K. Honda and D. Littman, The Microbiome in Infectious Disease and Inflammation, Annual Review of Immunology, vol.30, issue.1, pp.759-795, 2012.
DOI : 10.1146/annurev-immunol-020711-074937

H. Sokol, B. Pigneur, L. Watterlot, O. Lakhdari, and L. Bermudez-humaran, 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.105, issue.43, pp.16731-16736, 2008.
DOI : 10.1073/pnas.0804812105
URL : https://hal.archives-ouvertes.fr/hal-00652961

B. Willing, J. Halfvarson, J. Dicksved, M. Rosenquist, and G. Jarnerot, Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn??s disease, Inflammatory Bowel Diseases, vol.15, issue.5, pp.653-660, 2009.
DOI : 10.1002/ibd.20783

C. Manichanh, N. Borruel, F. Casellas, and F. Guarner, The gut microbiota in IBD, Nature Reviews Gastroenterology & Hepatology, vol.252, issue.10, pp.599-608, 2012.
DOI : 10.1038/nrgastro.2012.152

Y. Nagano, K. Itoh, and K. Honda, The induction of Treg cells by gut-indigenous Clostridium, Current Opinion in Immunology, vol.24, issue.4, pp.392-397, 2012.
DOI : 10.1016/j.coi.2012.05.007

S. Sakaguchi, T. Yamaguchi, T. Nomura, and M. Ono, Regulatory T Cells and Immune Tolerance, Cell, vol.133, issue.5, pp.775-787, 2008.
DOI : 10.1016/j.cell.2008.05.009

S. Josefowicz, L. Lu, and A. Rudensky, Regulatory T Cells: Mechanisms of Differentiation and Function, Annual Review of Immunology, vol.30, issue.1, pp.531-564, 2012.
DOI : 10.1146/annurev.immunol.25.022106.141623

A. Bilate and J. Lafaille, Regulatory T Cells in Immune Tolerance, Annual Review of Immunology, vol.30, issue.1, pp.733-758, 2012.
DOI : 10.1146/annurev-immunol-020711-075043

K. Atarashi, T. Tanoue, T. Shima, A. Imaoka, and T. Kuwahara, Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species, Science, vol.331, issue.6015, pp.337-341, 2011.
DOI : 10.1126/science.1198469

S. Lathrop, S. Bloom, S. Rao, K. Nutsch, and C. Lio, Peripheral education of the immune system by colonic commensal microbiota, Nature, vol.3, issue.7368, pp.250-254, 2011.
DOI : 10.1038/nature10434

T. Tanoue and K. Honda, Induction of Treg cells in the mouse colonic mucosa: A central mechanism to maintain host???microbiota homeostasis, Seminars in Immunology, vol.24, issue.1, pp.50-57, 2012.
DOI : 10.1016/j.smim.2011.11.009

J. Buckner, Mechanisms of impaired regulation by CD4+CD25+FOXP3+ regulatory T cells in human autoimmune diseases, Nature Reviews Immunology, vol.3, issue.12, pp.849-859, 2010.
DOI : 10.1038/nri2889

M. Roncarolo, S. Gregori, M. Battaglia, R. Bacchetta, and K. Fleischhauer, Interleukin???10???secreting type 1 regulatory T cells in rodents and humans, Immunological Reviews, vol.169, issue.1, pp.28-50, 2006.
DOI : 10.1067/mai.2003.1570

K. Fujio, T. Okamura, and K. Yamamoto, The Family of IL-10-Secreting CD4+ T Cells, Adv Immunol, vol.105, pp.99-130, 2010.
DOI : 10.1016/S0065-2776(10)05004-2

G. Das, M. Augustine, J. Das, K. Bottomly, and P. Ray, An important regulatory role for CD4+CD8???? T cells in the intestinal epithelial layer in the prevention of inflammatory bowel disease, Proceedings of the National Academy of Sciences, vol.100, issue.9, pp.5324-5329, 2003.
DOI : 10.1073/pnas.0831037100

C. Maynard, L. Harrington, K. Janowski, J. Oliver, and C. Zindl, Regulatory T cells expressing interleukin 10 develop from Foxp3+ and Foxp3??? precursor cells in the absence of interleukin 10, Nature Immunology, vol.171, issue.9, pp.931-941, 2007.
DOI : 10.1016/j.immuni.2006.09.013

A. Franke, T. Balschun, C. Sina, D. Ellinghaus, and R. Hasler, Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL), Nature Genetics, vol.74, issue.4, pp.292-294, 2010.
DOI : 10.1038/ng.553

E. Glocker, D. Kotlarz, K. Boztug, E. Gertz, and A. Schaffer, Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor, New England Journal of Medicine, vol.361, issue.21, pp.2033-2045, 2009.
DOI : 10.1056/NEJMoa0907206

Y. Parel and C. Chizzolini, CD4+ CD8+ double positive (DP) T cells in health and disease, Autoimmunity Reviews, vol.3, issue.3, pp.215-220, 2004.
DOI : 10.1016/j.autrev.2003.09.001

M. Suni, S. Ghanekar, D. Houck, H. Maecker, and S. Wormsley, CD4+CD8dim T lymphocytes exhibit enhanced cytokine expression, proliferation and cytotoxic activity in response to HCMV and HIV-1 antigens, European Journal of Immunology, vol.180, issue.8, pp.2512-2520, 2001.
DOI : 10.1002/1521-4141(200108)31:8<2512::AID-IMMU2512>3.0.CO;2-M

