ALTERED MICROBIOME OF CHRONIC PELVIC PAIN

• US 20150284781A1
• Filed: 04/02/2015
• Published: 10/08/2015
• Est. Priority Date: 04/02/2014
• Status: Active Grant

• Current Assignee: Board of Trustees of The University of Illinois, Northwestern University
• Original Assignee: Board of Trustees of The University of Illinois, Northwestern University
• Inventors: Klumpp, David J., Schaeffer, Anthony J., White, Bryan A.
• Granted Patent: US 9,783,858 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 2035/115 Probiotics
• CPC Class Codes: A61K 35/74 Bacteria therapeutic use of a bacterial protein A61K38/00
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/689 for bacteria

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).

Claims

1. A method comprising:

testing, or having tested a stool sample from a subject suspected of suffering from interstitial cystitis (IC) and/or interstitial cystitis/bladder pain syndrome (IC/BPS), to determine the level of bacteria from at least one bacterial species from a bacterial genus,

wherein said bacterial genus is selected from the group consisting of;

Odoribacter, Faecalibacterium, Colinsella, Eggerthella, Lactonifactor, and Roseburia.

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.

21. The method of claim 1, further comprising comparing the level of bacteria to healthy control population levels.

7-8. -8. (canceled)

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.

12-15. -15. (canceled)

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.