I. Sekirov, S. L. Russell, L. C. Antunes, and B. B. Finlay, Gut Microbiota in Health and Disease, Physiol. Rev, vol.90, pp.859-904, 2010.

N. Cerf-bensussan and V. Gaboriau-routhiau, The immune system and the gut microbiota: friends or foes?, Nat. Rev. Immunol, vol.10, pp.735-779, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01204303

J. H. Cummings, Microbial Digestion of Complex Carbohydrates in Man, Proc. Nutr. Soc, vol.43, pp.35-44, 1984.

M. J. Albert, V. I. Mathan, and S. J. Baker, Vitamin B12 synthesis by human small intestinal bacteria, Nature, vol.283, pp.781-782, 1980.

F. Bäckhed, The gut microbiota as an environmental factor that regulates fat storage, Proc. Natl. Acad. Sci. USA, vol.101, pp.15718-15741, 2004.

L. V. Hooper, T. Midtvedt, and J. I. Gordon, How host-microbial interactions shape the nutrient environment of the mammalian intestine, Annu. Rev. Nutr, vol.22, pp.283-307, 2002.

D. Kelly, M. I. Delday, and I. Mulder, Microbes and microbial effector molecules in treatment of inflammatory disorders, Immunol. Rev, vol.245, pp.27-44, 2012.

L. Chatelier and E. , Richness of human gut microbiome correlates with metabolic markers, Nature, vol.500, pp.541-547, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01190602

P. D. Cani, N. M. Delzenne, J. Amar, and R. Burcelin, Role of gut microflora in the development of obesity and insulin resistance following high-fat diet feeding, Pathol. Biol, vol.56, pp.305-314, 2008.
URL : https://hal.archives-ouvertes.fr/inserm-00408892

J. R. Brestoff and D. Artis, Commensal bacteria at the interface of host metabolism and the immune system, Nat. Immunol, vol.14, pp.676-84, 2013.

L. Kjer-nielsen, MR1 presents microbial vitamin B metabolites to MAIT cells, Nature, vol.491, pp.717-740, 2012.

S. I. Sayin, Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist, Cell Metab, vol.17, pp.225-260, 2013.

C. Dreyer, Control of the peroxisomal ? -oxidation pathway by a novel family of nuclear hormone receptors, Cell, vol.68, pp.879-87, 1992.

L. Fajas, The organization, promoter analysis, and expression of the human PPARgamma gene, J Biol Chem, vol.272, pp.18779-89, 1997.

L. Dubuquoy, PPARgamma as a new therapeutic target in inflammatory bowel diseases, Gut, vol.55, pp.1341-1350, 2006.

P. Sarraf, Loss-of-function mutations in PPAR gamma associated with human colon cancer, Mol. Cell, vol.3, pp.799-804, 1999.

D. Kelly, Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPARgamma and RelA, Nat. Immunol, vol.5, pp.104-116, 2004.

F. Backhed, J. K. Manchester, C. F. Semenkovich, and J. I. Gordon, Mechanisms underlying the resistance to diet-induced obesity in germ-free mice, Proc Natl Acad Sci, vol.104, pp.979-84, 2007.

K. Wada, A. Nakajima, and R. S. Blumberg, ? and inflammatory bowel disease: a new therapeutic PPAR? target for ulcerative colitis and Crohn's disease, vol.7, pp.329-360, 2001.

P. Sarraf, E. Mueller, and D. Jones, Differentiation and reversal of malignant changes in colon cancer through PPAR?, Nat. Med, vol.4, pp.1046-52, 1998.

M. L. Slattery, PPARgamma and colon and rectal cancer: associations with specific tumor mutations, aspirin, ibuprofen and insulin-related genes (United States), Cancer Causes Control, vol.17, pp.239-288, 2006.

S. I. Anghel and W. Wahli, Fat poetry: a kingdom for PPAR gamma, Cell Res, vol.17, pp.486-511, 2007.

O. Lakhdari, Identification of NF-? B Modulation Capabilities within Human Intestinal Commensal Bacteria, J. Biomed. Biotechnol, p.282356, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000996

M. Nepelska, Butyrate Produced by Commensal Bacteria Potentiates Phorbol Esters Induced AP-1 Response in Human Intestinal Epithelial Cells, PLoS One, vol.7, p.52869, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190699

A. Korecka, ANGPTL4 expression induced by butyrate and rosiglitazone in human intestinal epithelial cells utilizes independent pathways, Am. J. Physiol. Gastrointest. Liver Physiol, vol.304, pp.1025-1062, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01001518

D. R. Donohoe, The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon, Cell Metab, vol.13, pp.517-543, 2011.

A. and S. , Short chain fatty acids stimulate Angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating PPAR?, Mol. Cell. Biol, vol.33, pp.1303-1319, 2013.

