, Regional ileitis, The American Journal of Medicine, vol.13, issue.5, pp.583-90, 1952.
DOI : 10.1016/0002-9343(52)90025-9
, Serologic Testing with ANCA, ASCA, and Anti-OmpC in Children and Young Adults with Crohn's Disease and Ulcerative Colitis: Diagnostic Value and Correlation with Disease Phenotype, The American Journal of Gastroenterology, vol.42, issue.11, pp.99-2235, 2004.
DOI : 10.1111/j.1572-0241.2001.04043.x
, The Utility of Biomarkers in the Diagnosis and Therapy of Inflammatory Bowel Disease, Gastroenterology, vol.140, issue.6, pp.1817-1826, 2011.
DOI : 10.1053/j.gastro.2010.11.058
, Inflammatory Bowel Disease, New England Journal of Medicine, vol.347, issue.6, pp.417-446, 2002.
DOI : 10.1056/NEJMra020831
, Maladies inflammatoires chroniques de l'intestin Geographical variations of inflammatory bowel disease in France: a study based on national health insurance data, Inflamm Bowel Dis, issue.3, pp.12-218, 2006.
, Azathioprine and 6-mercaptopurine in Crohn disease. A meta-analysis
, Methotrexate for the Treatment of Crohn's Disease, New England Journal of Medicine, vol.332, issue.5, pp.292-299, 1995.
DOI : 10.1056/NEJM199502023320503
, Influence of Immunogenicity on the Long-Term Efficacy of Infliximab in Crohn's Disease, New England Journal of Medicine, vol.348, issue.7, pp.348-601, 2003.
DOI : 10.1056/NEJMoa020888
, Interleukin 12 is expressed and actively released by Crohn's disease intestinal lamina propria mononuclear cells, Gastroenterology, vol.112, issue.4, pp.1169-78, 1997.
DOI : 10.1016/S0016-5085(97)70128-8
, Expression of Interleukin-12-Related Cytokine Transcripts in Inflammatory Bowel Disease: Elevated Interleukin-23p19 and Interleukin-27p28 in Crohn??s Disease But Not in Ulcerative Colitis, Inflammatory Bowel Diseases, vol.11, issue.1, pp.16-235, 2002.
DOI : 10.1097/00054725-200501000-00003
, Intestinal epithelial cells as producers but not targets of chronic TNF suffice to cause murine Crohn-like pathology, Proceedings of the National Academy of Sciences, vol.108, issue.13, pp.5396-401, 1997.
DOI : 10.1073/pnas.1007811108
, Blockade of interleukin 6 trans signaling suppresses T-cell resistance against apoptosis in chronic intestinal inflammation: Evidence in Crohn disease and experimental colitis in vivo, Nature Medicine, vol.16, issue.11, pp.583-591, 2000.
DOI : 10.1038/nm1110-1341
, Enhanced production of IL-8 in chronic but not in early ileal lesions of Crohn's disease (CD), Clinical and Experimental Immunology, vol.59, issue.2, pp.180-185, 2000.
DOI : 10.1016/S0167-5699(98)01285-7
, Proinflammatory Cytokines in the Pathogenesis of Inflammatory Bowel Diseases, Gastroenterology, vol.140, issue.6, pp.1756-67, 2011.
DOI : 10.1053/j.gastro.2011.02.016
, Functional diversity of helper T lymphocytes, Nature, vol.383, issue.6603, pp.383-787, 1996.
DOI : 10.1038/383787a0
, Biology of human TH1 and TH2 cells IL-23 drives a pathogenic T cell population that induces autoimmune inflammation, J Clin Immunol J Exp Med, vol.15, issue.2012, pp.121-130, 1995.
, Mechanisms of Disease: pathogenesis of Crohn's disease and ulcerative colitis, Nature Clinical Practice Gastroenterology & Hepatology, vol.124, issue.7, pp.390-407, 2006.
DOI : 10.1038/ncpgasthep0528
, Unravelling the pathogenesis of inflammatory bowel disease, Nature, vol.124, issue.7152, pp.448-427, 2007.
DOI : 10.1038/nature06005
, Inflammatory Bowel Disease, Annual Review of Immunology, vol.28, issue.1, pp.573-621, 2010.
DOI : 10.1146/annurev-immunol-030409-101225
, The genetic basis of inflammatory bowel disease Genetic epidemiology in inflammatory bowel disease Ulcerative colitis and Crohn's disease in an unselected population of monozygotic and dizygotic twins. A study of heritability and the influence of smoking, Dig Dis Dig Dis Gut, vol.27, issue.1667, pp.428-470, 1988.
, CARD15/NOD2 Mutations in Crohn's Disease, Annals of the New York Academy of Sciences, vol.45, issue.1, pp.9-18, 1072.
DOI : 10.1016/S0016-5085(98)70019-8
, Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease, Nature Nature, issue.41168376837, pp.599-603, 2001.
, Genetic aspects of Crohn's disease: a review. Immuno-analyse et Biologie Spécialisée, pp.137-150, 2007.
, Nod2 Is a General Sensor of Peptidoglycan through Muramyl Dipeptide (MDP) Detection, Journal of Biological Chemistry, vol.278, issue.11, pp.8869-72, 2003.
DOI : 10.1074/jbc.C200651200
, Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition, The EMBO Journal, vol.23, issue.7, pp.1587-97, 2004.
