G. Kaplan, The global burden of IBD: from 2015 to 2025, Nature Reviews Gastroenterology & Hepatology, vol.19, issue.12, pp.720-727, 2015.
DOI : 10.1007/s10198-014-0595-3

A. Barrie and M. Regueiro, Biologic therapy in the management of extraintestinal manifestations of inflammatory bowel disease, Inflammatory Bowel Diseases, vol.13, issue.11, pp.1424-1429, 2007.
DOI : 10.1002/ibd.20196

S. Ardizzone, P. Puttini, A. Cassinotti, and G. Porro, Extraintestinal manifestations of inflammatory bowel disease. Digestive and Liver Disease, pp.253-259, 2008.

F. Veloso, Extraintestinal manifestations of inflammatory bowel disease: Do they influence treatment and outcome?, World Journal of Gastroenterology, vol.17, issue.22, pp.2702-2707, 2011.
DOI : 10.3748/wjg.v17.i22.2702

S. Vavricka, L. Brun, P. Ballabeni, V. Pittet, P. Vavricka et al., Frequency and Risk Factors for Extraintestinal Manifestations in the Swiss Inflammatory Bowel Disease Cohort, The American Journal of Gastroenterology, vol.107, issue.1, pp.110-119, 2010.
DOI : 10.1016/j.crohns.2007.10.006

I. Vind, L. Riis, J. T. Knudsen, E. Pedersen, N. Elkjaer et al., Increasing Incidences of Inflammatory Bowel Disease and Decreasing Surgery Rates in Copenhagen City and County, 2003-2005: A Population-Based Study from the Danish Crohn Colitis Database, The American Journal of Gastroenterology, vol.128, issue.6, pp.1274-1282, 2003.
DOI : 10.1053/j.gastro.2005.03.003

U. Monsén, J. Sorstad, G. Hellers, and C. Johansson, Extracolonic diagnoses in ulcerative colitis: an epidemiological study, Am J Gastroenterol, vol.85, pp.711-716, 1990.

R. Peluso, F. Manguso, M. Vitiello, S. Iervolino, D. Minno et al., Management of arthropathy in inflammatory bowel diseases. Therapeutic Advances in Chronic Disease, pp.65-77, 2015.

R. Peluso, D. Minno, M. Iervolino, S. Manguso, F. Tramontano et al., Enteropathic Spondyloarthritis: From Diagnosis to Treatment, Clinical and Developmental Immunology, vol.97, issue.1, pp.1-12, 2013.
DOI : 10.1016/j.amjmed.2012.03.015

URL : http://doi.org/10.1155/2013/631408

T. Orchard, B. Wordsworth, and D. Jewell, Peripheral arthropathies in inflammatory bowel disease: their articular distribution and natural history, Gut, vol.42, issue.3, pp.387-391, 1998.
DOI : 10.1136/gut.42.3.387

C. Petersen and J. Round, Defining dysbiosis and its influence on host immunity and disease, Cellular Microbiology, vol.27, issue.Suppl. 1, pp.1024-1033, 2014.
DOI : 10.1016/j.bpg.2013.03.003

URL : http://onlinelibrary.wiley.com/doi/10.1111/cmi.12308/pdf

T. Gill, M. Asquith, J. Rosenbaum, and R. Colbert, The intestinal microbiome in spondyloarthritis, Current Opinion in Rheumatology, vol.27, issue.4, pp.319-325, 2015.
DOI : 10.1097/BOR.0000000000000187

N. Nagalingam, J. Kao, and V. Young, Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis, Inflammatory Bowel Diseases, vol.17, issue.4, pp.917-926, 2011.
DOI : 10.1002/ibd.21462

B. Zheng, J. Van-bergenhenegouwen, S. Overbeek, H. Van-de-kant, J. Garssen et al., Bifidobacterium breve Attenuates Murine Dextran Sodium Sulfate-Induced Colitis and Increases Regulatory T Cell Responses, PLoS ONE, vol.1207, issue.5, pp.95441-24787575, 2014.
DOI : 10.1371/journal.pone.0095441.s003

URL : https://doi.org/10.1371/journal.pone.0095441

M. Asquith, P. Stauffer, S. Davin, C. Mitchell, L. Mdphd et al., Perturbed Mucosal Immunity and Dysbiosis Accompany Clinical Disease in a Rat Model of Spondyloarthritis, Arthritis & Rheumatology, vol.8, issue.1, p.26992013, 2016.
DOI : 10.1371/journal.pone.0076520

I. Doro?y?ska, M. Majewska-szczepanik, K. Marci?ska, and M. Szczepanik, Partial depletion of natural gut flora by antibiotic aggravates collagen induced arthritis (CIA) in mice, Pharmacological Reports, vol.66, issue.2, pp.250-255, 2014.
DOI : 10.1016/j.pharep.2013.09.007

H. Sokol, V. Leducq, H. Aschard, H. Pham, S. Jegou et al., Fungal microbiota dysbiosis in IBD, Gut, vol.6, issue.6, pp.2015-310746, 2016.
DOI : 10.1136/gutjnl-2015-310746

URL : https://hal.archives-ouvertes.fr/hal-01270909

B. Lamas, M. Richard, V. Leducq, H. Pham, M. Michel et al., CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands, Nature Medicine, vol.3, issue.6, pp.598-605
DOI : 10.1373/clinchem.2004.037465

URL : https://hal.archives-ouvertes.fr/hal-01314089

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

D. Mcdonald, M. Price, J. Goodrich, E. Nawrocki, T. Desantis et al., An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, The ISME Journal, vol.180, issue.3, pp.610-618, 2012.
DOI : 10.1038/nature08656

