H. R. Singh, Y. Gutierrez, A. N. Lu, F. Bahalim, L. M. Farzadfar et al., National, regional, and global trends in body-mass index since 1980: Systematic analysis of health examination surveys and epidemiological studies with 960 countryyears and 9.1 million participants, Lancet, vol.377, pp.557-567, 2011.

W. Van-treuren, R. Walters, C. B. Knight, A. C. Newgard, J. I. Heath et al., Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, vol.341, p.1241214, 2013.

J. E. Druesne, V. W. Van-hylckama-vlieg, A. K. Bloks, H. G. Groen, E. G. Heilig et al., Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome, Gastroenterology, vol.143, pp.913-919, 2012.

N. H. Cook, I. D. Hunt, A. J. Caterson, L. H. Holmes, and . Storlien, Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice, PLoS One, vol.7, p.34233, 2012.

A. W. Janssen and S. Kersten, The role of the gut microbiota in metabolic health, The FASEB Journal, vol.29, issue.8, pp.3111-3123, 2015.
DOI : 10.1096/fj.14-269514

F. Sommer and F. Bäckhed, The gut microbiota ? masters of host development and physiology, Nature Reviews Microbiology, vol.13, issue.4, pp.227-265, 2013.
DOI : 10.1038/nri3349

J. C. Clemente, L. K. Ursell, L. W. Parfrey, and R. Knight, The Impact of the Gut Microbiota on Human Health: An Integrative View, Cell, vol.148, issue.6, pp.1258-1270, 2012.
DOI : 10.1016/j.cell.2012.01.035

L. Biedermann and G. Rogler, The intestinal microbiota: its role in health and disease, European Journal of Pediatrics, vol.30, issue.2, pp.151-167, 2015.
DOI : 10.1097/MOG.0000000000000048

J. Tang, A. J. Didonato, S. L. Lusis, and . Hazen, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, vol.472, pp.57-63, 2011.

A. W. Janssen and S. Kersten, Potential mediators linking gut bacteria to metabolic health: a critical view, The Journal of Physiology, vol.157, issue.Suppl, pp.477-487, 2017.
DOI : 10.1016/j.vetmic.2011.10.024
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5233664

D. Schuppan and J. M. Schattenberg, Non-alcoholic steatohepatitis: Pathogenesis and novel therapeutic approaches, Journal of Gastroenterology and Hepatology, vol.32, issue.Suppl. 2, pp.68-76, 2013.
DOI : 10.1111/j.1478-3231.2011.02730.x

H. Tilg and A. R. Moschen, Evolution of inflammation in nonalcoholic fatty liver disease: The multiple parallel hits hypothesis, Hepatology, vol.11, issue.5, pp.1836-1846, 2010.
DOI : 10.1002/hep.23535

F. Nassir and J. Ibdah, Role of Mitochondria in Nonalcoholic Fatty Liver Disease, International Journal of Molecular Sciences, vol.13, issue.5, pp.8713-8742, 2014.
DOI : 10.1016/j.mito.2013.09.002

W. Jiang, N. Wu, X. Wang, Y. Chi, Y. Zhang et al., Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease, Scientific Reports, vol.92, issue.1, pp.1-7, 2015.
DOI : 10.1038/labinvest.2012.12

J. P. Mcgilvray and . Allard, Intestinal microbiota in patients with nonalcoholic fatty liver disease, Hepatology, vol.58, pp.120-127, 2013.

. Gonzalez, Intestinal farnesoid X receptor signaling promotes nonalcoholic fatty liver disease, J. Clin. Invest, vol.125, pp.386-402, 2015.

M. Hoffman and R. , Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity, Nature, vol.482, pp.179-85, 2012.

. Svegliati-baroni, Dysbiosis contributes to fibrogenesis in the course of chronic liver injury in mice, Hepatology, vol.59, pp.1738-1749, 2014.

