Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis

References

• Li J, Butcher J, Mack D, Stintzi A. Functional impacts of the intestinal microbiome in the pathogenesis of inflammatory bowel disease. Inflamm Bowel Dis 2015; 21:139-53; PMID:25248007; http://dx.doi.org/10.1097/MIB.0000000000000215
   PubMed Web of Science ®Google Scholar
• Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491:119-24; PMID:23128233; http://dx.doi.org/10.1038/nature11582
   PubMed Web of Science ®Google Scholar
• Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 2011; 17:179-84; PMID:20839241; http://dx.doi.org/10.1002/ibd.21339
   PubMed Web of Science ®Google Scholar
• 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; 139:1844-54 e1; PMID:20816835; http://dx.doi.org/10.1053/j.gastro.2010.08.049
   PubMed Web of Science ®Google Scholar
• Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Folsch UR, Timmis KN, Schreiber S. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004; 53:685-93; PMID:15082587; http://dx.doi.org/10.1136/gut.2003.025403
   PubMed Web of Science ®Google Scholar
• 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 U S A 2007; 104:13780-5; PMID:17699621; http://dx.doi.org/10.1073/pnas.0706625104
   PubMed Web of Science ®Google Scholar
• Lepage P, Seksik P, Sutren M, de la Cochetière M-F, Jian R, Marteau P, Doré J. Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with Ibd. Inflamm Bowel Dis 2005; 11:473-80; PMID:15867587; http://dx.doi.org/10.1097/01.MIB.0000159662.62651.06
   PubMed Web of Science ®Google Scholar
• Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J Med Microbiol 2006; 55:1141-9; PMID:16849736; http://dx.doi.org/10.1099/jmm.0.46498-0
   PubMed Web of Science ®Google Scholar
• Varela E, Manichanh C, Gallart M, Torrejon A, Borruel N, Casellas F, Guarner F, Antolin M. Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis. Aliment Pharmacol Ther 2013; 38:151-61; PMID:23725320; http://dx.doi.org/10.1111/apt.12365
   PubMed Web of Science ®Google Scholar
• Hansen R, Russell RK, Reiff C, Louis P, McIntosh F, Berry SH, Mukhopadhya I, Bisset WM, Barclay AR, Bishop J, et al. Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis. Am J Gastroenterol 2012; 107:1913-22; PMID:23044767; http://dx.doi.org/10.1038/ajg.2012.335
   PubMed Web of Science ®Google Scholar
• Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, Leleiko N, Kenche H, Stolfi A, Wine E. Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis 2012; 18:1799-808; PMID:22170749; http://dx.doi.org/10.1002/ibd.22860
   PubMed Web of Science ®Google Scholar
• Lepage P, Hasler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Dore J, Raedler A, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011; 141:227-36; PMID:21621540; http://dx.doi.org/10.1053/j.gastro.2011.04.011
   PubMed Web of Science ®Google Scholar
• Ott SJ, Plamondon S, Hart A, Begun A, Rehman A, Kamm MA, Schreiber S. Dynamics of the mucosa-associated flora in ulcerative colitis patients during remission and clinical relapse. J Clin Microbiol 2008; 46:3510-3; PMID:18701655; http://dx.doi.org/10.1128/JCM.01512-08
   PubMed Web of Science ®Google Scholar
• Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 2008; 105:16731-6; PMID:18936492; http://dx.doi.org/10.1073/pnas.0804812105
   PubMed Web of Science ®Google Scholar
• Chen L, Wang W, Zhou R, Ng SC, Li J, Huang M, Zhou F, Wang X, Shen B,   M AK, et al. Characteristics of fecal and mucosa-associated microbiota in chinese patients with inflammatory bowel disease. Medicine 2014; 93:e51; PMID:25121355; http://dx.doi.org/10.1097/MD.0000000000000051
   PubMed Web of Science ®Google Scholar
• Fite A, Macfarlane S, Furrie E, Bahrami B, Cummings JH, Steinke DT, Macfarlane GT. Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration. J Clin Microbiol 2013; 51:849-56; PMID:23269735; http://dx.doi.org/10.1128/JCM.02574-12
   PubMed Web of Science ®Google Scholar
• Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, Ballet V, Claes K, Van Immerseel F, Verbeke K, et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut 2014; 63:1275-83; PMID:24021287; http://dx.doi.org/10.1136/gutjnl-2013-304833
   PubMed Web of Science ®Google Scholar
• Lopez-Siles M, Martinez-Medina M, Busquets D, Sabat-Mir M, Duncan SH, Flint HJ, Aldeguer X, Garcia-Gil LJ. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes. Int J Med Microbiol 2014; 304:464-75; PMID:24713205; http://dx.doi.org/10.1016/j.ijmm.2014.02.009
   PubMed Web of Science ®Google Scholar
• Wang M, Molin G, Ahrne S, Adawi D, Jeppsson B. High proportions of proinflammatory bacteria on the colonic mucosa in a young patient with ulcerative colitis as revealed by cloning and sequencing of 16S rRNA genes. Dig Dis Sci 2007; 52:620-7; PMID:17265126; http://dx.doi.org/10.1007/s10620-006-9461-1