DOI : 10.1038/sj.emboj.7600175
, Expression of NOD2 in Paneth cells: a possible link to Crohn's ileitis, Gut, vol.52, issue.11, pp.52-1591, 2003.
DOI : 10.1136/gut.52.11.1591
, Nod2-Dependent Th2 Polarization of Antigen-Specific Immunity, The Journal of Immunology, vol.181, issue.11, pp.181-7925, 2008.
DOI : 10.4049/jimmunol.181.11.7925
, Identification of an innate T helper type 17 response to intestinal bacterial pathogens, Nature Medicine, vol.178, issue.7, pp.837-881, 2011.
DOI : 10.1111/j.1462-5822.2007.01071.x
, Direct bacterial killing in vitro by recombinant Nod2 is compromised by Crohn's disease-associated mutations Nod-like receptors: cytosolic watchdogs for immunity against pathogens NOD2, an intracellular innate immune sensor involved in host defense and Crohn's disease, PLoS One PLoS Pathog Mucosal Immunol, vol.5, issue.312 45, pp.152-194, 2007.
, NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry, Nat Med Nat Immunol, vol.16, issue.111, pp.55-62, 2010.
, A NOD2-NALP1 complex mediates caspase-1-dependent IL-1beta secretion in response to Bacillus anthracis infection and muramyl dipeptide Nucleotide-binding oligomerization domain-2 modulates specific TLR pathways for the induction of cytokine release, Proc Natl Acad Sci U S A J Immunol, vol.105, issue.2210, pp.174-6518, 2005.
, Dual roles of NOD2 in TLR4-mediated signal transduction and -induced inflammatory gene expression in macrophages, Cellular Microbiology, vol.69, issue.5, pp.717-747, 2011.
DOI : 10.1111/j.1462-5822.2010.01567.x
, NOD2 is a negative regulator of Toll-like receptor 2???mediated T helper type 1 responses, Nature Immunology, vol.52, issue.8, pp.800-808, 2004.
DOI : 10.1016/S0006-291X(02)02807-3
, Secretory Mediators Regulate Nod2-Induced Tolerance in Human Macrophages, Gastroenterology, vol.140, issue.1, pp.231-272, 2010.
DOI : 10.1053/j.gastro.2010.09.009
, Nod2 suppresses Borrelia burgdorferi mediated murine Lyme arthritis and carditis through the induction of tolerance Nod2 is essential for temporal development of intestinal microbial communities, PLoS One Gut, vol.6, issue.210, pp.60-1354, 2011.
, Evidence for the involvement of NOD2 in regulating colonic epithelial cell growth and survival, World J Gastroenterol, issue.38, pp.14-5834, 2008.
, Intestinal homeostasis and its breakdown in inflammatory bowel disease, Nature, vol.8, issue.7351, pp.474-298, 2011.
DOI : 10.1038/nature10208
, CARD15/NOD2 Mutational Analysis and Genotype-Phenotype Correlation in 612 Patients with Inflammatory Bowel Disease, The American Journal of Human Genetics, vol.70, issue.4, pp.845-57, 2002.
DOI : 10.1086/339432
, The prevalence of genetic and serologic markers in an unselected European population-based cohort of IBD patients, Gastroenterol Clin Biol Inflamm Bowel Dis, vol.29, issue.131, pp.6-7, 2005.
, Prevalence of CARD15/NOD2 Mutations in Caucasian Healthy People, The American Journal of Gastroenterology, vol.39, issue.34, pp.1259-67, 2007.
DOI : 10.1111/j.1572-0241.2005.00224.x
, Estimating the odds ratios of Crohn disease for the main CARD15/NOD2 mutations using a conditional maximum likelihood method in pedigrees collected via affected family members, European Journal of Human Genetics, vol.51, issue.8, pp.15-864, 2007.
DOI : 10.1038/sj.ejhg.5201839
, The contribution of NOD2 gene mutations to the risk and site of disease in inflammatory bowel disease, Gastroenterology, vol.122, issue.4, pp.867-74, 2002.
DOI : 10.1053/gast.2002.32415
, NOD2 mutations predict the risk for surgery in pediatric-onset Crohn's disease NOD2 Polymorphism Predicts Response to Treatment in Crohn's Disease- First Steps to a Personalized Therapy Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract, J Pediatr Surg Dig Dis Sci Science, issue.85710, pp.45-1591, 2005.
, Innate immunity in inflammatory bowel disease, World Journal of Gastroenterology, vol.13, issue.42, pp.5577-80, 2007.
DOI : 10.3748/wjg.v13.i42.5577
, Nod2 mutation in Crohn's disease potentiates NF-kappaB activity and IL- 1beta processing Crohn's disease-associated Nod2 mutants reduce IL10 transcription, Science Nat Immunol, vol.307, issue.655, pp.734-742, 2005.
, NOD2 (CARD15) mutations in Crohn's disease are associated with diminished mucosal alpha-defensin expression, Gut, issue.11, pp.53-1658, 2004.
, Human beta-defensin 2 but not beta-defensin 1 is expressed preferentially in colonic mucosa of inflammatory bowel disease, Eur J Gastroenterol Hepatol, issue.7, pp.14-745, 2002.
, MDP-NOD2 stimulation induces HNP-1 secretion, which contributes to NOD2 antibacterial function, Inflammatory Bowel Diseases, vol.16, issue.5, pp.736-778, 2008.
