Loftus EV: Clinical epidemiology of inflammatory bowel disease: Incidence, prevalence, and environmental influences. Gastroenterology. 2004, 126: 1504-1517. 10.1053/j.gastro.2004.01.063.
Article
PubMed
Google Scholar
Pizzi LT, Weston CM, Goldfarb NI, Moretti D, Cobb N, Howell JB, Infantolino A, Dimarino AJ, Cohen S: Impact of chronic conditions on quality of life in patients with inflammatory bowel disease. Inflamm Bowel Dis. 2006, 12: 47-52. 10.1097/01.MIB.0000191670.04605.e7.
Article
PubMed
Google Scholar
Halfvarson J, Bodin L, Tysk C, Lindberg E, Järnerot G: Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. Gastroenterology. 2003, 124: 1767-1773. 10.1016/S0016-5085(03)00385-8.
Article
PubMed
Google Scholar
Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, et al: Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008, 40: 955-962. 10.1038/ng.175.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xavier RJ, Podolsky DK: Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007, 448: 427-434. 10.1038/nature06005.
Article
PubMed
CAS
Google Scholar
Sartor RB: Pathogenesis and immune mechanisms of chronic inflammatory bowel diseases. Am J Gastroenterol. 1997, 92 (12 Suppl): 5S-11S.
PubMed
CAS
Google Scholar
Bouma G, Strober W: The immunological and genetic basis of inflammatory bowel disease. Nat Rev Immunol. 2003, 3: 521-533. 10.1038/nri1132.
Article
PubMed
CAS
Google Scholar
Cho JH: The genetics and immunopathogenesis of inflammatory bowel disease. Nat Rev Immunol. 2008, 8: 458-466. 10.1038/nri2340.
Article
PubMed
CAS
Google Scholar
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI: Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Micro. 2008, 6: 776-788. 10.1038/nrmicro1978.
Article
CAS
Google Scholar
Dethlefsen L, Eckburg PB, Bik EM, Relman DA: Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006, 21: 517-523. 10.1016/j.tree.2006.06.013.
Article
PubMed
Google Scholar
Tlaskalová-Hogenová H, Stepánková R, Hudcovic T, Tucková L, Cukrowska B, Lodinová-Zádníková R, Kozáková H, Rossmann P, Bártová J, Sokol D, Funda DP, Borovská D, Reháková Z, Sinkora J, Hofman J, Drastich P, Kokesová A: Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunol Lett. 2004, 93: 97-108.
Article
PubMed
Google Scholar
Canny GO, McCormick BA: Bacteria in the intestine, helpful residents or enemies from within?. Infect Immun. 2008, 76: 3360-3373. 10.1128/IAI.00187-08.
Article
PubMed
CAS
PubMed Central
Google Scholar
Harper PH, Lee EC, Kettlewell MG, Bennett MK, Jewell DP: Role of the faecal stream in the maintenance of Crohn's colitis. Gut. 1985, 26: 279-284. 10.1136/gut.26.3.279.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nell S, Suerbaum S, Josenhans C: The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models. Nat Rev Microbiol. 2010, 8: 564-577. 10.1038/nrmicro2403.
Article
PubMed
CAS
Google Scholar
Schultsz C, Van Den Berg FM, Ten Kate FW, Tytgat GN, Dankert J: The intestinal mucus layer from patients with inflammatory bowel disease harbors high numbers of bacteria compared with controls. Gastroenterology. 1999, 117: 1089-1097. 10.1016/S0016-5085(99)70393-8.
Article
PubMed
CAS
Google Scholar
Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, Weber J, Hoffmann U, Schreiber S, Dietel M, Lochs H: Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002, 122: 44-54. 10.1053/gast.2002.30294.
Article
PubMed
Google Scholar
Sartor RB: Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008, 134: 577-594. 10.1053/j.gastro.2007.11.059.
Article
PubMed
CAS
Google Scholar
Rutgeerts P, Hiele M, Geboes K, Peeters M, Penninckx F, Aerts R, Kerremans R: Controlled trial of Metronidazole treatment for prevention of Crohn's recurrence after ileal resection. Gastroenterology. 1995, 108: 1617-1621. 10.1016/0016-5085(95)90121-3.