N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky et al., Metagenomic biomarker discovery and explanation, Genome Biology, vol.12, issue.6, p.21702898, 2011.
DOI : 10.1101/gr.112730.110

URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2011-12-6-r60?site=genomebiology.biomedcentral.com

S. Vavricka, A. Schoepfer, M. Scharl, P. Lakatos, A. Navarini et al., Extraintestinal Manifestations of Inflammatory Bowel Disease, Inflammatory Bowel Diseases, vol.21, issue.8, pp.1982-1992, 2015.
DOI : 10.1097/MIB.0000000000000392

P. Gionchetti, C. Calabrese, and F. Rizzello, Inflammatory Bowel Diseases and Spondyloarthropathies, The Journal of Rheumatology Supplement, vol.93, issue.0, pp.21-23, 2015.
DOI : 10.3899/jrheum.150628

B. Schroeder and F. Bäckhed, Signals from the gut microbiota to distant organs in physiology and disease, Nature Medicine, vol.22, issue.10, pp.1079-1089, 2016.
DOI : 10.1038/nm.4185

I. Koboziev, R. Webb, C. Furr, K. Grisham, and M. , Role of the enteric microbiota in intestinal homeostasis and inflammation, Free Radical Biology and Medicine, vol.68, pp.122-133, 2014.
DOI : 10.1016/j.freeradbiomed.2013.11.008

P. Eckburg, E. Bik, C. Bernstein, E. Purdom, L. Dethlefsen et al., Diversity of the Human Intestinal Microbial Flora, Science, vol.308, issue.5728, pp.1635-1638, 2005.
DOI : 10.1126/science.1110591

Y. Yeom, B. Kim, S. Kim, and Y. Kim, Sasa quelpaertensis leaf extract regulates microbial dysbiosis by modulating the composition and diversity of the microbiota in dextran sulfate sodium-induced colitis mice, BMC Complementary and Alternative Medicine, vol.126, issue.1, pp.481-27884149, 2016.
DOI : 10.1053/j.gastro.2004.03.024

P. Munyaka, M. Rabbi, E. Khafipour, and J. Ghia, Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice, Journal of Basic Microbiology, vol.39, issue.9, pp.986-998, 2016.
DOI : 10.1136/gut.39.2.234

H. Sokol, P. Seksik, J. Furet, O. Firmesse, I. Nion-larmurier et al., Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflammatory Bowel Diseases, vol.15, issue.8, pp.1183-1189, 2009.
DOI : 10.1002/ibd.20903

URL : https://hal.archives-ouvertes.fr/hal-00657435

X. Morgan, T. Tickle, H. Sokol, D. Gevers, K. Devaney et al., Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biology, vol.13, issue.9, p.23013615, 2012.
DOI : 10.1186/gb-2011-12-6-r60

URL : https://hal.archives-ouvertes.fr/hal-00736429

H. Sokol, B. Pigneur, L. Watterlot, O. Lakhdari, L. Bermúdez-humarán et al., Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients, Proceedings of the National Academy of Sciences, vol.41, issue.4, pp.16731-16736, 2008.
DOI : 10.1136/gut.41.4.487

URL : https://hal.archives-ouvertes.fr/hal-00652961

A. Darfeuille-michaud, J. Boudeau, P. Bulois, C. Neut, A. Glasser et al., High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn???s disease, Gastroenterology, vol.127, issue.2, pp.412-421, 2004.
DOI : 10.1053/j.gastro.2004.04.061

J. Scher, D. Littman, and S. Abramson, Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases, Arthritis & Rheumatology, vol.132, issue.Suppl 1, pp.35-45, 2015.
DOI : 10.1053/j.gastro.2006.11.022

S. Stebbings, K. Munro, M. Simon, G. Tannock, J. Highton et al., Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis, Rheumatology, vol.41, issue.12, pp.1395-1401, 2002.
DOI : 10.1093/rheumatology/41.12.1395

M. Costello, F. Ciccia, D. Willner, N. Warrington, P. Robinson et al., Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis, Arthritis & Rheumatology, vol.8, issue.3, pp.686-691, 2014.
DOI : 10.2217/ijr.12.84

E. Vieira-sousa, L. Van-duivenvoorde, J. Fonseca, R. Lories, and D. Baeten, Review: Animal Models as a Tool to Dissect Pivotal Pathways Driving Spondyloarthritis, Arthritis & Rheumatology, vol.54, issue.Suppl, pp.2813-2827, 2015.
DOI : 10.1002/art.21897

S. Brusca, S. Abramson, and J. Scher, Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity, Current Opinion in Rheumatology, vol.26, issue.1, pp.101-107, 2014.
DOI : 10.1097/BOR.0000000000000008

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011633/pdf

L. Chen, Y. Zou, J. Peng, F. Lu, Y. Yin et al., Lactobacillus acidophilus suppresses colitis-associated activation of the IL-23/Th17 axis, Journal of Immunology Research, vol.2015, pp.909514-909524, 2015.

D. Ahl, H. Liu, O. Schreiber, S. Roos, M. Phillipson et al., increases mucus thickness and ameliorates dextran sulphate sodium-induced colitis in mice, Acta Physiologica, vol.121, issue.4, pp.300-310, 2016.
DOI : 10.1172/JCI44031

Y. Belkaid and T. Hand, Role of the Microbiota in Immunity and Inflammation. Cell, pp.121-141, 2014.