DOI : 10.1002/ibd.21144
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895931
, NOD2 gene variants are a risk factor for culture-positive spontaneous bacterial peritonitis and monomicrobial bacterascites in cirrhosis Genetics of Crohn disease, an archetypal inflammatory barrier disease, Liver Int Nat Rev Genet, issue.65, pp.376-88, 2005.
, Nucleotide-Binding Oligomerization Domain-2 Inhibits Toll-Like Receptor-4 Signaling in the Intestinal Epithelium, Gastroenterology, vol.139, issue.3, pp.904-921, 2010.
DOI : 10.1053/j.gastro.2010.05.038
, A Crohn's disease???associated NOD2 mutation suppresses transcription of human IL10 by inhibiting activity of the nuclear ribonucleoprotein hnRNP-A1, Nature Immunology, vol.63, issue.5, pp.471-480, 2009.
DOI : 10.1002/eji.200425229
, CARD15 mutations in Blau syndrome The future of genetic studies of complex human diseases, Nat Genet Science, vol.29, issue.15281, pp.273-1516, 1996.
, Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease, Nature Genetics, vol.29, issue.2, pp.223-231, 2001.
DOI : 10.1038/ng1001-223
, XBP1 Links ER Stress to Intestinal Inflammation and Confers Genetic Risk for Human Inflammatory Bowel Disease, Cell, vol.134, issue.5, pp.743-56, 2008.
DOI : 10.1016/j.cell.2008.07.021
, Common variants in the NLRP3 region contribute to Crohn's disease susceptibility, Nature Genetics, vol.52, issue.1, pp.71-77, 2009.
DOI : 10.1073/pnas.88.16.7276
, A Genome-Wide Association Study Identifies IL23R as an Inflammatory Bowel Disease Gene, Science, vol.314, issue.5804, pp.314-1461, 2006.
DOI : 10.1126/science.1135245
, Crohn disease: A current perspective on genetics, autophagy and immunity, Autophagy, vol.7, issue.4, pp.355-74, 2008.
DOI : 10.4161/auto.7.4.13074
, A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells, Nature, vol.102, issue.7219, pp.456-259, 2008.
DOI : 10.1038/nature07416
, ATG16L1 and NOD2 interact in an autophagy-dependent, anti-bacterial pathway implicated in Crohn's disease pathogenesis A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease Towards a molecular risk map--recent advances on the etiology of inflammatory bowel disease, Gastroenterology Nat Genet Semin Immunol, vol.85, issue.216, pp.242-247, 2009.
, Importance of disrupted intestinal barrier in inflammatory bowel diseases, Inflammatory Bowel Diseases, vol.17, issue.1, pp.362-81, 2011.
DOI : 10.1002/ibd.21403
, Production of Short Chain Fatty Acids by the Intestinal Microflora During the First 2 Years of Human Life, Journal of Pediatric Gastroenterology and Nutrition, vol.15, issue.4, pp.395-403, 1992.
DOI : 10.1097/00005176-199211000-00005
, Reduced Enterobacterial and Increased Staphylococcal Colonization of the Infantile Bowel: An Effect of Hygienic Lifestyle?, Pediatric Research, vol.9, issue.54, pp.96-101, 2006.
DOI : 10.1203/01.pdr.0000191137.12774.b2
, Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age, Diversity of the human intestinal microbial flora. Science, pp.308-1635, 2005.
DOI : 10.1016/j.jaci.2011.04.060
, Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization, Applied and Environmental Microbiology, vol.66, issue.5, pp.2263-2269, 2000.
DOI : 10.1128/AEM.66.5.2263-2266.2000
, Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes, FEMS Microbiology Ecology, vol.43, issue.2, pp.237-282, 2003.
DOI : 10.1111/j.1574-6941.2003.tb01063.x
, Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection, Cell, vol.127, issue.2, pp.423-456, 2006.
DOI : 10.1016/j.cell.2006.08.043
, Biodiversity of the Mucosa-Associated Microbiota Is Stable Along the Distal Digestive Tract in Healthy Individuals and Patients With Ibd, Inflammatory Bowel Diseases, vol.11, issue.5, pp.473-80, 2005.
DOI : 10.1097/01.MIB.0000159662.62651.06
, Enterotypes of the human gut microbiome, Nature, issue.7346, pp.473-174, 2011.
URL : https://hal.archives-ouvertes.fr/cea-00903625
, The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing Characteristics of human intestinal Escherichia coli with changing environments, PLoS Biol Environ Microbiol, issue.6118, pp.10-2132, 2008.
, Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut, Nature Reviews Immunology, vol.118, issue.6, pp.411-431, 2008.
DOI : 10.1038/nri2316
, Influence of intestinal bacteria on induction of regulatory T cells: lessons from a transfer model of colitis, Gut, vol.54, issue.11, pp.54-1546, 2005.
DOI : 10.1136/gut.2004.059451
, The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.105-15064, 2008.
DOI : 10.1073/pnas.0803124105
, The intestinal mucus layer from patients with inflammatory bowel disease harbors high numbers of bacteria compared with controls, Gastroenterology, vol.117, issue.5, pp.1089-97, 1999.
DOI : 10.1016/S0016-5085(99)70393-8
, The claudins, Genome Biology, vol.10, issue.8, p.235, 2009.
DOI : 10.1186/gb-2009-10-8-235
, Occludin is required for cytokine-induced regulation of tight junction barriers, Journal of Cell Science, vol.123, issue.16, pp.2844-52, 2010.