Article
PubMed
CAS
Google Scholar
Stringer EE, Nicholson TJ, Armstrong D: Efficacy of topical Metronidazole (10 percent) in the treatment of anorectal Crohn's disease. Dis Colon Rectum. 2005, 48: 970-974. 10.1007/s10350-004-0873-8.
Article
PubMed
Google Scholar
Feller M, Huwiler K, Stephan R, Altpeter E, Shang A, Furrer H, Pfyffer GE, Jemmi T, Baumgartner A, Egger M: Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis. Lancet Infect Dis. 2007, 7: 607-613. 10.1016/S1473-3099(07)70211-6.
Article
PubMed
Google Scholar
Barnich N, Darfeuille-Michaud A: Adherent-invasive Escherichia coli and Crohn's disease. Curr Opin Gastroenterol. 2007, 23: 16-20. 10.1097/MOG.0b013e3280105a38.
Article
PubMed
Google Scholar
Tamboli CP, Neut C, Desreumaux P, Colombel JF: Dysbiosis in inflammatory bowel disease. Gut. 2004, 53: 1-4. 10.1136/gut.53.1.1.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sartor RB, Muehlbauer M: Microbial host interactions in IBD: implications for pathogenesis and therapy. Curr Gastroenterol Rep. 2007, 9: 497-507. 10.1007/s11894-007-0066-4.
Article
PubMed
Google Scholar
Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Fölsch 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: 685-693. 10.1136/gut.2003.025403.
Article
PubMed
CAS
PubMed Central
Google Scholar
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J: Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut. 2006, 55: 205-211. 10.1136/gut.2005.073817.
Article
PubMed
CAS
PubMed Central
Google Scholar
Scanlan PD, Shanahan F, O'Mahony C, Marchesi JR: Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol. 2006, 44: 3980-3988. 10.1128/JCM.00312-06.
Article
PubMed
CAS
PubMed Central
Google Scholar
Martinez C, Antolin M, Santos J, Torrejon A, Casellas F, Borruel N, Guarner F, Malagelada JR: Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission. Am J Gastroenterol. 2008, 103: 643-648. 10.1111/j.1572-0241.2007.01592.x.
Article
PubMed
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al: A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010, 464: 59-65. 10.1038/nature08821.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ: Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J Clin Microbiol. 2006, 44: 4136-4141. 10.1128/JCM.01004-06.
Article
PubMed
CAS
PubMed Central
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 USA. 2007, 104: 13780-13785. 10.1073/pnas.0706625104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Doré J: Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 2009, 15: 1183-1189. 10.1002/ibd.20903.
Article
PubMed
CAS
Google Scholar
Poxton IR, Brown R, Sawyerr A, Ferguson A: Mucosa-associated bacterial flora of the human colon. J Med Microbiol. 1997, 46: 85-91. 10.1099/00222615-46-1-85.
Article
PubMed
CAS
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: 3401-3407. 10.1128/AEM.68.7.3401-3407.2002.
Article
PubMed
CAS
PubMed Central
Google Scholar
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA: Diversity of the human intestinal microbial flora. Science. 2005, 308: 1635-1638. 10.1126/science.1110591.
Article
PubMed
PubMed Central
Google Scholar
Wang M, Ahrné S, Jeppsson B, Molin G: Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Micro Ecol. 2005, 54: 219-231. 10.1016/j.femsec.2005.03.012.
Article
CAS
Google Scholar
Lepage P, Seksik P, Sutren M, de la Cochetière MF, 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: 473-480. 10.1097/01.MIB.0000159662.62651.06.
Article
PubMed
Google Scholar
Green GL, Brostoff J, Hudspith B, Michael M, Mylonaki M, Rayment N, Staines N, Sanderson J, Rampton DS, Bruce KD: Molecular characterization of the bacteria adherent to human colorectal mucosa. J Appl Micro. 2006, 100: 460-469. 10.1111/j.1365-2672.2005.02783.x.
Article
CAS
Google Scholar
Schloss PD, Larget BR, Handelsman J: Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol. 2004, 70: 5485-5492. 10.1128/AEM.70.9.5485-5492.2004.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hamady M, Lozupone C, Knight R: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010, 4: 17-27. 10.1038/ismej.2009.97.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009, 75: 7537-7541. 10.1128/AEM.01541-09.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, D141-145. 10.1093/nar/gkn879. 37 Database
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottière HM, Doré 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. 10.1073/pnas.0804812105.