A. Klinder, Fecal water as a non-invasive biomarker in nutritional intervention: comparison of preparation methods and refinement of different endpoints, Nutr. Cancer, vol.57, pp.158-67, 2007.

J. H. Cummings, E. W. Pomare, W. J. Branch, C. P. Naylor, and G. T. Macfarlane, Short chain fatty acids in human large intestine, portal, hepatic and venous blood, Gut, vol.28, pp.1221-1228, 1987.

F. Backhed, The gut microbiota as an environmental factor that regulates fat storage, Proc Natl Acad Sci, vol.101, pp.15718-15741, 2004.

A. Are, Enterococcus faecalis from newborn babies regulate endogenous PPARgamma activity and IL-10 levels in colonic epithelial cells, Proc. Natl. Acad. Sci. USA 105, pp.1943-1951, 2008.

K. A. Burns and J. P. Vanden-heuvel, Modulation of PPAR activity via phosphorylation, Biochim. Biophys. Acta, vol.1771, pp.952-60, 2007.

W. Jia, H. Li, L. Zhao, and J. K. Nicholson, Gut microbiota: a potential new territory for drug targeting, Nat Rev Drug Discov, vol.7, pp.123-132, 2008.

H. M. Blottière, W. M. De-vos, S. D. Ehrlich, and J. Doré, Human intestinal metagenomics: state of the art and future, Curr. Opin. Microbiol, vol.16, pp.232-241, 2013.

D. Shao and M. A. Lazar, Modulating nuclear receptor function: may the phos be with you, J. Clin. Invest, vol.103, pp.1617-1625, 1999.

S. Lalevée, C. Ferry, and C. Rochette-egly, Phosphorylation control of nuclear receptors, Methods Mol. Biol, vol.647, pp.251-66, 2010.

M. Adams, M. J. Reginato, D. Shao, M. A. Lazar, and V. K. Chatterjee, Transcriptional activation by peroxisome proliferator-activated receptor gamma is inhibited by phosphorylation at a consensus mitogen-activated protein kinase site, J. Biol. Chem, vol.272, pp.5128-5160, 1997.

B. Zhang, Insulin-and mitogen-activated protein kinase-mediated phosphorylation and activation of peroxisome proliferatoractivated receptor gamma, J. Biol. Chem, vol.271, pp.31771-31775, 1996.

, Scientific RepoRts |, vol.7, p.43199

C. J. Marshall, Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation, Cell, vol.80, pp.179-85, 1995.

J. Raingeaud, Pro-inflammatory cytokines and environmental stress cause p38 mitogen-activated protein kinase activation by dual phosphorylation on tyrosine and threonine, J. Biol. Chem, vol.270, pp.7420-7426, 1995.

L. Aronsson, Decreased fat storage by Lactobacillus paracasei is associated with increased levels of angiopoietin-like 4 protein (ANGPTL4), PLoS One, vol.5, 2010.

P. Desreumaux, Attenuation of colon inflammation through activators of the retinoid X receptor (RXR)/peroxisome proliferator-activated receptor gamma (PPARgamma) heterodimer. A basis for new therapeutic strategies, J. Exp. Med, vol.193, pp.827-865, 2001.

C. G. Su, A novel therapy for colitis utilizing PPAR-gamma ligands to inhibit the epithelial inflammatory response, J. Clin. Invest, vol.104, pp.383-392, 1999.

M. Adachi, Peroxisome proliferator activated receptor gamma in colonic epithelial cells protects against experimental inflammatory bowel disease, Gut, vol.55, pp.1104-1117, 2006.

V. Annese, F. Rogai, A. Settesoldi, and S. Bagnoli, PPAR? in Inflammatory Bowel Disease, PPAR Res, p.620839, 2012.

V. Andersen, Polymorphisms in NF-? B, PXR, LXR, PPAR? and risk of inflammatory bowel disease, World J. Gastroenterol, vol.17, pp.197-206, 2011.

J. U. Scher, Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis, vol.2, p.1202, 2013.

P. S. Kumar, New bacterial species associated with chronic periodontitis, J. Dent. Res, vol.82, pp.338-382, 2003.

T. Pédron, A Crypt-Specific Core Microbiota Resides in the Mouse Colon, vol.3, pp.116-128, 2012.

R. E. Hungate and . The-anaerobic, Growth (Lakeland), 1950.

B. Couvigny, Commensal Streptococcus salivarius Modulates PPAR? Transcriptional Activity in Human Intestinal Epithelial Cells, PLoS One, vol.10, p.125371, 2015.