K. Nomura and T. Yamanouchi, The role of fructose-enriched diets in mechanisms of nonalcoholic fatty liver disease, The Journal of Nutritional Biochemistry, vol.23, issue.3, pp.203-211, 2012.
DOI : 10.1016/j.jnutbio.2011.09.006

P. Song, Y. Zhang, and C. D. Klaassen, Dose-Response of Five Bile Acids on Serum and Liver Bile Acid Concentrations and Hepatotoxicty in Mice, Toxicological Sciences, vol.123, issue.2, pp.359-367, 2011.
DOI : 10.1093/toxsci/kfr177

S. Rakoff-nahoum, J. Paglino, F. Eslami-varzaneh, S. Edberg, and R. Medzhitov, Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis, Cell, vol.118, issue.2, pp.229-241, 2004.
DOI : 10.1016/j.cell.2004.07.002

A. Land, A. Hoek, and U. J. Tietge, Presence of bile acids in human follicular fluid and their relation with embryo development in modified natural cycle IVF, 2015.

Z. Wang, B. S. Levison, J. E. Hazen, L. Donahue, X. M. Li et al., Measurement of trimethylamine-N-oxide by stable isotope dilution liquid chromatography tandem mass spectrometry, Analytical Biochemistry, vol.455, pp.35-40, 2014.
DOI : 10.1016/j.ab.2014.03.016

L. Wu, J. D. Li, W. H. Smith, J. A. Tang, A. J. Didonato et al., 2014. ?-Butyrobetaine Is a Proatherogenic Intermediate in Gut Microbial Metabolism of L-Carnitine to TMAO, Cell Metab, vol.20, pp.799-812
URL : https://hal.archives-ouvertes.fr/hal-01491331

M. J. Govers, R. Van, and . Meet, Effects of dietary calcium and phosphate on the intestinal interactions between calcium, phosphate, fatty acids, and bile acids., Gut, vol.34, issue.3, pp.365-370, 1993.
DOI : 10.1136/gut.34.3.365

H. Van-meer, G. Boehm, F. Stellaard, A. Vriesema, J. Knol et al., Prebiotic oligosaccharides and the enterohepatic circulation of bile salts in rats, AJP: Gastrointestinal and Liver Physiology, vol.294, issue.2, pp.540-547, 2008.
DOI : 10.1152/ajpgi.00396.2007

B. M. Bolstad, R. A. Irizarry, M. , and T. P. Speed, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, vol.19, issue.2, pp.185-193, 2003.
DOI : 10.1093/bioinformatics/19.2.185

R. A. Irizarry, B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs et al., Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Research, vol.31, issue.4, p.15, 2003.
DOI : 10.1093/nar/gng015
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150247/pdf

T. P. Myers, H. Speed, S. J. Akil, F. Watson, and . Meng, Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data, Nucleic Acids Res, vol.33, pp.1-9, 2005.

M. A. Sartor, C. R. Tomlinson, S. C. Wesselkamper, S. Sivaganesan, G. D. Leikauf et al., Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments, BMC Bioinformatics, vol.7, issue.1, p.538, 2006.
DOI : 10.1186/1471-2105-7-538

J. D. Storey and R. Tibshirani, Statistical significance for genomewide studies, Proceedings of the National Academy of Sciences, vol.23, issue.1, pp.9440-9445, 2003.
DOI : 10.1002/gepi.1124
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC170937

I. S. Jamall, V. N. Finelli, and S. S. Hee, A simple method to determine nanogram levels of 4-hydroxyproline in biological tissues, Analytical Biochemistry, vol.112, issue.1, pp.70-75, 1981.
DOI : 10.1016/0003-2697(81)90261-X

J. Crandall, C. Hyams, R. Huttenhower, R. J. Knight, and . Xavier, The treatmentnaive microbiome in new-onset Crohn's disease, Cell Host Microbe, vol.15, pp.382-392, 2014.

