Altered microbiome of chronic pelvic pain

Abstract

Provided herein are kits, compositions, and methods for diagnosing and treating interstitial cystitis (IC) and/or interstitial cystitis/bladder pain syndrome (IC/BPS) based on finding lower levels of certain bacteria in a subject's stool sample (e.g., O. splanchnicus, F. prausnitzii, C. aerofaciens, E. sinensis, L. longoviformis, and R. intestinalis). In certain embodiments, then present invention provides probiotic formulations containing live bacteria (e.g., from O. splanchnicus, F. prausnitzii, C. aerofaciens, E. sinensis, L. longoviformis, and R. intestinalis).

We claim: 
     
         1 . A method comprising:
 a) testing, or having a stool sample from a subject tested, to determine the level of bacteria from at least one bacterial species from a bacterial genus compared to healthy control population levels,   wherein said bacterial genus is selected from the group consisting of:  Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor , and  Roseburia , and   b) performing at least one of the following:
 i) generating a report that indicates that said subject has or is at risk of interstitial cystitis (IC) and/or interstitial cystitis/bladder pain syndrome (IC/BPS) based on finding a reduced level of said at least one bacterial species in said stool sample compared to said control; 
 ii) generating a report that indicates that said subject does not have or is not at risk of IC and/or IC/BPS based on finding a non-reduced level of said at least one bacterial species in said stool sample compared to said control; 
 iii) diagnosing and/or informing said subject that they have or are at risk for IC and/or IC/BPS based on finding a reduced level of said at least one bacterial species in said stool sample compared to said control; 
 iv) informing said subject that they do not have or are not at risk for IC and/or IC/BPS based on finding a non-reduced level of said at least one bacterial species in said stool sample compared to said control; and 
 v) prescribing and or administering a probiotic and/or therapeutic agent targeting IC and/or IC/BPS to said subject based on finding a reduced level of said at least one bacterial species in said stool sample compared to said control. 
   
     
     
         2 . The method of  claim 1 , wherein said at least one species is selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         3 . The method of  claim 1 , wherein said at least one species is at least two species selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         4 . The method of  claim 1 , wherein said at least one species is at least five species selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         5 . The method of  claim 1 , wherein said stool sample is tested with a sequencing assay specific to ribosomal rRNA of said at least one species. 
     
     
         6 . The method of  claim 1 , wherein said subject has symptoms of IDC and/or IC/BPS. 
     
     
         7 . The method of  claim 1 , wherein said probiotic comprises live bacteria from said at least one species. 
     
     
         8 . The method of  claim 1 , wherein said therapeutic agent comprises a stool specimen from a healthy individual. 
     
     
         9 . A composition comprising: i) a capsule formulated for human consumption, and ii) a probiotic formulation contained within said capsule, wherein said probiotic formulation comprises live bacteria from at least one species from a genus of bacteria, wherein said genus of bacteria is selected from the group consisting of:  Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor , and  Roseburia.    
     
     
         10 . The composition of  claim 9 , wherein at least one species is selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         11 . The composition of  claim 9 , wherein said at least one species is at least two species selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         12 . A system comprising:
 i) a report that indicates that said subject has or is at risk of interstitial cystitis (IC) and/or interstitial cystitis/bladder pain syndrome (IC/BPS) based on finding a reduced level of at least one species of bacteria from a genus of bacteria in said stool sample compared to said control, wherein said genus of bacteria is selected from the group consisting of:  Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor , and  Roseburia ; and   ii) a probiotic or therapeutic agent targeting IC and/or IC/BPS.   
     
     
         13 . The system of  claim 12 , wherein said probiotic comprises live bacteria from said genus of bacteria 
     
     
         14 . The system of  claim 12 , wherein at least one species is selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         15 . The system of  claim 12 , wherein said at least one species is at least two species selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         16 . A system or composition comprising:
 a) first diagnostic reagents able to detect a first species of bacteria from a genus of bacteria, wherein said genus of bacteria are selected from the group consisting of:  Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor , and  Roseburia ; and   b) second diagnostic reagents able to detect a second species from a genus of bacteria, wherein said second species is different from said first species, and wherein said genus of bacteria is selected from the group consisting of:  Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor , and  Roseburia.      
     
     
         17 . The system or composition of  claim 16 , wherein said first and second species of bacteria are selected from the group consisting of:  Odoribacter splanchnicus, Faecalibacterium prausnitzii, Colinsella aerofaciens, Eggerthella sinensis, Lactonifactor longoviformis , and  Roseburia intestinalis.    
     
     
         18 . The system or composition of  claim 16 , wherein said first and second diagnostic reagents comprise primer pairs, or nucleic acid probes, specific for said first and second species of bacteria respectively. 
     
     
         19 . The system or composition of  claim 16 , wherein first and second diagnostic reagents comprise antibodies specific for said first and second species of bacteria respectively. 
     
     
         20 . The system or composition of  claim 16 , wherein said first and second diagnostic reagents are in separate wells of a multi-well plate.