DOI : 10.1242/jcs.065581
, Changes in expression and distribution of claudin 2, 5 and 8 lead to discontinuous tight junctions and barrier dysfunction in active Crohn's disease, Gut, vol.56, issue.1, pp.61-72, 2007.
DOI : 10.1136/gut.2006.094375
, Modulating the intestinal immune system: the role of lymphotoxin and GALT organs, Gut, vol.53, issue.3, pp.456-65, 2004.
DOI : 10.1136/gut.2003.023671
, Peyer's Patches: The Immune Sensors of the Intestine, International Journal of Inflammation, vol.2, issue.1, p.823710, 2010.
DOI : 10.1182/blood-2004-11-4565
, Nod2 regulates the host response towards microflora by modulating T cell function and epithelial permeability in mouse Peyer's patches, Gut, vol.59, issue.2, pp.207-224, 2010.
DOI : 10.1136/gut.2008.171546
, Obesity, visceral fat and Crohn??s disease, Current Opinion in Clinical Nutrition and Metabolic Care, vol.13, issue.5, pp.574-80, 2010.
DOI : 10.1097/MCO.0b013e32833cf0f4
, Is Crohn??s creeping fat an adipose tissue?, Inflammatory Bowel Diseases, vol.17, issue.3, pp.747-57, 2011.
DOI : 10.1002/ibd.21413
URL : http://prodinra.inra.fr/ft/F38B201E-9C95-4869-96B1-58D154F3BEC7
, The path to Crohn??s disease: Is mucosal pathology a secondary event?, Inflammatory Bowel Diseases, vol.16, issue.5, pp.896-902, 2009.
DOI : 10.1002/ibd.21171
, Mesenteric fat in Crohn's disease: a pathogenetic hallmark or an innocent bystander?, Gut, vol.56, issue.4, pp.577-83, 2007.
DOI : 10.1136/gut.2005.082925
, Intestinal permeability in patients with Crohn's disease and their healthy relatives, Gastroenterology, vol.97, issue.4, pp.927-958, 1989.
DOI : 10.1016/0016-5085(89)91499-6
, Abnormal intestinal permeability predicts relapse in inactive Crohn disease, Scand J Gastroenterol, issue.11, pp.35-1163, 2000.
, Defensins and inflammation: The role of defensins in inflammatory bowel disease, Journal of Gastroenterology and Hepatology, vol.56, issue.2, pp.202-210, 2009.
DOI : 10.1111/j.1440-1746.2008.05772.x
, Mucosal flora in inflammatory bowel disease, Gastroenterology, vol.122, issue.1, pp.44-54, 2002.
DOI : 10.1053/gast.2002.30294
, Role of the faecal stream in the maintenance of Crohn's colitis., Gut, vol.26, issue.3, pp.279-84, 1985.
DOI : 10.1136/gut.26.3.279
, Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum, The Lancet, vol.338, issue.8770, pp.338-771, 1991.
DOI : 10.1016/0140-6736(91)90663-A
, Saccharomyces boulardii in maintenance treatment of Crohn's disease, Digestive Diseases and Sciences, vol.45, issue.7, pp.1462-1466, 2000.
DOI : 10.1023/A:1005588911207
, Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine, Gut, vol.53, issue.11, pp.53-1617, 2004.
DOI : 10.1136/gut.2003.037747
, Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice, Infect Immun, issue.11, pp.66-5224, 1998.
, Mucosal colonisation with Lactobacillus casei mitigates barrier injury induced by exposure to trinitronbenzene sulphonic acid, Gut, vol.54, issue.7, pp.955-964, 2005.
DOI : 10.1136/gut.2004.056101
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1774610
, Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria, Gastroenterology, vol.128, issue.4, pp.891-906, 2005.
DOI : 10.1053/j.gastro.2005.02.009
, Lactobacillus species prevents colitis in interleukin 10 gene???deficient mice, Gastroenterology, vol.116, issue.5, pp.1107-1121, 1999.
DOI : 10.1016/S0016-5085(99)70013-2
, Tolerance exists towards resident intestinal flora but is broken in active inflammatory bowel disease (IBD), Clinical & Experimental Immunology, vol.19, issue.3, pp.448-55, 1995.
DOI : 10.1111/j.1365-2249.1995.tb03836.x
, Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria., Gut, vol.38, issue.3, pp.365-75, 1996.
DOI : 10.1136/gut.38.3.365
, Presence of bacterial 16S ribosomal RNA gene segments in human intestinal lymph follicles, Scand J Gastroenterol, issue.8, pp.35-824, 2000.
, Bacterial translocation in patients with Crohn's disease undergoing surgery, Dis Colon Rectum, issue.12, pp.45-1665, 2002.
, Association of the NOD2 genotype with bacterial translocation via altered cell-cell contacts in Crohn's disease patients, Inflamm Bowel Dis, issue.8, pp.16-1311, 2010.
, Mucosal and Invading Bacteria in Patients with Inflammatory Bowel Disease Compared with Controls, Scandinavian Journal of Gastroenterology, vol.37, issue.9, pp.1034-1075, 2002.
DOI : 10.1080/003655202320378220
, Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine, Cell, vol.141, issue.7, pp.141-1135, 2010.
DOI : 10.1016/j.cell.2010.05.009
URL : http://doi.org/10.1016/j.cell.2010.05.009
, The role of infection in the aetiology of inflammatory bowel disease, Journal of Gastroenterology, vol.46, issue.4, pp.266-76, 2010.
