, Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest

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H. M. Blottiè-re, B. Buecher, J. Galmiche, and C. Cherbut, Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation, Proc Nutr Soc, vol.62, pp.101-106, 2003.

P. M. Smith, M. R. Howitt, N. Panikov, M. Michaud, C. A. Gallini et al., The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science, vol.341, pp.569-573, 2013.

J. Qin, R. Li, J. Raes, M. Arumugam, K. S. Burgdorf et al., A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010.
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J. Li, H. Jia, X. Cai, H. Zhong, Q. Feng et al., An integrated catalog of reference genes in the human gut microbiome, Nat Biotechnol, vol.32, pp.834-841, 2014.
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, The second catalog of human gut microbial genes derived from metagenomic sequencing of feces from 1267 individuals from three continents and composed of 10 million non-redundant genes

P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen et al., Diversity of the human intestinal microbial flora, Science, vol.308, pp.1635-1638, 2005.

A. Suau, R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson et al., Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut, Appl Environ Microbiol, vol.65, pp.4799-4807, 1999.

R. E. Ley, M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey et al., Evolution of mammals and their gut microbes, Science, vol.320, pp.1647-1651, 2008.

J. Tap, S. Mondot, F. Levenez, E. Pelletier, C. Caron et al., Towards the human intestinal microbiota phylogenetic core, Environ Microbiol, vol.11, pp.2574-2584, 2009.

P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan et al., A core gut microbiome in obese and lean twins, Nature, vol.457, pp.480-484, 2009.

L. A. Omoniyi, K. A. Jewell, O. A. Isah, A. P. Neumann, C. Onwuka et al., An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass-and treebased diets, J Appl Microbiol, vol.116, pp.1094-1105, 2014.

G. D. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y. Chen et al., Linking longterm dietary patterns with gut microbial enterotypes, Science, vol.334, pp.105-108, 2011.

L. A. David, C. F. Maurice, R. N. Carmody, D. B. Gootenberg, J. E. Button et al., Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.505, pp.559-563, 2014.

, A 16S ribosomal RNA-based metagenomic study showing that a shortterm diet of animal or plant products impacts on microbial community structure and functions

S. F. Clarke, E. F. Murphy, O. O'sullivan, A. J. Lucey, M. Humphreys et al., Exercise and associated dietary extremes impact on gut microbial diversity, Gut, vol.63, pp.1913-1920, 2014.

M. Arumugam, J. Raes, E. Pelletier, L. Paslier, D. Yamada et al., Enterotypes of the human gut microbiome, Nature, vol.473, pp.174-180, 2011.
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, An initially controversial whole metagenomic sequencing study showing a stratification of human fecal microbiome in at least three clusters named enterotypes

J. H. Bond, R. R. Engel, and M. D. Levitt, Factors influencing pulmonary methane excretion in man. An indirect method of studying the in situ metabolism of the methane-producing colonic bacteria, J Exp Med, vol.133, pp.572-588, 1971.

M. D. Levitt, J. K. Furne, M. Kuskowski, and J. Ruddy, Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements, Clin Gastroenterol Hepatol, vol.4, pp.123-129, 2006.

J. L. Round and S. K. Mazmanian, Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota, Proc Natl Acad Sci, vol.107, pp.12204-12209, 2010.

E. Lé-cuyer, S. Rakotobe, H. Lengliné--garnier, C. Lebreton, M. Picard et al., Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses, Immunity, vol.40, pp.608-620, 2014.

, A study in mice showing SFB ability to induce and stimulate intestinal lymphoid tissues that cooperate to generate potent IgA and Th17

T. Pelaseyed, J. H. Bergströ-m, J. K. Gustafsson, A. Ermund, G. M. Birchenough et al., The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system, Immunol Rev, vol.260, pp.8-20, 2014.

J. L. Mcauley, S. K. Linden, C. W. Png, R. M. King, H. L. Pennington et al., MUC1 cell surface mucin is a critical element of the mucosal barrier to infection, J Clin Invest, vol.117, pp.2313-2324, 2007.