   PubMed Web of Science ®Google Scholar
• Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13:R79; PMID:23013615; http://dx.doi.org/10.1186/gb-2012-13-9-r79
   PubMed Web of Science ®Google Scholar
• Nwosu FC, Thorkildsen LT, Avershina E, Ricanek P, Perminow G, Brackmann S, Vatn MH, Rudi K. Age-dependent fecal bacterial correlation to inflammatory bowel disease for newly diagnosed untreated children. Gastroenterol Res Pract 2013; 2013:302398; PMID:23690761; http://dx.doi.org/10.1155/2013/302398
   PubMed Web of Science ®Google Scholar
• Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014; 15:382-92; PMID:24629344; http://dx.doi.org/10.1016/j.chom.2014.02.005
   PubMed Web of Science ®Google Scholar
• Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002; 68:3401-7; PMID:12089021; http://dx.doi.org/10.1128/AEM.68.7.3401-3407.2002
   PubMed Web of Science ®Google Scholar
• Kellermayer R, Mir SA, Nagy-Szakal D, Cox SB, Dowd SE, Kaplan JL, Sun Y, Reddy S, Bronsky J, Winter HS. Microbiota separation and C-reactive protein elevation in treatment-naive pediatric granulomatous Crohn disease. J Pediatr Gastroenterol Nutr 2012; 55:243-50; PMID:22699834; http://dx.doi.org/10.1097/MPG.0b013e3182617c16
   PubMed Web of Science ®Google Scholar
• Derrien M, Vaughan EE, Plugge CM, de Vos WM. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 2004; 54:1469-76; PMID:15388697; http://dx.doi.org/10.1099/ijs.0.02873-0
   PubMed Web of Science ®Google Scholar
• van Passel MW, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, et al. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PloS One 2011; 6:e16876; PMID:21390229
   PubMed Web of Science ®Google Scholar
• Collado MC, Derrien M, Isolauri E, de Vos WM, Salminen S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol 2007; 73:7767-70; PMID:17933936; http://dx.doi.org/10.1128/AEM.01477-07
   PubMed Web of Science ®Google Scholar
• Derrien M, Van Baarlen P, Hooiveld G, Norin E, Muller M, de Vos WM. Modulation of Mucosal Immune Response, Tolerance, and Proliferation in Mice Colonized by the Mucin-Degrader Akkermansia muciniphila. Front Microbiol 2011; 2:166; PMID:21904534; http://dx.doi.org/10.3389/fmicb.2011.00166
   PubMed Web of Science ®Google Scholar
• Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin TH. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 2010; 105:2420-8; PMID:20648002; http://dx.doi.org/10.1038/ajg.2010.281
   PubMed Web of Science ®Google Scholar
• Rajilic-Stojanovic M, Shanahan F, Guarner F, de Vos WM. Phylogenetic analysis of dysbiosis in ulcerative colitis during remission. Inflamm Bowel Dis 2013; 19:481-8; PMID:23385241; http://dx.doi.org/10.1097/MIB.0b013e31827fec6d
   PubMed Web of Science ®Google Scholar
• James SL, Christophersen CT, Bird AR, Conlon MA, Rosella O, Gibson PR, Muir JG. Abnormal fibre usage in UC in remission. Gut 2014; 64:562-70; PMID:25037189; http://dx.doi.org/10.1136/gutjnl-2014-307198
   PubMed Web of Science ®Google Scholar
• Vigsnaes LK, Brynskov J, Steenholdt C, Wilcks A, Licht TR. Gram-negative bacteria account for main differences between faecal microbiota from patients with ulcerative colitis and healthy controls. Benef Microbes 2012; 3:287-97; PMID:22968374; http://dx.doi.org/10.3920/BM2012.0018
   PubMed Web of Science ®Google Scholar
• Dorofeyev AE, Vasilenko IV, Rassokhina OA, Kondratiuk RB. Mucosal barrier in ulcerative colitis and Crohn's disease. Gastroenterol Res Pract 2013; 2013:431231; PMID:23737764; http://dx.doi.org/10.1155/2013/431231
   PubMed Web of Science ®Google Scholar
• Ganesh BP, Klopfleisch R, Loh G, Blaut M. Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella Typhimurium-infected gnotobiotic mice. PloS One 2013; 8:e74963; PMID:24040367
   PubMed Web of Science ®Google Scholar
• Kang CS, Ban M, Choi EJ, Moon HG, Jeon JS, Kim DK, Park SK, Jeon SG, Roh TY, Myung SJ, et al. Extracellular vesicles derived from gut microbiota, especially Akkermansia muciniphila, protect the progression of dextran sulfate sodium-induced colitis. PloS One 2013; 8:e76520; PMID:24204633
   PubMed Web of Science ®Google Scholar
• Rehman A, Rausch P, Wang J, Skieceviciene J, Kiudelis G, Bhagalia K, Amarapurkar D, Kupcinskas L, Schreiber S, Rosenstiel P, et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut 2015; 65:238-48; PMID:25567118
   PubMed Web of Science ®Google Scholar
• Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol 2014; 12:661-72; PMID:25198138; http://dx.doi.org/10.1038/nrmicro3344
   PubMed Web of Science ®Google Scholar
• Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, et al. Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function. Cell Host Microbe 2015; PMID:25865369