DOI : 10.1007/s00535-009-0191-y
, Crohn's disease: the cold chain hypothesis, The Lancet, vol.362, issue.9400, pp.2012-2017, 2003.
DOI : 10.1016/S0140-6736(03)15024-6
, Does Mycobacterium avium subspecies paratuberculosis cause Crohn's disease? Gut, pp.896-904, 2005.
, Culture of Mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn's disease, The Lancet, vol.364, issue.9439, pp.364-1039, 2004.
DOI : 10.1016/S0140-6736(04)17058-X
, The Fecal Microbiota of Irritable Bowel Syndrome Patients Differs Significantly From That of Healthy Subjects, Gastroenterology, vol.133, issue.1, pp.24-33, 2007.
DOI : 10.1053/j.gastro.2007.04.005
, Obesity alters gut microbial ecology, Proceedings of the National Academy of Sciences, vol.102, issue.31, pp.11070-11075, 2005.
DOI : 10.1073/pnas.0504978102
, Innate immunity and intestinal microbiota in the development of Type 1 diabetes, Nature, vol.7, issue.7216, pp.455-1109, 2008.
DOI : 10.1038/nature07336
, Disease outcomes as a consequence of environmental influences on the development of the immune system, Curr Opin Allergy Clin Immunol, issue.93, pp.185-194, 2009.
, Microbial Influences in Inflammatory Bowel Diseases, Gastroenterology, vol.134, issue.2, pp.577-94, 2008.
DOI : 10.1053/j.gastro.2007.11.059
, The intestinal flora in inflammatory bowel disease: normal or abnormal?, Curr Opin Gastroenterol, vol.21, issue.4, pp.414-422, 2005.
, The role of mucosal immunity and host genetics in defining intestinal commensal bacteria, Current Opinion in Gastroenterology, vol.26, issue.6, pp.564-71, 2010.
DOI : 10.1097/MOG.0b013e32833f1195
, 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, issue.12, pp.12-1136, 2006.
, hybridization study in mice, World Journal of Gastroenterology, vol.11, issue.8, pp.1131-1171, 2005.
DOI : 10.3748/wjg.v11.i8.1131
, Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases, Proceedings of the National Academy of Sciences, vol.104, issue.34, pp.13780-13785, 2007.
DOI : 10.1073/pnas.0706625104
, Dysbiosis in inflammatory bowel disease, Gut, vol.53, issue.1, pp.1-4, 2004.
DOI : 10.1136/gut.53.1.1
, Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease, The American Journal of Gastroenterology, vol.119, issue.4, pp.939-985, 2002.
DOI : 10.1023/A:1026632704628
, Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon, Gut, vol.52, issue.2, pp.237-279, 2003.
DOI : 10.1136/gut.52.2.237
, High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease, Gut, vol.56, issue.5, pp.669-75, 2007.
DOI : 10.1136/gut.2006.099796
, Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach, Gut, vol.55, issue.2, pp.205-216, 2006.
DOI : 10.1136/gut.2005.073817
, Reduced microbial diversity in inflammatory bowel diseases, Gut, issue.8, pp.55-1207, 2006.
, Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis, Journal of Clinical Microbiology, vol.44, issue.11, pp.44-4136, 2006.
DOI : 10.1128/JCM.01004-06
, Specificities of the fecal microbiota in inflammatory bowel disease, Inflammatory Bowel Diseases, vol.12, issue.2, pp.106-117, 2006.
DOI : 10.1097/01.MIB.0000200323.38139.c6
, Nod2 is required for the regulation of commensal microbiota in the intestine, Proceedings of the National Academy of Sciences, vol.106, issue.37, pp.106-15813, 2009.
DOI : 10.1073/pnas.0907722106
, Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases, Inflammatory Bowel Diseases, vol.17, issue.1, pp.179-84, 2010.
DOI : 10.1002/ibd.21339
, Pathogenic Escherichia coli, Nat Rev Microbiol, issue.22, pp.123-163, 2004.
, Enteroaggregative Escherichia coli expresses a novel flagellin that causes IL-8 release from intestinal epithelial cells, Journal of Clinical Investigation, vol.105, issue.12, pp.1769-77, 2000.
DOI : 10.1172/JCI8892
, Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease, Gastroenterology, vol.115, issue.6, pp.1405-1418, 1998.
DOI : 10.1016/S0016-5085(98)70019-8
, 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, The ISME Journal, vol.62, issue.5, pp.403-421, 2007.
DOI : 10.1073/pnas.252529799
, Invasive Escherichia coli are a feature of Crohn's disease, Laboratory Investigation, vol.115, issue.10, pp.1042-54, 2007.
DOI : 10.1038/labinvest.3700661
, Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease, Infect Immun, vol.67, issue.9, pp.4499-509, 1999.
, High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn???s disease, Gastroenterology, vol.127, issue.2, pp.412-433, 2004.
DOI : 10.1053/j.gastro.2004.04.061
, 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, Inflammatory Bowel Diseases, vol.15, issue.6, pp.15-872, 2009.
DOI : 10.1002/ibd.20860
, Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease, Inflammatory Bowel Diseases, vol.18, issue.5, 2011.
DOI : 10.1002/ibd.21899
, Adherent Invasive Escherichia coli Strains from Patients with Crohn's Disease Survive and Replicate within Macrophages without Inducing Host Cell Death, Infection and Immunity, vol.69, issue.9, pp.69-5529, 2001.
