Stool-based biomarkers of interstitial cystitis/bladder pain syndrome

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Braundmeier Fleming, A ^a   Russell, Nathan T ^a   Yang, Wenbin ^b   Nas, Megan Y ^b   Yaggie, Ryan E ^b   Berry, Matthew ^a   Bachrach, Laurie ^b   Flury, Sarah C ^b   Marko, Darlene S ^b   Bushell, Colleen B ^a   Welge, Michael E ^a   White, Bryan A ^a   Schaeffer, Anthony J ^b   Klumpp, David J ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; RIBOSOME DNA; RNA 16S;

ADULT; BACTERIUM; BLADDER; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FECES; FEMALE; GENETICS; HUMAN; INTERSTITIAL CYSTITIS; METABOLOME; METAGENOMICS; MICROBIOLOGY; MIDDLE AGED; PATHOLOGY; PHYLOGENY; QUESTIONNAIRE; YOUNG ADULT;

ADULT; BACTERIA; BIOMARKERS; CLUSTER ANALYSIS; CYSTITIS, INTERSTITIAL; DNA, RIBOSOMAL; FECES; FEMALE; HUMANS; METABOLOME; METAGENOMICS; MIDDLE AGED; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SURVEYS AND QUESTIONNAIRES; URINARY BLADDER; YOUNG ADULT;

EID: 84970028963     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep26083     Document Type: Article

References (56)