   PubMed Web of Science ®Google Scholar
• Kumari R, Ahuja V, Paul J. Fluctuations in butyrate-producing bacteria in ulcerative colitis patients of North India. World J Gastroenterol 2013; 19:3404-14; PMID:23801832; http://dx.doi.org/10.3748/wjg.v19.i22.3404
   PubMed Web of Science ®Google Scholar
• Schaible TD, Harris RA, Dowd SE, Smith CW, Kellermayer R. Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes. Hum Mol Genet 2011; 20:1687-96; PMID:21296867; http://dx.doi.org/10.1093/hmg/ddr044
   PubMed Web of Science ®Google Scholar
• Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res 2014; 21:15-25; PMID:24013298; http://dx.doi.org/10.1093/dnares/dst037
   PubMed Web of Science ®Google Scholar
• Song CH, Vadheim CM, Snape WJ, Heiner DC. Antibodies in patients with inflammatory bowel disease and the apparent influence of medications. J Clin Lab Immunol 1995; 46:143-54; PMID:8733027
   PubMedGoogle Scholar
• Davenport M, Poles J, Leung JM, Wolff MJ, Abidi WM, Ullman T, Mayer L, Cho I, Loke P. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 2014; 20:723-31; PMID:24583479; http://dx.doi.org/10.1097/MIB.0000000000000011
   PubMed Web of Science ®Google Scholar
• Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013; 31:814-21; PMID:23975157; http://dx.doi.org/10.1038/nbt.2676
   PubMed Web of Science ®Google Scholar
• Rajca S, Grondin V, Louis E, Vernier-Massouille G, Grimaud JC, Bouhnik Y, Laharie D, Dupas JL, Pillant H, Picon L, et al. Alterations in the intestinal microbiome (dysbiosis) as a predictor of relapse after infliximab withdrawal in Crohn's disease. Inflamm Bowel Dis 2014; 20:978-86; PMID:24788220
   PubMed Web of Science ®Google Scholar
• Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, et al. Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. FASEB J 2012; 26:1960-9; PMID:22267340; http://dx.doi.org/10.1096/fj.10-177980
   PubMed Web of Science ®Google Scholar
• Carmody RN, Gerber GK, Luevano JM, Jr., Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota. Cell Host Microbe 2014; PMID:25532804
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335-6; PMID:20383131; http://dx.doi.org/10.1038/nmeth.f.303
   PubMed Web of Science ®Google Scholar
• Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell 2014; 158:250-62; PMID:25036628; http://dx.doi.org/10.1016/j.cell.2014.06.037
   PubMed Web of Science ®Google Scholar
• DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-72; PMID:16820507; http://dx.doi.org/10.1128/AEM.03006-05
   PubMed Web of Science ®Google Scholar
• McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012; 6:610-8; PMID:22134646; http://dx.doi.org/10.1038/ismej.2011.139
   PubMed Web of Science ®Google Scholar
• Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21:494-504; PMID:21212162; http://dx.doi.org/10.1101/gr.112730.110
   PubMed Web of Science ®Google Scholar
• Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005; 71:8228-35; PMID:16332807; http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005
   PubMed Web of Science ®Google Scholar
• Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. EMPeror: a tool for visualizing high-throughput microbial community data. GigaScience 2013; 2:16; PMID:24280061; http://dx.doi.org/10.1186/2047-217X-2-16
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Knight R, Kelley ST. Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PloS One 2011; 6:e16900; PMID:21383980
   PubMedGoogle Scholar
• Goecks J, Nekrutenko A, Taylor J, Galaxy T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010; 11:R86; PMID:20738864; http://dx.doi.org/10.1186/gb-2010-11-8-r86
   PubMed Web of Science ®Google Scholar
• Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Current protocols in molecular biology / edited by Frederick M Ausubel [et al] 2010; Chapter 19:Unit 19 0 1-21.
   Google Scholar
• Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res 2002; 12:47-56; PMID:11779830; http://dx.doi.org/10.1101/gr.203201
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28:27-30; PMID:10592173; http://dx.doi.org/10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014; 42:D199-205; PMID:24214961; http://dx.doi.org/10.1093/nar/gkt1076
   PubMed Web of Science ®Google Scholar
• Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 2014; 30:3123-4; PMID:25061070; http://dx.doi.org/10.1093/bioinformatics/btu494
   PubMed Web of Science ®Google Scholar
• Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12:R60; PMID:21702898; http://dx.doi.org/10.1186/gb-2011-12-6-r60
   PubMed Web of Science ®Google Scholar
• White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 2009; 5:e1000352; PMID:19360128; http://dx.doi.org/10.1371/journal.pcbi.1000352
   PubMed Web of Science ®Google Scholar