Background/Aim: We analyzed the fecal microbiota profiles of pediatric patients with inflammatory bowel disease. Method: Terminal restriction fragment length polymorphism analysis was performed in 10 fecal samples from Crohn’s disease (CD), 14 samples from ulcerative colitis (UC) and 27 samples from healthy individuals. The bacterial diversity was evaluated by the Shannon diversity index. Result: In CD patients, a setting of similarity generated three major clusters. The majority of CD patients were classified into CD clusters I and II (9 out of 10), but the majority of healthy individuals (21 of 27) were classified into CD cluster III. In UC patients, a setting of similarity also generated three major UC clusters, but each cluster was not characteristic for UC patients or healthy individuals. The changes in simulated bacterial composition indicated that the class Clostridia, including the genus Faecalibacterium, was significantly decreased in CD patients as compared to UC patients and/or healthy individuals. The genus Bacteroides was also decreased as compared to healthy individuals. The bacterial diversity measured by the Shannon diversity index was significantly reduced in CD patients as compared to healthy individuals. Conclusion: The gut microbiota profile of pediatric CD patients was different from that of healthy children.

Sands BE: Inflammatory bowel disease: past, present, and future. J Gastroenterol 2007;42:16–25.
Mayer L: Evolving paradigms in the pathogenesis of IBD. J Gastroenterol 2010;45:9–16.
Hibi T, Ogata H: Novel pathophysiological concepts of inflammatory bowel disease. J Gastroenterol 2006;41:10–16.
Podolsky DK: Inflammatory bowel disease. N Engl J Med 2002;347:417–429.
Hamilton MJ, Snapper SB, Blumberg RS: Update on biologic pathways in inflammatory bowel disease and their therapeutic relevance. J Gastroenterol 2012;47:1–8.
Kobori A, Yagi Y, Imaeda H, Ban H, Bamba S, Tsujikawa T, Saito Y, Fujiyama Y, Andoh A: Interleukin-33 expression is specifically enhanced in inflamed mucosa of ulcerative colitis. J Gastroenterol 2010;45:999–1007.
Sartor RB: Microbial influences in inflammatory bowel diseases. Gastroenterology 2008;134:577–594.
Mizoguchi A, Mizoguchi E: Inflammatory bowel disease, past, present and future: Lessons from animal models. J Gastroenterol 2008;43:1–17.
Sartor RB: Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol 2006;3:390–407.
Wirtz S, Neurath MF: Mouse models of inflammatory bowel disease. Adv Drug Deliv Rev 2007;59:1073–1083.
Braun J, Wei B: Body traffic: ecology, genetics, and immunity in inflammatory bowel disease. Annu Rev Pathol 2007;2:401–429.
Seksik P, Sokol H, Lepage P, Vasquez N, Manichanh C, Mangin I, Pochart P, Dore J, Marteau P: Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease. Aliment Pharmacol Ther 2006;24(suppl 3):11–18.
Elson CO, Cong Y, McCracken VJ, Dimmitt RA, Lorenz RG, Weaver CT: Experimental models of inflammatory bowel disease reveal innate, adaptive, and regulatory mechanisms of host dialogue with the microbiota. Immunol Rev 2005;206:260–276.
Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nunez G, Cho JH: A frameshift mutation in nod2 associated with susceptibility to Crohn’s disease. Nature 2001;411:603–606.
Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S, Stone CD, Brunt EM, Xavier RJ, Sleckman BP, Li E, Mizushima N, Stappenbeck TS, Virgin HWT: A key role for autophagy and the autophagy gene atg16l1 in mouse and human intestinal paneth cells. Nature 2008;456:259–263.
Kabi A, Nickerson KP, Homer CR, McDonald C: Digesting the genetics of inflammatory bowel disease: insights from studies of autophagy risk genes. Inflamm Bowel Dis 2011;18:782–792.
Andoh A, Imaeda H, Aomatsu T, Inatomi O, Bamba S, Sasaki M, Saito Y, Tsujikawa T, Fujiyama Y: Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn’s disease using terminal restriction fragment length polymorphism analysis. J Gastroenterol 2011;46:479–486.
Sekirov I, Russell SL, Antunes LC, Finlay BB: Gut microbiota in health and disease. Physiol Rev 2010;90:859–904.
Mahida YR, Rolfe VE: Host-bacterial interactions in inflammatory bowel disease. Clin Sci (Lond) 2004;107:331–341.
Andoh A, Benno Y, Kanauchi O, Fujiyama Y: Recent advances in molecular approaches to gut microbiota in inflammatory bowel disease. Curr Pharm Des 2009;15:2066–2073.
Hayashi H, Sakamoto M, Kitahara M, Benno Y: Molecular analysis of fecal microbiota in elderly individuals using 16s rDNA library and T-RFLP. Microbiol Immunol 2003;47:557–570.
Sakamoto M, Takeuchi Y, Umeda M, Ishikawa I, Benno Y: Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J Med Microbiol 2003;52:79–89.
Li F, Hullar MA, Lampe JW: Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. J Microbiol Methods 2007;68:303–311.
Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y: Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J Med Microbiol 2005;54:1093–1101.
