Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome
Vijay Shankar, Nicholas V Reo, Oleg Paliy, Vijay Shankar, Nicholas V Reo, Oleg Paliy
Abstract
Background: We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy age-matched controls. Here we explored whether observed fecal microbiota and metabolite differences between these two adolescent populations can be used to discriminate between IBS and health.
Findings: We constructed individual microbiota- and metabolite-based sample classification models based on the partial least squares multivariate analysis and then applied a Bayesian approach to integrate individual models into a single classifier. The resulting combined classification achieved 84 % accuracy of correct sample group assignment and 86 % prediction for IBS-D in cross-validation tests. The performance of the cumulative classification model was further validated by the de novo analysis of stool samples from a small independent IBS-D cohort.
Conclusion: High-throughput microbial and metabolite profiling of subject stool samples can be used to facilitate IBS diagnosis.
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References
- Quigley EM, Abdel-Hamid H, Barbara G, Bhatia SJ, Boeckxstaens G, De Giorgio R, et al. A global perspective on irritable bowel syndrome: a consensus statement of the World Gastroenterology Organisation Summit Task Force on irritable bowel syndrome. J Clin Gastroenterol. 2012;46:356–366. doi: 10.1097/MCG.0b013e318247157c.
- Grundmann O, Yoon SL. Irritable bowel syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners. J Gastroenterol Hepatol. 2010;25:691–699. doi: 10.1111/j.1440-1746.2009.06120.x.
- Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC. Functional bowel disorders. Gastroenterology. 2006;130:1480–1491. doi: 10.1053/j.gastro.2005.11.061.
- Reddymasu SC, Sostarich S, McCallum RW. Small intestinal bacterial overgrowth in irritable bowel syndrome: are there any predictors? BMC Gastroenterol. 2010;10:23. doi: 10.1186/1471-230X-10-23.
- Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology. 2010;156:3205–3215. doi: 10.1099/mic.0.043257-0.
- Rigsbee L, Agans R, Shankar V, Kenche H, Khamis HJ, Michail S, et al. Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome. Am J Gastroenterol. 2012;107:1740–1751. doi: 10.1038/ajg.2012.287.
- Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011;141:1782–1791. doi: 10.1053/j.gastro.2011.06.072.
- Jeffery IB, O'Toole PW, Ohman L, Claesson MJ, Deane J, Quigley EM, et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut. 2012;61:997–1006. doi: 10.1136/gutjnl-2011-301501.
- Jahng J, Jung IS, Choi EJ, Conklin JL, Park H. The effects of methane and hydrogen gases produced by enteric bacteria on ileal motility and colonic transit time. Neurogastroenterol Motil. 2012;24:185–E192. doi: 10.1111/j.1365-2982.2011.01819.x.
- Treem WR, Ahsan N, Kastoff G, Hyams JS. Fecal short-chain fatty acids in patients with diarrhea-predominant irritable bowel syndrome: in vitro studies of carbohydrate fermentation. J Pediatr Gastroenterol Nutr. 1996;23:280–286. doi: 10.1097/00005176-199610000-00013.
- Bala L, Ghoshal UC, Ghoshal U, Tripathi P, Misra A, Gowda GA, et al. Malabsorption syndrome with and without small intestinal bacterial overgrowth: a study on upper-gut aspirate using 1H NMR spectroscopy. Magn Reson Med. 2006;56:738–744. doi: 10.1002/mrm.21041.
- Shankar V, Homer D, Rigsbee L, Khamis HJ, Michail S, Raymer M, et al. The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome. Isme J. 2015;9:1899–1903. doi: 10.1038/ismej.2014.258.
- Scarpellini E, Giorgio V, Gabrielli M, Lauritano EC, Pantanella A, Fundaro C, et al. Prevalence of small intestinal bacterial overgrowth in children with irritable bowel syndrome: a case-control study. J Pediatr. 2009;155:416–420. doi: 10.1016/j.jpeds.2009.03.033.
- Cremonini F, Talley NJ. Irritable bowel syndrome: epidemiology, natural history, health care seeking and emerging risk factors. Gastroenterol Clin North Am. 2005;34:189–204. doi: 10.1016/j.gtc.2005.02.008.
- Shankar V, Agans R, Holmes B, Raymer M, Paliy O. Do gut microbial communities differ in pediatric IBS and health? Gut Microbes. 2013;4:347–352. doi: 10.4161/gmic.24827.
- Rigsbee L, Agans R, Foy BD, Paliy O. Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. FEMS Microbiol Ecol. 2011;75:332–342. doi: 10.1111/j.1574-6941.2010.01009.x.
- Sood R, Gracie DJ, Law GR, Ford AC. Systematic review with meta-analysis: the accuracy of diagnosing irritable bowel syndrome with symptoms, biomarkers and/or psychological markers. Aliment Pharmacol Ther. 2015;42:491–503. doi: 10.1111/apt.13283.
- Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, et al. Alterations of the human gut microbiome in liver cirrhosis. Nature. 2014;513:59–64. doi: 10.1038/nature13568.
Source: PubMed