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

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

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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

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Unravelling the pathogenesis of inflammatory bowel disease

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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

The Wellcome Trust Case Control Consortium, U.K.

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

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

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

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

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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

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

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

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

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

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

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XBP1 Links ER Stress to Intestinal Inflammation and Confers Genetic Risk for Human Inflammatory Bowel Disease

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

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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

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

Mucosal flora in inflammatory bowel disease

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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

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

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

Enteric defensins are essential regulators of intestinal microbial ecology

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

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

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

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

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

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

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

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The genetics and immunopathogenesis of inflammatory bowel disease

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

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

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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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Bacterial flagellin is a dominant antigen in Crohn disease

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

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

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Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut

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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?

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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

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

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

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

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

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

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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.2007.08.002 · Cited by 501

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

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

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

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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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Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly

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Inflammatory bowel disease

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T cell receptor-alpha beta-deficient mice fail to develop colitis in the absence of a microbial environment.

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Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM

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