Article
PubMed
CAS
PubMed Central
Google Scholar
Eckburg PB, Relman DA: The role of microbes in Crohn's disease. Clin Infect Dis. 2007, 44: 256-262. 10.1086/510385.
Article
PubMed
CAS
Google Scholar
Loubinoux J, Bronowicki J, Pereira IAC, Mougenel J, Le Faou AE: Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. FEMS Micro Ecol. 2002, 40: 107-112. 10.1111/j.1574-6941.2002.tb00942.x.
Article
CAS
Google Scholar
Seksik P, Rigottier-Gois L, Gramet G, Sutren M, Pochart P, Marteau P, Jian R, Doré J: Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut. 2003, 52: 237-242. 10.1136/gut.52.2.237.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mangin I, Bonnet R, Seksik P, Rigottier-Gois L, Sutren M, Bouhnik Y, Neut C, Collins MD, Colombel JF, Marteau P, Doré J: Molecular inventory of faecal microflora in patients with Crohn's disease. FEMS Micro Ecol. 2004, 50: 25-36. 10.1016/j.femsec.2004.05.005.
Article
CAS
Google Scholar
Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H: Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol. 2005, 43: 3380-3389. 10.1128/JCM.43.7.3380-3389.2005.
Article
PubMed
PubMed Central
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: 1141-1149. 10.1099/jmm.0.46498-0.
Article
PubMed
Google Scholar
Lucke K, Miehlke S, Jacobs E, Schuppler M: Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis. J Med Microbiol. 2006, 55: 617-624. 10.1099/jmm.0.46198-0.
Article
PubMed
CAS
Google Scholar
Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia-Gil LJ: Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis. 2006, 12: 1136-1145. 10.1097/01.mib.0000235828.09305.0c.
Article
PubMed
Google Scholar
Sokol H, Lepage P, Seksik P, Doré J, Marteau P: Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis. J Clin Microbiol. 2006, 44: 3172-3177. 10.1128/JCM.02600-05.
Article
PubMed
CAS
PubMed Central
Google Scholar
Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, Berg D, Schukken Y, Scherl E, Simpson KW: Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J. 2007, 1: 403-418. 10.1038/ismej.2007.52.
Article
PubMed
CAS
Google Scholar
Kotlowski R, Bernstein CN, Sepehri S, Krause DO: High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut. 2007, 56: 669-675. 10.1136/gut.2006.099796.
Article
PubMed
CAS
PubMed Central
Google Scholar
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 analysis. Aliment Pharmacol Ther. 2009, 29: 75-82. 10.1111/j.1365-2036.2008.03860.x.
Article
PubMed
CAS
Google Scholar
Martinez-Medina M, Aldeguer X, Lopez-Siles M, González-Huix F, López-Oliu C, Dahbi G, Blanco JE, Blanco J, Garcia-Gil LJ, Darfeuille-Michaud A: Molecular diversity of Escherichia coli in the human gut: New ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease. Inflamm Bowel Dis. 2009, 15: 872-882. 10.1002/ibd.20860.
Article
PubMed
Google Scholar
Dicksved J, Halfvarson J, Rosenquist M, Järnerot 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. 10.1038/ismej.2008.37.
Article
PubMed
CAS
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: 3510-3513. 10.1128/JCM.01512-08.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mylonaki M, Rayment NB, Rampton DS, Hudspith BN, Brostoff J: Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease. Inflamm Bowel Dis. 2005, 11: 481-487. 10.1097/01.MIB.0000159663.62651.4f.
Article
PubMed
Google Scholar
Sepehri S, Kotlowski R, Bernstein CN, Krause DO: Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis. 2007, 13: 675-683. 10.1002/ibd.20101.
Article
PubMed
Google Scholar
Seksik P, Lepage P, de la Cochetière MF, Bourreille A, Sutren M, Galmiche JP, Doré J, Marteau P: Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA. J Clin Microbiol. 2005, 43: 4654-4658. 10.1128/JCM.43.9.4654-4658.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sokol H, Lepage P, Seksik P, Doré J, Marteau P: Molecular comparison of dominant microbiota associated with injured versus healthy mucosa in ulcerative colitis. Gut. 2007, 56: 152-154. 10.1136/gut.2006.109686.