1. Clemens, J. Q., Markossian, T. & Calhoun, E. A. Comparison of economic impact of chronic prostatitis/chronic pelvic pain syndrome and interstitial cystitis/painful bladder syndrome. Urology 73, 743-746, doi: S0090-4295(08)01836-010. 1016/j. urology. 2008. 11. 007 (2009).
2. Berry, S. H. et al. Prevalence of symptoms of bladder pain syndrome/interstitial cystitis among adult females in the United States. J Urol 186, 540-544, doi: 10. 1016/j. juro. 2011. 03. 132 (2011).
3. Rabin, C., O'Leary, A., Neighbors, C. & Whitmore, K. Pain and depression experienced by women with interstitial cystitis. Women & health 31, 67-81 (2000).
4. Watkins, K. E. et al. Depressive disorders and panic attacks in women with bladder pain syndrome/interstitial cystitis: A populationbased sample. General hospital psychiatry 33, 143-149, doi: 10. 1016/j. genhosppsych. 2011. 01. 004 (2011).
5. Rothrock, N. E., Lutgendorf, S. K., Hoffman, A. & Kreder, K. J. Depressive symptoms and quality of life in patients with interstitial cystitis. J Urol 167, 1763-1767 (2002).
6. Hanno, P. Campbell-Walsh Urology Vol. 1 (eds Wein, A. J. et al. ) Ch. 14, 334-370 (Elsevier, 2016).
7. Leiby, B. E., Landis, J. R., Propert, K. J. & Tomaszewski, J. E. Discovery of morphological subgroups that correlate with severity of symptoms in interstitial cystitis: A proposed biopsy classification system. J Urol 177, 142-148 (2007).
8. Tomaszewski, J. E. et al. Biopsy features are associated with primary symptoms in interstitial cystitis: results from the interstitial cystitis database study. Urology 57, 67-81 (2001).
9. Yilmaz, U., Liu, Y. W., Berger, R. E. & Yang, C. C. Autonomic nervous system changes in men with chronic pelvic pain syndrome. J Urol 177, 2170-2174; discussion 2174, doi: 10. 1016/j. juro. 2007. 01. 144 (2007).
10. Dimitrakov, J. et al. Adrenocortical hormone abnormalities in men with chronic prostatitis/chronic pelvic pain syndrome. Urology 71, 261-266, doi: 10. 1016/j. urology. 2007. 09. 025 (2008).
11. Lutgendorf, S. K. et al. Diurnal cortisol variations and symptoms in patients with interstitial cystitis. J Urol 167, 1338-1343 (2002).
12. Anderson, R. U., Orenberg, E. K., Chan, C. A., Morey, A. & Flores, V. Psychometric profiles and hypothalamic-pituitary-adrenal axis function in men with chronic prostatitis/chronic pelvic pain syndrome. J Urol 179, 956-960, doi: 10. 1016/j. juro. 2007. 10. 084 (2008).
13. Buffington, C. A. Idiopathic cystitis in domestic cats-beyond the lower urinary tract. Journal of veterinary internal medicine/ American College of Veterinary Internal Medicine 25, 784-796, doi: 10. 1111/j. 1939-1676. 2011. 0732. x (2011).
14. Clemens, J. Q. et al. The MAPP research network: A novel study of urologic chronic pelvic pain syndromes. BMC urology 14 (2014).
15. Landis, J. R. et al. The MAPP research network: design, patient characterization and operations. BMC urology 14, 58, doi: 10. 1186/1471-2490-14-58 (2014).
16. Blaser, M., Bork, P., Fraser, C., Knight, R. & Wang, J. The microbiome explored: recent insights and future challenges. Nat Rev Microbiol 11, 213-217, doi: 10. 1038/nrmicro2973 (2013).
17. Human Microbiome Project, C. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214, doi: 10. 1038/nature11234 (2012).
18. Haiser, H. J., Seim, K. L., Balskus, E. P. & Turnbaugh, P. J. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes 5, 233-238, doi: 10. 4161/gmic. 27915 (2014).
19. Hilt, E. et al. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. Journal of clinical microbiology, doi: 10. 1128/JCM. 02876-13 (2013).
20. Rudick, C. N. et al. Host-pathogen interactions mediating pain of urinary tract infection. The Journal of infectious diseases 201, 1240-1249, doi: 10. 1086/651275 (2010).
21. Rudick, C. N. et al. O-antigen modulates infection-induced pain states. PLoS ONE 7, e41273, doi: 10. 1371/journal. pone. 0041273 (2012).
22. Malykhina, A. P. Neural mechanisms of pelvic organ cross-sensitization. Neuroscience 149, 660-672, doi: 10. 1016/j. neuroscience. 2007. 07. 053 (2007).
23. Malykhina, A. P. et al. Differential effects of intravesical resiniferatoxin on excitability of bladder spinal neurons upon colon-bladder cross-sensitization. Brain research 1491, 213-224, doi: 10. 1016/j. brainres. 2012. 11. 003 (2013).
24. Pezzone, M. A., Liang, R. & Fraser, M. O. A model of neural cross-talk and irritation in the pelvis: implications for the overlap of chronic pelvic pain disorders. Gastroenterology 128, 1953-1964 (2005).
25. Rudick, C. N. et al. Uropathogenic Escherichia coli induces chronic pelvic pain. Infect Immun 79, 628-635, doi: IAI. 00910-10 10. 1128/IAI. 00910-10 (2011).
26. Rudick, C. N., Chen, M. C., Mongiu, A. K. & Klumpp, D. J. Organ Crosstalk Modulates Pelvic Pain. Am J Physiol Regul Integr Comp Physiol 293, R1191-1198 (2007).