DOI : 10.1128/IAI.69.9.5529-5537.2001
, Escherichia coli isolated from a Crohn's disease patient adheres, invades, and induces inflammatory responses in polarized intestinal epithelial cells, International Journal of Medical Microbiology, vol.298, issue.5-6, pp.298-303, 2008.
DOI : 10.1016/j.ijmm.2007.05.011
, The Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 replicates in mature phagolysosomes within J774 macrophages, Cellular Microbiology, vol.23, issue.3, pp.471-84, 2006.
DOI : 10.1016/j.bbrc.2003.07.023
, Replication of Crohn's disease-associated AIEC within macrophages is dependent on TNF-alpha secretion, Lab Invest, 2011.
, Adherent-invasive Escherichia coli isolated from Crohn's disease patients induce granulomas in vitro, Cellular Microbiology, vol.23, issue.5, pp.1252-61, 2007.
DOI : 10.1038/ni1092
, Adherent-invasive Escherichia coli, strain LF82 disrupts apical junctional complexes in polarized epithelia, BMC Microbiology, vol.9, issue.1, p.180, 2009.
DOI : 10.1186/1471-2180-9-180
, Adherent-invasive Escherichia coli: a putative new E. coli pathotype associated with Crohn's disease, International Journal of Medical Microbiology, vol.292, issue.3-4, pp.3-4, 2002.
DOI : 10.1078/1438-4221-00201
, Complete Genome Sequence of Adherent Invasive Escherichia coli UM146 Isolated from Ileal Crohn's Disease Biopsy Tissue, Journal of Bacteriology, vol.193, issue.2, p.583, 2011.
DOI : 10.1128/JB.01290-10
, Complete genome sequence of Crohn's disease-associated adherentinvasive E. coli strain LF82, PLoS One, vol.5, issue.9, 2010.
, Biofilm formation as a novel phenotypic feature of adherentinvasive Escherichia coli (AIEC), BMC Microbiol, issue.9, p.202, 2009.
, Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM, J Exp Med, issue.10, pp.206-2179, 2009.
, Abnormal CEACAM6 expression in Crohn disease patients favors gut colonization and inflammation by adherent-invasive E. coli. Virulence, pp.281-283, 2010.
, Abnormally expressed ER stress response chaperone Gp96 in CD favours adherent-invasive Escherichia coli invasion, Gut, vol.59, issue.10, pp.59-1355, 2010.
DOI : 10.1136/gut.2010.207456
URL : https://hal.archives-ouvertes.fr/hal-01218270
, Crohn disease???associated adherent-invasive E. coli bacteria target mouse and human Peyer???s patches via long polar fimbriae, Journal of Clinical Investigation, vol.121, issue.3, pp.966-75, 2011.
DOI : 10.1172/JCI44632DS1
, Ex??vivo intestinal adhesion of Escherichia coli LF82 in Crohn???s disease, Microbial Pathogenesis, vol.51, issue.6, pp.51-426, 2011.
DOI : 10.1016/j.micpath.2011.08.006
, A Role for the RNA Chaperone Hfq in Controlling Adherent-Invasive Escherichia coli Colonization and Virulence, PLoS ONE, vol.294, issue.1, p.16387, 2011.
DOI : 10.1371/journal.pone.0016387.s001
, Lactobacillus casei DN-114 001 Inhibits the Ability of Adherent-Invasive Escherichia coli Isolated from Crohn's Disease Patients To Adhere to and To Invade Intestinal Epithelial Cells, Applied and Environmental Microbiology, vol.71, issue.6, pp.71-2880, 2005.
DOI : 10.1128/AEM.71.6.2880-2887.2005
, Inhibitory effect of probiotic Escherichia coli strain Nissle 1917 on adhesion to and invasion of intestinal epithelial cells by adherent-invasive E. coli strains isolated from patients with Crohn's disease, Alimentary Pharmacology and Therapeutics, vol.95, issue.15, pp.45-56, 2003.
DOI : 10.1136/gut.49.1.47
, The Probiotic Escherichia coli Nissle 1917 Reduces Pathogen Invasion and Modulates Cytokine Expression in Caco-2 Cells Infected with Crohn's Disease-Associated E. coli LF82, Applied and Environmental Microbiology, vol.77, issue.7, pp.77-2541, 2011.
DOI : 10.1128/AEM.01601-10
, CARD15 variants determine a disturbed early response of monocytes to adherent-invasive Escherichia coli strain LF82 in Crohn's disease, International Journal of Immunogenetics, vol.48, issue.3, pp.181-91, 2007.
DOI : 10.1128/IAI.69.4.2045-2053.2001
, Defects in autophagy favour adherent-invasive Escherichia coli persistence within macrophages leading to increased proinflammatory response, Cell Microbiol, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01227409
, Different intestinal permeability patterns in relatives and spouses of patients with Crohn's disease: an inherited defect in mucosal defence?, Gut, vol.44, issue.1, pp.96-100, 1999.
DOI : 10.1136/gut.44.1.96
, The Obligate Anaerobic Faecal Flora of Patients with Crohn's Disease and Their First-Degree Relatives, Scandinavian Journal of Gastroenterology, vol.89, issue.9, pp.1125-1156, 1988.
DOI : 10.3109/00365528809090179
, Inflammatory Bowel Disease in the South Asian Pediatric Population of British Columbia, The American Journal of Gastroenterology, vol.100, issue.5, pp.1077-83, 2007.
