consisting of LUCA111, LUCA011, LUCA015, LUCA009, LUCA102, LUCA006, LUCA059, LUCA103, and LUCA008. 
   
     
     
         34 . The method of  claim 33 , wherein the cancer of the female genitourinary system is a human papillomavirus (HPV)-caused cancer. 
     
     
         35 . The method of  claim 33 , wherein the cancer of the female genitourinary system is cervical cancer. 
     
     
         36 . The method of  claim 33 , wherein the live biotherapeutic formulation further comprises at least one of an antimicrobial agent, a redox potential control agent, a pH buffer configured to maintain a healthy pH of the vaginal environment, a pharmaceutically acceptable carrier, an agent adapted to reduce or remove free ammonia from the vaginal environment, and a growth promoter. 
     
     
         37 . The method of  claim 33 , wherein the administering step achieves an improvement in the genitourinary health of the subject selected from the group consisting of decreasing ammonia in the vaginal environment of the subject, reducing inflammation in the subject, suppressing the growth or hampering the survival of at least one of  Gardnerella vaginalis  and  Prevotella bivia  in the vagina of the subject, and combinations thereof.