Turner D, Otley AR, Mack D, Hyams J, de Bruijne J, Uusoue K, Walters TD, Zachos M, Mamula P, Beaton DE, Steinhart AH, Griffiths AM: Development, validation, and evaluation of a pediatric ulcerative colitis activity index: a prospective multicenter study. Gastroenterology 2007;133:423–432.
Hyams JS, Ferry GD, Mandel FS, et al: Development and validation of a pediatric crohn’s disease activity index. J Pediatr Gastroenterol Nutr 1991;12:439–447.
Nagashima K, Hisada T, Sato M, Mochizuki J: Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl Environ Microbiol 2003;69:1251–1262.
Matsumoto M, Sakamoto M, Hayashi H, Benno Y: Novel phylogenetic assignment database for terminal-restriction fragment length polymorphism analysis of human colonic microbiota. J Microbiol Methods 2005;61:305–319.
Marsh TL, Saxman P, Cole J, Tiedje J: Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol 2000;66:3616– 3620.
Hill TC, Walsh KA, Harris JA, Moffett BF: Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 2003;43:1–11.
Dean-Ross D, Mills AL: Bacterial community structure and function along a heavy metal gradient. Appl Environ Microbiol 1989;55:2002–2009.
Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, Jarnerot G, Tysk C, Jansson JK, Engstrand L: A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010;139:1844–1854 e1841.
Dicksved J, Floistrup H, Bergstrom A, Rosenquist M, Pershagen G, Scheynius A, Roos S, Alm JS, Engstrand L, Braun-Fahrlander C, von Mutius E, Jansson JK: Molecular fingerprinting of the fecal microbiota of children raised according to different lifestyles. Appl Environ Microbiol 2007;73:2284–2289.
Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK: Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J 2008;2:716–727.
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI: A core gut microbiome in obese and lean twins. Nature 2009;457:480–484.
Nagalingam NA, Lynch SV: Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 2012;18:968–984.
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR: Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 2007;104:13780–13785.
Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L: High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 2011;11:7.
Nishikawa J, Kudo T, Sakata S, Benno Y, Sugiyama T: Diversity of mucosa-associated microbiota in active and inactive ulcerative colitis. Scand J Gastroenterol 2009;44:180–186.
Andoh A, Sakata S, Koizumi Y, Mitsuyama K, Fujiyama Y, Benno Y: Terminal restriction fragment length polymorphism analysis of the diversity of fecal microbiota in patients with ulcerative colitis. Inflamm Bowel Dis 2007;13:955–962.
Andoh A, Tsujikawa T, Sasaki M, Mitsuyama K, Suzuki Y, Matsui T, Matsumoto T, Benno Y, Fujiyama Y: Fecal microbiota profile of crohn’s disease determined by terminal restriction fragment length polymorphism (T-RFLP) analysis. Aliment Pharmacol Ther 2008;29:75–82.
Zilbauer M, Jenke A, Wenzel G, Goedde D, Postberg J, Phillips AD, Lucas M, Noble-Jamieson G, Torrente F, Salvestrini C, Heuschkel R, Wirth S: Intestinal alpha-defensin expression in pediatric inflammatory bowel disease. Inflamm Bowel Dis 2011;17:2076–2086.
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K, Honda K: Induction of colonic regulatory t cells by indigenous clostridium species. Science 2011;331:337–341.
Hall JA, Bouladoux N, Sun CM, Wohlfert EA, Blank RB, Zhu Q, Grigg ME, Berzofsky JA, Belkaid Y: Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity 2008;29:637–649.
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottiere HM, Dore J, Marteau P, Seksik P, Langella P: Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 2008;105:16731–16736.
Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Dore J: Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009;15:1183–1189.
De Preter V, Arijs I, Windey K, Vanhove W, Vermeire S, Schuit F, Rutgeerts P, Verbeke K: Impaired butyrate oxidation in ulcerative colitis is due to decreased butyrate uptake and a defect in the oxidation pathway. Inflamm Bowel Dis 2012;18:1127—1136.
De Preter V, Arijs I, Windey K, Vanhove W, Vermeire S, Schuit F, Rutgeerts P, Verbeke K: Decreased mucosal sulfide detoxification is related to an impaired butyrate oxidation in ulcerative colitis. Inflamm Bowel Dis 2012 Mar 20. doi: 10.1002/ibd.22949 [Epub ahead of print].
Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y: Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007;6:546–551.
Andoh A, Fujiyama Y, Hata K, Araki Y, Takaya H, Shimada M, Bamba T: Counter-regulatory effect of sodium butyrate on tumour necrosis factor-alpha (TNF-alpha)-induced complement C3 and factor B biosynthesis in human intestinal epithelial cells. Clin Exp Immunol 1999;118:23–29.
Kawamura T, Andoh A, Nishida A, Shioya M, Yagi Y, Nishimura T, Hashimoto T, Tsujikawa T, Yasui H, Fujiyama Y: Inhibitory effects of short-chain fatty acids on matrix metalloproteinase secretion from human colonic subepithelial myofibroblasts. Dig Dis Sci 2009;54:238–245.
You do not currently have access to this content.