J. Yatsunenko, R. Zaneveld, and . Knight, QIIME allows analysis of highthroughput community sequencing data, Nat. Methods, vol.7, pp.335-336, 2010.

. Huttenhower, Metagenomic biomarker discovery and explanation, Genome Biol, vol.12, p.60, 2011.

T. M. Pryce, S. Palladino, I. D. Kay, and G. W. Coombs, Rapid identification of fungi by sequencing the ITS1 and ITS2 regions using an automated capillary electrophoresis system, Medical Mycology, vol.41, issue.5, pp.369-381, 2003.
DOI : 10.1080/13693780310001600435

D. Haenen, C. Souza, J. Zhang, S. J. Koopmans, G. Bosch et al., Resistant Starch Induces Catabolic but Suppresses Immune and Cell Division Pathways and Changes the Microbiome in the Proximal Colon of Male Pigs, Journal of Nutrition, vol.143, issue.12, pp.1889-1898, 2013.
DOI : 10.3945/jn.113.182154

G. Masuoko and . Gores, Fast food diet mouse: novel small animal model of NASH with ballooning, progressive fibrosis, and high physiological fidelity to the human condition, AJP Gastrointest. Liver Physiol, vol.301, pp.825-834, 2011.

N. Kawanishi, H. Yano, T. Mizokami, M. Takahashi, E. Oyanagi et al., Exercise training attenuates hepatic inflammation, fibrosis and macrophage infiltration during diet induced-obesity in mice, Brain, Behavior, and Immunity, vol.26, issue.6, pp.931-972, 2012.
DOI : 10.1016/j.bbi.2012.04.006

C. Savard, E. Tartaglione, R. Kuver, W. G. Haigh, G. C. Farrell et al., Synergistic interaction of dietary cholesterol and dietary fat in inducing experimental steatohepatitis, Hepatology, vol.278, issue.1, pp.81-92, 2013.
DOI : 10.1074/jbc.M306022200

S. Bashiardes, H. Shapiro, S. Rozin, O. Shibolet, and E. Elinav, Non-alcoholic fatty liver and the gut microbiota, Molecular Metabolism, vol.5, issue.9, pp.782-794, 2016.
DOI : 10.1016/j.molmet.2016.06.003

L. Hazen, Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat. Med, vol.19, pp.576-85, 2013.

W. H. Tang, Z. Wang, D. J. Kennedy, Y. Wu, J. Buffa et al., Gut Microbiota-Dependent Trimethylamine N-Oxide (TMAO) Pathway Contributes to Both Development of Renal Insufficiency and Mortality Risk in Chronic Kidney Disease, Circulation Research, vol.116, issue.3, pp.448-455, 2015.
DOI : 10.1161/CIRCRESAHA.116.305360

E. Lau, D. Carvalho, and P. Freitas, Gut Microbiota: Association with NAFLD and Metabolic Disturbances, BioMed Research International, vol.119, issue.5, 2015.
DOI : 10.1053/gast.2000.19267
URL : http://doi.org/10.1155/2015/979515

G. J. Müller and . Hooiveld, Comparison of the effects of five dietary fibers on mucosal transcriptional profiles, and luminal microbiota composition and SCFA concentrations in murine colon, Mol. Nutr. Food Res, vol.59, pp.1590-1602, 2015.

M. Dumas, R. H. Barton, A. Toye, O. Cloarec, C. Blancher et al., Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice, Proc. Natl. Acad. Sci, 2006.
DOI : 10.1016/S0169-7439(98)00109-9

X. Gao, X. Liu, J. Xu, C. Xue, Y. Xue et al., Dietary trimethylamine N-oxide exacerbates impaired glucose tolerance in mice fed a high fat diet, Journal of Bioscience and Bioengineering, vol.118, issue.4, pp.476-481, 2014.
DOI : 10.1016/j.jbiosc.2014.03.001

. Anania, Loss of Junctional Adhesion Molecule A Promotes Severe Steatohepatitis in Mice on a Diet High in Saturated Fat, Fructose, and Cholesterol, Gastroenterology, vol.151, pp.733-746, 2016.