DOI : 10.1136/adc.88.11.995
, Smoking in Crohn's disease: effect on localisation and clinical course., Gut, vol.33, issue.6, pp.779-82, 1992.
DOI : 10.1136/gut.33.6.779
, Appendectomy is followed by increased risk of Crohn's disease, Gastroenterology, vol.124, issue.1, pp.40-46, 2003.
DOI : 10.1053/gast.2003.50021
, Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases, Gut, vol.57, issue.9, pp.1185-91, 2008.
DOI : 10.1136/gut.2007.122143
, Lifestyle-related disease in Crohn???s disease: Relapse prevention by a semi-vegetarian diet, World Journal of Gastroenterology, vol.16, issue.20, pp.16-2484, 2010.
DOI : 10.3748/wjg.v16.i20.2484
, Imbalances in Dietary Consumption of Fatty Acids, Vegetables, and Fruits Are Associated With Risk for Crohn's Disease in Children, The American Journal of Gastroenterology, vol.12, issue.170, pp.2016-2041, 2007.
DOI : 10.1136/gut.2004.054353
, Human nutrition, the gut microbiome and the immune system, Nature, vol.455, issue.7351, pp.474-327, 2011.
DOI : 10.1038/nature10213
, Health effects of air pollution, Journal of Allergy and Clinical Immunology, vol.114, issue.5, pp.1116-1139, 2004.
DOI : 10.1016/j.jaci.2004.08.030
, Hygiene hypothesis in inflammatory bowel disease: A critical review of the literature, World Journal of Gastroenterology, vol.14, issue.2, pp.165-73, 2008.
DOI : 10.3748/wjg.14.165
, Childhood Hygiene Is Associated With the Risk for Inflammatory Bowel Disease: A Population-Based Study, The American Journal of Gastroenterology, vol.299, issue.7, pp.1775-82, 2008.
DOI : 10.1111/j.1572-0241.2008.01905.x
, Childhood infections and the risk of inflammatory bowel disease, Digestive Diseases and Sciences, vol.86, issue.3, pp.555-60, 1994.
DOI : 10.1007/BF02088342
, PERINATAL RISK FACTORS FOR INFLAMMATORY BOWEL DISEASE: A CASE-CONTROL STUDY, American Journal of Epidemiology, vol.132, issue.6, pp.1111-1120, 1990.
DOI : 10.1093/oxfordjournals.aje.a115754
, Infectious Gastroenteritis and Risk of Developing Inflammatory Bowel Disease, Gastroenterology, vol.135, issue.3, pp.781-787, 2008.
DOI : 10.1053/j.gastro.2008.05.081
, Increased Short- and Long-Term Risk of Inflammatory Bowel Disease After Salmonella or Campylobacter Gastroenteritis, Gastroenterology, vol.137, issue.2, pp.495-501, 2009.
DOI : 10.1053/j.gastro.2009.04.001
, Bacterial Biofilm Suppression with Antibiotics for Ulcerative and Indeterminate Colitis: Consequences of Aggressive Treatment, Archives of Medical Research, vol.39, issue.2, pp.198-204, 2008.
DOI : 10.1016/j.arcmed.2007.08.001
, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proceedings of the National Academy of Sciences, vol.108, issue.Supplement_1, pp.4554-61, 2011.
DOI : 10.1073/pnas.1000087107
, Antibiotic use and the development of Crohn's disease, Gut, vol.53, issue.2, pp.246-50, 2004.
DOI : 10.1136/gut.2003.025239
, Early-life exposures associated with antibiotic use and risk of subsequent Crohn's disease, Scandinavian Journal of Gastroenterology, vol.15, issue.8, pp.43-961, 2008.
DOI : 10.1542/peds.2005-2824
, Association Between the Use of Antibiotics in the First Year of Life and Pediatric Inflammatory Bowel Disease, The American Journal of Gastroenterology, vol.69, issue.12, pp.105-2687, 2010.
DOI : 10.1542/peds.99.3.318
, Antibiotic use and inflammatory bowel diseases in childhood, Gut, vol.60, issue.1, pp.49-54, 2011.
DOI : 10.1136/gut.2010.219683
, Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection, Infection and Immunity, vol.76, issue.10, pp.76-4726, 2008.
DOI : 10.1128/IAI.00319-08
, Antibiotic Treatment Alters the Colonic Mucus Layer and Predisposes the Host to Exacerbated Citrobacter rodentium-Induced Colitis, Infection and Immunity, vol.79, issue.4, pp.1536-1581, 2011.
DOI : 10.1128/IAI.01104-10
, Risk of upper gastrointestinal bleeding and perforation associated with individual non-steroidal anti-inflammatory drugs, Lancet, issue.8900, pp.343-769, 1994.
, Aspirin in the aetiology of Crohn???s disease and ulcerative colitis: a European prospective cohort study, Alimentary Pharmacology & Therapeutics, vol.125, issue.Suppl., pp.34-649, 2011.
DOI : 10.1111/j.1365-2036.2011.04784.x
, Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation, Brain, Behavior, and Immunity, vol.25, issue.3, pp.397-407, 2011.
DOI : 10.1016/j.bbi.2010.10.023
, Review article: mechanisms of initiation and perpetuation of gut inflammation by stress, Aliment Pharmacol Ther, issue.12, pp.16-2017, 2002.