Article
PubMed
CAS
PubMed Central
Google Scholar
Vasquez N, Mangin I, Lepage P, Seksik P, Duong JP, Blum S, Schiffrin E, Suau A, Allez M, Vernier G, Tréton X, Doré J, Marteau P, Pochart P: Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Inflamm Bowel Dis. 2007, 13: 684-692. 10.1002/ibd.20084.
Article
PubMed
Google Scholar
Bent SJ, Forney LJ: The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J. 2008, 2: 689-695. 10.1038/ismej.2008.44.
Article
PubMed
CAS
Google Scholar
Marzorati M, Wittebolle L, Boon N, Daffonchio D, Verstraete W: How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ Microbiol. 2008, 10: 1571-1581. 10.1111/j.1462-2920.2008.01572.x.
Article
PubMed
CAS
Google Scholar
Farris MH, Olson JB: Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers. Lett Appl Microbiol. 2007, 45: 376-381. 10.1111/j.1472-765X.2007.02198.x.
Article
PubMed
CAS
Google Scholar
Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ: Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol. 2008, 74: 2461-2470. 10.1128/AEM.02272-07.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cadwell K, Patel KK, Maloney NS, Liu TC, Ng AC, Storer CE, Head RD, Xavier R, Stappenbeck TS, Virgin HW: Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell. 2010, 141: 1135-1145. 10.1016/j.cell.2010.05.009.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kleessen B, Kroesen AJ, Buhr HJ, Blaut M: Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand J Gastroenterol. 2002, 37: 1034-1041. 10.1080/003655202320378220.
Article
PubMed
CAS
Google Scholar
Winter SE, Keestra AM, Tsolis RM, Bäumler AJ: The blessings and curses of intestinal inflammation. Cell Host Microbe. 2010, 8: 36-43. 10.1016/j.chom.2010.06.003.
Article
PubMed
CAS
PubMed Central
Google Scholar
Swidsinski A, Loening-Baucke V, Theissig F, Engelhardt H, Bengmark S, Koch S, Lochs H, Dörffel Y: Comparative study of the intestinal mucus barrier in normal and inflamed colon. Gut. 2007, 56: 343-350. 10.1136/gut.2006.098160.
Article
PubMed
PubMed Central
Google Scholar
Peterson DA, McNulty NP, Guruge JL, Gordon JI: IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007, 2: 328-339. 10.1016/j.chom.2007.09.013.
Article
PubMed
CAS
Google Scholar
Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD: Salmonella enterica serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol. 2007, 5: 2177-2189. 10.1371/journal.pbio.0050244.
Article
PubMed
CAS
Google Scholar
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB: Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe. 2007, 2: 119-129. 10.1016/j.chom.2007.06.010.
Article
PubMed
CAS
Google Scholar
Artis D: Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat Rev Immunol. 2008, 8: 411-420. 10.1038/nri2316.
Article
PubMed
CAS
Google Scholar
Kaser A, Zeissig S, Blumberg RS: Inflammatory bowel disease. Annu Rev Immunol. 2010, 28: 573-621. 10.1146/annurev-immunol-030409-101225.
Article
PubMed
CAS
PubMed Central
Google Scholar
Baron JH, Connell AM, Lennard-Jones JE: Variation between observers in describing mucosal appearances in proctocolitis. BMJ. 1964, 5375: 89-92. 10.1136/bmj.1.5375.89.
Article
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: 5069-5072. 10.1128/AEM.03006-05.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, et al: ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32: 1363-1371. 10.1093/nar/gkh293.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ: New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol. 2006, 72: 5734-5741. 10.1128/AEM.00556-06.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ: At least 1 in 20 sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol. 2005, 71: 7724-7736. 10.1128/AEM.71.12.7724-7736.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schloss PD, Handelsman J: Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005, 71: 1501-1506. 10.1128/AEM.71.3.1501-1506.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL: NCBI BLAST: a better web interface. Nucleic Acids Res. 2008, W5-W9. 10.1093/nar/gkn201. 36 Web server
Letunic I, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007, 23: 127-128. 10.1093/bioinformatics/btl529.
Article
PubMed
CAS
Google Scholar
Nadkarni MA, Martin FE, Jacques NA, Hunter N: Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002, 148: 257-266.
Article
PubMed
CAS
Google Scholar