M. Senju, K. Wu, Y. Mahida, and D. Jewell, Coexpression of CD4 and CD8 on peripheral blood T cells and lamina propria T cells in inflammatory bowel disease by two colour immunofluorescence and flow cytometric analysis., Gut, vol.32, issue.8, pp.918-922, 1991.
DOI : 10.1136/gut.32.8.918

J. Carton, B. Byrne, L. Madrigal-estebas, O. Donoghue, D. et al., CD4+CD8+ human small intestinal T cells are decreased in coeliac patients, with CD8 expression downregulated on intra-epithelial T cells in the active disease, European Journal of Gastroenterology & Hepatology, vol.16, issue.10, pp.961-968, 2004.
DOI : 10.1097/00042737-200410000-00003

G. Sarrabayrouse, M. Corvaisier, L. Ouisse, C. Bossard, L. Mevel et al., Tumor-reactive CD4+CD8????+ CD103+ ????T cells: A prevalent tumor-reactive T-cell subset in metastatic colorectal cancers, International Journal of Cancer, vol.4, issue.suppl 1, pp.2923-2932, 2011.
DOI : 10.1002/ijc.25640

T. Yamaguchi, J. Wing, and S. Sakaguchi, Two modes of immune suppression by Foxp3+ regulatory T cells under inflammatory or non-inflammatory conditions, Seminars in Immunology, vol.23, issue.6, pp.424-430, 2011.
DOI : 10.1016/j.smim.2011.10.002

S. Miquel, R. Martin, O. Rossi, L. Bermudez-humaran, and J. Chatel, Faecalibacterium prausnitzii and human intestinal health, Current Opinion in Microbiology, vol.16, issue.3, pp.255-261, 2013.
DOI : 10.1016/j.mib.2013.06.003
URL : https://hal.archives-ouvertes.fr/hal-00842645

K. Atarashi, T. Tanoue, K. Oshima, W. Suda, and Y. Nagano, Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature, vol.158, issue.7461, pp.232-236, 2013.
DOI : 10.1038/nature12331

C. Lambert, M. Ibrahim, C. Iobagiu, and C. Genin, Erratum Significance of Unconventional Peripheral CD4+CD8dim T Cell Subsets, Journal of Clinical Immunology, vol.26, issue.3, pp.418-427, 2005.
DOI : 10.1007/s10875-006-9015-5

H. Sokol, P. Seksik, J. Furet, O. Firmesse, and I. Nion-larmurier, 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

K. Machiels, M. Joossens, J. Sabino, D. Preter, V. Arijs et al., A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis, Gut, 2013.

D. Mucida, M. Husain, S. Muroi, F. Van-wijk, and R. Shinnakasu, Transcriptional reprogramming of mature CD4+ helper T cells generates distinct MHC class II???restricted cytotoxic T lymphocytes, Nature Immunology, vol.158, issue.3, pp.281-289, 2013.
DOI : 10.1016/S0022-1759(03)00265-5

B. Reis, A. Rogoz, F. Costa-pinto, I. Taniuchi, and D. Mucida, Mutual expression of the transcription factors Runx3 and ThPOK regulates intestinal CD4+ T cell immunity, Nature Immunology, vol.175, issue.3, pp.271-280, 2013.
DOI : 10.1016/j.immuni.2008.05.010

W. Chen, F. Liu, Z. Ling, X. Tong, and C. Xiang, Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer, PLoS ONE, vol.682, issue.6, p.39743, 2012.
DOI : 10.1371/journal.pone.0039743.s004

S. Josefowicz, R. Niec, H. Kim, P. Treuting, and T. Chinen, Extrathymically generated regulatory T cells control mucosal TH2 inflammation, Nature, vol.11, issue.7385, pp.395-399, 2012.
DOI : 10.1038/nature10772

M. Koch, G. Tucker-heard, N. Perdue, J. Killebrew, and K. Urdahl, The transcription factor T-bet controls regulatory T cell homeostasis and function during type 1 inflammation, Nature Immunology, vol.446, issue.6, pp.595-602, 2009.
DOI : 10.1038/ni.1731

D. Campbell and M. Koch, Phenotypical and functional specialization of FOXP3+ regulatory T cells, Nature Reviews Immunology, vol.177, issue.2, pp.119-130, 2011.
DOI : 10.1038/nri2916

T. Duhen, R. Duhen, A. Lanzavecchia, F. Sallusto, and D. Campbell, Functionally distinct subsets of human FOXP3+ Treg cells that phenotypically mirror effector Th cells, Blood, vol.119, issue.19, pp.4430-4440, 2012.
DOI : 10.1182/blood-2011-11-392324

J. Zhao, C. Fett, K. Trandem, E. Fleming, and S. Perlman, T reg cells in the central nervous system during encephalomyelitis, The Journal of Experimental Medicine, vol.119, issue.8, pp.1571-1577, 2011.
DOI : 10.4049/jimmunol.0902164

C. Koenecke, C. Lee, K. Thamm, L. Fohse, and M. Schafferus, IFN-?? Production by Allogeneic Foxp3+ Regulatory T Cells Is Essential for Preventing Experimental Graft-versus-Host Disease, The Journal of Immunology, vol.189, issue.6, pp.2890-2896, 2012.
DOI : 10.4049/jimmunol.1200413

N. Gagliani, C. Magnani, S. Huber, M. Gianolini, and M. Pala, Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells, Nature Medicine, vol.184, issue.6, pp.739-746, 2013.
DOI : 10.1038/nm.3179

J. Fonteneau, L. Drean, E. , L. Guiner, S. Gervois et al., Heterogeneity of biologic responses of melanoma-specific CTL, J Immunol, vol.159, pp.2831-2839, 1997.