, The Role of Bacteria in the Pathogenesis of Inflammatory Bowel Disease, Gut and Liver, vol.4, issue.3, pp.295-306, 2010.
DOI : 10.5009/gnl.2010.4.3.295
, Inflammatory bowel disease-like enteritis and caecitis in a senescence accelerated mouse P1/Yit strain, Gut, vol.43, issue.1, pp.71-79, 1998.
DOI : 10.1136/gut.43.1.71
, Multiple immune abnormalities in tumor necrosis factor and lymphotoxin-?? double-deficient mice, International Immunology, vol.8, issue.1, pp.23-36, 1996.
DOI : 10.1093/intimm/8.1.23
, Lethal tuberculosis in interleukin-6-deficient mutant mice, Infect Immun, issue.11, pp.65-4843, 1997.
, Interleukin-10-deficient mice develop chronic enterocolitis, Cell, vol.75, issue.2, pp.263-74, 1993.
DOI : 10.1016/0092-8674(93)80068-P
, Muc2-Deficient Mice Spontaneously Develop Colitis, Indicating That MUC2 Is Critical for Colonic Protection, Gastroenterology, vol.131, issue.1, pp.117-146, 2006.
DOI : 10.1053/j.gastro.2006.04.020
, A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice, Gastroenterology, vol.98, issue.3, pp.98-694, 1990.
DOI : 10.1016/0016-5085(90)90290-H
, Bacteria Penetrate the Inner Mucus Layer before Inflammation in the Dextran Sulfate Colitis Model, PLoS ONE, vol.74, issue.8, p.12238, 2011.
DOI : 10.1371/journal.pone.0012238.s001
, Dysplasia and cancer in the dextran sulfate sodium mouse colitis model. Relevance to colitis-associated neoplasia in the human: a study of histopathology, B-catenin and p53 expression and the role of inflammation, Carcinogenesis, vol.21, issue.4, pp.757-68, 2000.
DOI : 10.1093/carcin/21.4.757
, Crohn's disease-associated Escherichia coli LF82 aggravates colitis in injured mouse colon via signaling by flagellin, Inflamm Bowel Dis, issue.8, pp.14-1051, 2008.
, Critical appraisal of the current practice in murine TNBS-induced colitis, Inflammatory Bowel Diseases, vol.12, issue.10, pp.12-995, 2006.
DOI : 10.1097/01.mib.0000227817.54969.5e
, Utility of the Citrobacter rodentium infection model in laboratory mice, Current Opinion in Gastroenterology, vol.24, issue.1, pp.32-39, 2008.
DOI : 10.1097/MOG.0b013e3282f2b0fb
, A mouse model for S. typhimurium-induced enterocolitis, Trends in Microbiology, vol.13, issue.10, pp.497-503, 2005.
DOI : 10.1016/j.tim.2005.08.008
, Helicobacter hepaticus infection in mice: models for understanding lower bowel inflammation and cancer, Mucosal Immunology, vol.67, issue.1, pp.22-30, 2011.
DOI : 10.1128/IAI.01091-06
, Mouse models of inflammatory bowel disease???, Advanced Drug Delivery Reviews, vol.59, issue.11, pp.1073-83, 2007.
DOI : 10.1016/j.addr.2007.07.003
, Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes, BMC Genomics, vol.11, issue.1, p.667, 2010.
DOI : 10.1186/1471-2164-11-667
, Adherent-invasive E. coli in Crohn disease: bacterial ???agent provocateur???, Journal of Clinical Investigation, vol.121, issue.3, pp.841-845, 2011.
DOI : 10.1172/JCI46333
, Shifting the balance: antibiotic effects on hostmicrobiota mutualism, Nat Rev Microbiol, issue.94, pp.233-276, 2011.
, Antibiotic administration alters the community structure of the gastrointestinal microbiota, Gut Microbes, vol.124, issue.4, pp.279-284, 2010.
DOI : 10.1128/AEM.00062-07
, Current Concepts of the Intestinal Microbiota and the Pathogenesis of Infection, Current Infectious Disease Reports, vol.25, issue.15, pp.28-34, 2011.
DOI : 10.1007/s11908-010-0147-7
, Antibiotic administration alters the community structure of the gastrointestinal microbiota, Gut Microbes, vol.124, issue.4, pp.279-284, 2011.
DOI : 10.1128/AEM.00062-07
, CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease, Journal of Clinical Investigation, vol.117, issue.6, pp.1566-74, 2007.
DOI : 10.1172/JCI30504
, Intestinal permeability and the prediction of relapse in Crohn's disease, Lancet, issue.8858, pp.341-1437, 1993.
, Increased uptake of non-pathogenicE. coli via the follicle-associated epithelium in longstanding ileal Crohn's disease, The Journal of Pathology, vol.117, issue.2, pp.135-179, 2008.
DOI : 10.1002/path.2337
, Antimicrobial peptide response to blood translocation of bacterial DNA in Crohn's disease is affected by NOD2/CARD15 genotype, Inflamm Bowel Dis, 2010.
, Induction and rescue of Nod2-dependent Th1-driven granulomatous inflammation of the ileum, Proceedings of the National Academy of Sciences, vol.107, issue.33, pp.14739-14783
DOI : 10.1073/pnas.1003363107
, Antibiotic overuse: Stop the killing of beneficial bacteria, Nature, vol.107, issue.7361, pp.476-393, 2011.
DOI : 10.1038/476393a
, Base Columbia (Bio-mérieux) 42, p.8