The Commensal Microbiota and Enteropathogens in the Pathogenesis of Inflammatory Bowel Diseases

A human gut microbial gene catalogue established by metagenomic sequencing

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Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

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Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease

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A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease

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IL-17 and th17 cells

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Metagenomic Analysis of the Human Distal Gut Microbiome

Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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<i>Faecalibacterium prausnitzii</i> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413 · see citing works

Unravelling the pathogenesis of inflammatory bowel disease

Xavier, R. J., & Podolsky, D. K. (2007) · Nature · doi:10.1038/nature06005 · Cited by 4,364 · see citing works

Interleukin-10-deficient mice develop chronic enterocolitis

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An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System

Mazmanian, S. K., Liu, C. H., Tzianabos, A. O., & Kasper, D. L. (2005) · Cell · doi:10.1016/j.cell.2005.05.007 · Cited by 2,910 · see citing works

The Wellcome Trust Case Control Consortium, U.K.

Mossman, K. (2008) · Scientific American · doi:10.1038/scientificamerican0108-42a · Cited by 2,714 · see citing works

Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach

Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277 · see citing works

Autophagy Is a Defense Mechanism Inhibiting BCG and Mycobacterium tuberculosis Survival in Infected Macrophages

Gutierrez, M. G., Master, S. S., Singh, S. B., Taylor, G. A., Colombo, M. I., & Deretic, V. (2004) · Cell · doi:10.1016/j.cell.2004.11.038 · Cited by 2,252 · see citing works

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1

Hampe, J., Franke, A., Rosenstiel, P. C., Till, A., Teuber, M., Huse, K., Albrecht, M., Gabriele Mayr, B., Vega, F. M. D. L., Briggs, J. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1954 · Cited by 1,899 · see citing works

Inflammatory bowel disease

Kaser, A., Zeissig, S., & Blumberg, R. S. (2010) · Annual Review of Immunology · doi:10.1146/annurev-immunol-030409-101225 · Cited by 1,806 · see citing works

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

Rioux, J. D., Xavier, R. J., Taylor, K. D., Silverberg, M. S., Goyette, P., Huett, A., Green, T., Kuballa, P., Barmada, M. M., Datta, L. W., et al. (2007) · Nature Genetics · doi:10.1038/ng2032 · Cited by 1,769 · see citing works

High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease

Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A.-L., Barnich, N., Bringer, M.-A., Swidsinski, A., Beaugerie, L., & Colombel, J.-F. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.04.061 · Cited by 1,566 · see citing works

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

Cadwell, K., Liu, J. Y., Brown, S. L., Miyoshi, H., Loh, J., Lennerz, J. K., Kishi, C., Kc, W., Carrero, J. A., Hunt, S., et al. (2008) · Nature · doi:10.1038/nature07416 · Cited by 1,542 · see citing works

Resident Enteric Bacteria Are Necessary for Development of Spontaneous Colitis and Immune System Activation in Interleukin-10-Deficient Mice

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The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., et al. (2009) · Immunity · doi:10.1016/j.immuni.2009.08.020 · Cited by 1,452 · see citing works

XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease

Kaser, A., Lee, A.-H., Franke, A., Glickman, J., Zeissig, S., Tilg, H., Nieuwenhuis, E., Higgins, D. E., Schreiber, S., Glimcher, L., et al. (2008) · Cell · doi:10.1016/j.cell.2008.07.021 · Cited by 1,442 · see citing works

Symbiotic bacteria direct expression of an intestinal bactericidal lectin

Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006) · Science · doi:10.1126/science.1127119 · Cited by 1,432 · see citing works

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

Png, C. W., Lindén, S. K., Gilshenan, K. S., Zoetendal, E. G., McSweeney, C. S., Sly, L. I., McGuckin, M. A., & Florin, T. H. J. (2010) · American Journal of Gastroenterology · doi:10.1038/ajg.2010.281 · Cited by 1,364 · see citing works

Mucosal flora in inflammatory bowel disease

Swidsinski, A. V., Ladhoff, A., Pernthaler, A., Swidsinski, S., Loening-Baucke, V. A., Ortner, M., Weber, J., Hoffmann, U., Schreiber, S., Dietel, M., et al. (2002) · Gastroenterology · doi:10.1053/gast.2002.30294 · Cited by 1,344 · see citing works

Host-Mediated Inflammation Disrupts the Intestinal Microbiota and Promotes the Overgrowth of Enterobacteriaceae

Lupp, C., Robertson, M. L., Wickham, M. E., Sekirov, I., Champion, O. L., Gaynor, E. C., & Finlay, B. B. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.06.010 · Cited by 1,310 · see citing works

Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry

Travassos, L. H., Carneiro, L. A. M., Ramjeet, M., Hussey, S., Kim, Y.-G., Magalhães, J. G., Yuan, L., Soares, F., Chea, E., Le Bourhis, L., et al. (2010) · Nature Immunology · doi:10.1038/ni.1823 · Cited by 1,306 · see citing works

Changes in expression and distribution of claudin 2, 5 and 8 lead to discontinuous tight junctions and barrier dysfunction in active Crohn’s disease

Zeißig, S., Bürgel, N., Günzel, D., Richter, J. F., Mankertz, J., Wahnschaffe, U., Kroesen, A. J., Zeitz, M., Fromm, M., & Schulzke, J. (2006) · Gut · doi:10.1136/gut.2006.094375 · Cited by 1,218 · see citing works

Enteric defensins are essential regulators of intestinal microbial ecology

Salzman, N. H., Hung, K., Haribhai, D., Chu, H., Karlsson-Sjöberg, J., Amir, E., Teggatz, P., Barman, M., Hayward, M., Eastwood, D., et al. (2010) · Nature Immunology · doi:10.1038/ni.1825 · Cited by 1,156 · see citing works

Mutations in T-cell antigen receptor genes α and β block thymocyte development at different stages

Mombaerts, P., Clarke, A. R., Rudnicki, M. A., Iacomini, J., Itohara, S., Lafaille, J. J., Wang, L., Ichikawa, Y., Jaenisch, R., Hooper, M., et al. (1992) · Nature · doi:10.1038/360225a0 · Cited by 1,114 · see citing works

Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics

Sartor, R. B. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.03.024 · Cited by 1,053 · see citing works

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048 · see citing works

NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation

Cooney, R. M., BAKER, J. T., Brain, O., Danis, B., Pichulik, T., Allan, P., Ferguson, D. J. P., Campbell, B. J., Jewell, D. P., & Simmons, A. (2009) · Nature Medicine · doi:10.1038/nm.2069 · Cited by 1,046 · see citing works

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

Willing, B. P., Dicksved, J., Halfvarson, J., Andersson, A. F., Lucio, M., Zheng, Z., Järnerot, G., Tysk, C., Jansson, J. K., & Engstrand, L. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.08.049 · Cited by 1,032 · see citing works

Spontaneous inflammatory disease in transgenic rats expressing HLA-B27 and human β2m: An animal model of HLA-B27-associated human disorders

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Reduced Paneth cell α-defensins in ileal Crohn's disease

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The genetics and immunopathogenesis of inflammatory bowel disease

Cho, J. H. (2008) · Nature Reviews Immunology · doi:10.1038/nri2340 · Cited by 940 · see citing works

Angiogenins: a new class of microbicidal proteins involved in innate immunity

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Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System

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Early lesions of recurrent Crohn's disease caused by infusion of intestinal contents in excluded ileum

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Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease

Darfeuille–Michaud, A., Neut, C., Barnich, N., Lederman, E., Martino, P. D., Desreumaux, P., Gambiez, L. P., Joly, B., Cortot, A., & Colombel, J.-F. (1998) · Gastroenterology · doi:10.1016/s0016-5085(98)70019-8 · Cited by 859 · see citing works

Normal luminal bacteria, especially Bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27/human beta2 microglobulin transgenic rats.

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IgA Response to Symbiotic Bacteria as a Mediator of Gut Homeostasis

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NOD2 (CARD15) mutations in Crohn’s disease are associated with diminished mucosal α-defensin expression

Wehkamp, J., Harder, J., Weichenthal, M., Schwab, M. G., Schäffeler, E., Schlee, M., Herrlinger, K. R., Stallmach, A., Noack, F., Fritz, P., et al. (2004) · Gut · doi:10.1136/gut.2003.032805 · Cited by 823 · see citing works

Bacterial flagellin is a dominant antigen in Crohn disease

Lodes, M. J., Cong, Y., Elson, C. O., Mohamath, R., Landers, C. J., Targan, S. R., Fort, M., & Hershberg, R. M. (2004) · Journal of Clinical Investigation · doi:10.1172/jci200420295 · Cited by 802 · see citing works

Increased Intestinal Permeability in Patients with Crohn's Disease and Their Relatives

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Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum

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Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon

Seksik, P., Rigottier‐Gois, L., Gramet, G., BRIEND‐SUTREN, M., Pochart, P., Marteau, P. R., Jian, R., & Dore, J. M. (2003) · Gut · doi:10.1136/gut.52.2.237 · Cited by 746 · see citing works

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

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Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut

Suzuki, K., Meek, B., Doi, Y., Muramatsu, M., Chiba, T., Honjo, T., & Fagarasan, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307317101 · Cited by 721 · see citing works

Enhanced Escherichia coli adherence and invasion in Crohn’s disease and colon cancer 1 1The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l’Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A. Darfeuille-Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn’s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens.As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn’s disease.