H. E. Jakobsson, A. M. Rodríguez-piñ-eiro, A. Schü-tte, A. Ermund, P. Boysen et al., The composition of the gut microbiota shapes the colon mucus barrier, EMBO Rep, vol.16, pp.164-177, 2015.

, A comparison of two mice colonies maintained in separate rooms and displaying different colonic mucus properties that were attributed to differences in their microbiome

G. Sellge and T. A. Kufer, PRR-signaling pathways -learning from microbial tactics, Semin Immunol, vol.27, pp.75-84, 2015.

D. Corridoni, K. O. Arseneau, M. G. Cifone, and F. Cominelli, The dual role of nod-like receptors in mucosal innate immunity and chronic intestinal inflammation, Front Immunol, vol.5, p.317, 2014.

M. Chieppa, M. Rescigno, A. Huang, and R. N. Germain, Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement, J Exp Med, vol.203, pp.2841-2852, 2006.

M. Rescigno, Intestinal microbiota and its effects on the immune system, Cell Microbiol, vol.16, pp.1004-1013, 2014.

J. L. Coombes, K. Siddiqui, C. V. Arancibia-cá-rcamo, J. Hall, C. Sun et al., A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-b-and retinoic acid-dependent mechanism, J Exp Med, vol.204, pp.1757-1764, 2007.

J. A. Hall, J. L. Cannons, J. R. Grainger, D. Santos, L. M. Hand et al., Essential role for retinoic acid in the promotion of CD4(+) T cell effector responses via retinoic acid receptor alpha, Immunity, vol.34, pp.435-447, 2011.

E. A. Kiss and C. Vonarbourg, Aryl hydrocarbon receptor: a molecular link between postnatal lymphoid follicle formation and diet, Gut Microbes, vol.3, pp.577-582, 2012.

T. Zelante, R. G. Iannitti, C. Cunha, D. Luca, A. Giovannini et al., Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22, Immunity, vol.39, pp.372-385, 2013.

, An elegant study showing that tryptophan metabolites impact on mucosal immunity through aryl-receptor dependent IL-22 production

L. Romani, T. Zelante, D. Luca, A. Iannitti, R. G. Moretti et al., Microbiota control of a tryptophan-AhR pathway in disease tolerance to fungi, Eur J Immunol, vol.44, pp.3192-3200, 2014.

S. Fukumoto, T. Toshimitsu, S. Matsuoka, A. Maruyama, K. Oh-oka et al., Identification of a probiotic bacteria-derived activator of the aryl hydrocarbon receptor that inhibits colitis, Immunol Cell Biol, vol.92, pp.460-465, 2014.

I. Monteleone, A. Rizzo, M. Sarra, G. Sica, P. Sileri et al., Aryl hydrocarbon receptor-induced signals up-regulate IL-22 production and inhibit inflammation in the gastrointestinal tract, Gastroenterology, vol.141, pp.237-248, 2011.

T. Takamura, D. Harama, S. Matsuoka, N. Shimokawa, Y. Nakamura et al., Activation of the aryl hydrocarbon receptor pathway may ameliorate dextran sodium sulfate-induced colitis in mice, Immunol Cell Biol, vol.88, pp.685-689, 2010.

Z. Wang, E. Klipfell, B. J. Bennett, R. Koeth, B. S. Levison et al., Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, vol.472, pp.57-63, 2011.

K. A. Romano, E. I. Vivas, D. Amador-noguez, and F. E. Rey, Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide, vol.6, p.2481, 2015.

H. Tilg and A. R. Moschen, Food, immunity, and the microbiome, Gastroenterology, vol.148, pp.1107-1119, 2015.

H. Sokol, P. Seksik, J. P. Furet, O. Firmesse, I. Nion-larmurier et al., Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflamm Bowel Dis, vol.15, pp.1183-1189, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00657435

S. Miquel, M. Leclerc, R. Martin, F. Chain, M. Lenoir et al., Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii, vol.6, pp.300-315, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01226343