27. Evaluation of 16S rDNA-based community profiling for human microbiome research. Plos One 7, e39315, doi: 10. 1371/journal. pone. 0039315 (2012).
28. Diaz-Uriate, R. S. & de Andres, S. Gene selection and classification of microarray data using random forest. BMC bioinformatics 7, 3 (2006).
29. Reshef, D. N. et al. Detecting novel associations in large data sets. Science 334, 1518-1524, doi: 10. 1126/science. 1205438 (2011).
30. Roessner, U., Wagner, C., Kopka, J., Trethewey, R. N. & Willmitzer, L. Technical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23, 131-142 (2000).
31. Xia, J., Mandal, R., Sinelnikov, I. V., Broadhurst, D. & Wishart, D. S. MetaboAnalyst 2. 0-a comprehensive server for metabolomic data analysis. Nucleic Acids Res 40, W127-133, doi: 10. 1093/nar/gks374 (2012).
32. Xia, J., Psychogios, N., Young, N. & Wishart, D. S. MetaboAnalyst: A web server for metabolomic data analysis and interpretation. Nucleic Acids Res 37, W652-660, doi: 10. 1093/nar/gkp356 (2009).
33. Xia, J., Sinelnikov, I. V., Han, B. & Wishart, D. S. MetaboAnalyst 3. 0-making metabolomics more meaningful. Nucleic Acids Res 43, W251-257, doi: 10. 1093/nar/gkv380 (2015).
34. Shorter, B., Lesser, M., Moldwin, R. M. & Kushner, L. Effect of comestibles on symptoms of interstitial cystitis. J Urol 178, 145-152, doi: 10. 1016/j. juro. 2007. 03. 020 (2007).
35. Friedlander, J. I., Shorter, B. & Moldwin, R. M. Diet and its role in interstitial cystitis/bladder pain syndrome (IC/BPS) and comorbid conditions. BJU international 109, 1584-1591, doi: 10. 1111/j. 1464-410X. 2011. 10860. x (2012).
36. Rudick, C. N., Pavlov, V. I., Chen, M. C. & Klumpp, D. J. Gender specific pelvic pain severity in neurogenic cystitis. J Urol 187, 715-724, doi: 10. 1016/j. juro. 2011. 10. 048 (2012).
37. Theoharides, T. C., Pang, X., Letourneau, R. & Sant, G. R. Interstitial cystitis: A neuroimmunoendocrine disorder. Annals of the New York Academy of Sciences 840, 619-634. (1998).
38. Cryan, J. F. & O'Mahony, S. M. The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil 23, 187-192, doi: 10. 1111/j. 1365-2982. 2010. 01664. x (2011).
39. Klumpp, D. J. & Rudick, C. N. Summation model of pelvic pain in interstitial cystitis. Nature clinical practice 5, 494-500, doi: 10. 1038/ncpuro1203 (2008).
40. Khan, M. T. et al. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J 6, 1578-1585, doi: 10. 1038/ismej. 2012. 5 (2012).
41. Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS 105, 16731-16736 (2008).
42. Sokol, H. et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflammatory bowel diseases 15, 1183-1189, doi: 10. 1002/ibd. 20903 (2009).
43. Willing, B. et al. Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflammatory bowel diseases 15, 653-660, doi: 10. 1002/ibd. 20783 (2009).
44. De Vadder, F. et al. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 156, 84-96, doi: 10. 1016/j. cell. 2013. 12. 016 (2014).
45. Kelly, C. J. et al. Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function. Cell Host Microbe 17, 662-671, doi: 10. 1016/j. chom. 2015. 03. 005 (2015).
46. Malinen, E. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World Journal of Gastroenterology 16, 4532, doi: 10. 3748/wjg. v16. i36. 4532 (2010).
47. Tamma, S. M., Shorter, B., Toh, K. L., Moldwin, R. & Gordon, B. Influence of polyunsaturated fatty acids on urologic inflammation. Int Urol Nephrol 47, 1753-1761, doi: 10. 1007/s11255-015-1108-8 (2015).
48. Klumpp, D. & Rudick, C. N. Dietary sensitivity of interstitial cystitis: bane and opportunity. European Urological Review 4, 54-56 (2009).
49. Clemens, J. Q. et al. The MAPP research network: A novel study of urologic chronic pelvic pain syndromes. BMC urology 14, 57, doi: 10. 1186/1471-2490-14-57 (2014).
50. Blankenberg, D. et al. Galaxy: A web-based genome analysis tool for experimentalists. Current protocols in molecular biology/edited by Frederick M. Ausubel. et al. Chapter 19, Unit 19 10 11-21, doi: 10. 1002/0471142727. mb1910s89 (2010).
51. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods 7, 335-336, doi: 10. 1038/nmeth. f. 303 (2010).
52. Meyer, F. et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics 9, 386, doi: 10. 1186/1471-2105-9-386 (2008).
53. Breiman, L. Random forests. Machine Learning 45, 5-32 (2001).
54. Nilsson, R., Pena, J., Bjorkegren, J. & Tegner, J. Consistent feature selection for pattern recognition in polynomial time. Journal of Machine Learning Research 8, 612 (2007).
55. Friedman, J. Greedy function approximation: A gradient boosting machine. The Annals of Statistics 29, 1189-1232 (2001).
56. Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31, 814-821, doi: 10. 1038/nbt. 2676 (2013).