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The immune system and the gut microbiota: friends or foes?

Cerf-Bensussan, N., & Gaboriau-Routhiau, V. (2010) · Nature Reviews Immunology · doi:10.1038/nri2850 · Cited by 704 · see citing works

Aberrant Mucin Assembly in Mice Causes Endoplasmic Reticulum Stress and Spontaneous Inflammation Resembling Ulcerative Colitis

Heazlewood, C. K., Cook, M. C., Eri, R., Price, G. R., Tauro, S. B., Taupin, D., Thornton, D. J., Png, C. W., Crockford, T. L., Cornall, R. J., et al. (2008) · PLoS Medicine · doi:10.1371/journal.pmed.0050054 · Cited by 701 · see citing works

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

Baumgart, M., Dogan, B., Rishniw, M., Weitzman, G., Bosworth, B. P., Yantiss, R. K., Orsi, R. H., Wiedmann, M., McDonough, P. L., Kim, S. G., et al. (2007) · The ISME Journal · doi:10.1038/ismej.2007.52 · Cited by 630 · see citing works

Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora

Fagarasan, S., Muramatsu, M., Suzuki, K., Nagaoka, H., Hiai, H., & Honjo, T. (2002) · Science · doi:10.1126/science.1077336 · Cited by 590 · see citing works

CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease

Barnich, N., Carvalho, F. A., Glasser, A.-L., Darcha, C., Jantscheff, P., Allez, M., Peeters, H., Bommelaer, G., Desreumaux, P., Colombel, J., et al. (2007) · Journal of Clinical Investigation · doi:10.1172/jci30504 · Cited by 590 · see citing works

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

Brest, P., Lapaquette, P., Souidi, M., Lebrigand, K., Cesaro, A., Vouret-Craviari, V., Mari, B., Barbry, P., Mosnier, J.-F., Hébuterne, X., et al. (2011) · Nature Genetics · doi:10.1038/ng.762 · Cited by 563 · see citing works

Association of antibody responses to microbial antigens and complications of small bowel Crohn’s disease

Mow, W. S., Vasiliauskas, E. A., Lin, Y.-C., Fleshner, P. R., Papadakis, K. A., Taylor, K. D., Landers, C. J., Abreu-Martin, M. T., Rotter, J. I., Yang, H., et al. (2004) · Gastroenterology · doi:10.1053/j.gastro.2003.11.015 · Cited by 517 · see citing works

Host-Mediated Inflammation Disrupts the Intestinal Microbiota and Promotes the Overgrowth of Enterobacteriaceae

Lupp, C., Robertson, M. L., Wickham, M. E., Sekirov, I., Champion, O. L., Gaynor, E. C., & Finlay, B. B. (2007) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2007.08.002 · Cited by 501 · see citing works

Adherent Invasive Escherichia coli Strains from Patients with Crohn's Disease Survive and Replicate within Macrophages without Inducing Host Cell Death

Glasser, A.-L., Boudeau, J., Barnich, N., Perruchot, M.-H., Colombel, J., & Darfeuille–Michaud, A. (2001) · Infection and Immunity · doi:10.1128/iai.69.9.5529-5537.2001 · Cited by 465 · see citing works

Invasive Ability of an Escherichia coli Strain Isolated from the Ileal Mucosa of a Patient with Crohn’s Disease

Boudeau, J., Glasser, A.-L., Masseret, E., Joly, B., & Darfeuille–Michaud, A. (1999) · Infection and Immunity · doi:10.1128/iai.67.9.4499-4509.1999 · Cited by 449 · see citing works

Increased Short- and Long-Term Risk of Inflammatory Bowel Disease After Salmonella or Campylobacter Gastroenteritis

Gradel, K. O., Nielsen, H. L., Schønheyder, H. C., Ejlertsen, T., Kristensen, B., & Nielsen, H. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.04.001 · Cited by 424 · see citing works

High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease

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Molecular diversity of Escherichia coli in the human gut: New ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohnʼs disease

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CD4+ T Cells Reactive to Enteric Bacterial Antigens in Spontaneously Colitic C3H/HeJBir Mice: Increased T Helper Cell Type 1 Response and Ability to Transfer Disease

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Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease

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Comparative study of the intestinal mucus barrier in normal and inflamed colon

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Inflammatory bowel disease is associated with changes of enterocytic junctions

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Lymphoid Development in Mice Congenitally Lacking T Cell Receptor αβ-Expressing Cells

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Two-Year Combination Antibiotic Therapy With Clarithromycin, Rifabutin, and Clofazimine for Crohn’s Disease

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Inflammatory bowel disease

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