M. Mouzaki, A. Y. Wang, R. Bandsma, E. M. Comelli, B. M. Arendt et al., Bile Acids and Dysbiosis in Non-Alcoholic Fatty Liver Disease, PLOS ONE, vol.6, issue.8, p.151829, 2016.
DOI : 10.1371/journal.pone.0151829.s001

M. M. Aranha, H. Cortez-pinto, A. Costa, I. B. Da-silva, M. E. Camilo et al., Bile acid levels are increased in the liver of patients with steatohepatitis, European Journal of Gastroenterology & Hepatology, vol.20, issue.6, pp.519-525, 2008.
DOI : 10.1097/MEG.0b013e3282f4710a

P. Fickert, A. Fuchsbichler, H. Marschall, M. Wagner, G. Zollner et al., Lithocholic Acid Feeding Induces Segmental Bile Duct Obstruction and Destructive Cholangitis in Mice, The American Journal of Pathology, vol.168, issue.2, pp.410-422, 2006.
DOI : 10.2353/ajpath.2006.050404
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1606500

. Moshage, Metformin Protects Rat Hepatocytes against Bile Acid-Induced 39, 2013.

T. Sodeman, S. F. Bronk, P. J. Roberts, H. Miyoshi, and G. J. Gores, Bile salts mediate hepatocyte apoptosis by increasing cell surface trafficking of Fas, Am.J Physiol Gastrointest.Liver Physiol, vol.278, pp.992-999, 2000.

J. Gores, The Bile Acid Glycochenodeoxycholate Induces TRAIL-Receptor 2 / DR5 Expression and Apoptosis, J. Biol. Chem, vol.276, pp.38610-38618, 2001.

J. R. Swann, E. J. Want, F. M. Geier, K. Spagou, I. D. Wilson et al., Systemic gut microbial modulation of bile acid metabolism in host tissue compartments, Proceedings of the National Academy of Sciences, vol.30, issue.1, pp.4523-4553, 2011.
DOI : 10.1093/nar/30.1.207

S. I. Sayin, A. Wahlström, J. Felin, S. Jäntti, H. Marschall et al., Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist, Cell Metabolism, vol.17, issue.2, pp.225-235, 2013.
DOI : 10.1016/j.cmet.2013.01.003

Y. Zhang, P. B. Limaye, H. J. Renaud, and C. D. Klaassen, Effect of various antibiotics on modulation of intestinal microbiota and bile acid profile in mice, Toxicology and Applied Pharmacology, vol.277, issue.2, 2014.
DOI : 10.1016/j.taap.2014.03.009

D. E. Fouts, M. Torralba, K. E. Nelson, D. A. Brenner, and B. Schnabl, Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease, Journal of Hepatology, vol.56, issue.6, pp.1283-1292, 2012.
DOI : 10.1016/j.jhep.2012.01.019

J. Henao-mejia, E. Elinav, C. A. Thaiss, and R. A. , The Intestinal Microbiota in Chronic Liver Disease, Adv. Immunol, vol.117, pp.73-97, 2013.
DOI : 10.1016/B978-0-12-410524-9.00003-7

. Hekmatdoost, Synbiotic supplementation in nonalcoholic fatty liver disease : a randomized, double-blind, placebo-controlled pilot study, Am J Clin Nutr, vol.99, pp.535-542, 2014.

T. Nishimura and . Asano, Lactobacillus casei strain Shirota protects against nonalcoholic steatohepatitis development in a rodent model, Am. J. Physiol, 2013.

J. Noack, B. Kleessen, J. Proll, G. Dongowski, and M. Blaut, Dietary guar gum and pectin stimulate intestinal microbial polyamine synthesis in rats, J. Nutr, vol.128, pp.1385-91, 1998.

Y. Ohashi, K. Sumitani, M. Tokunaga, N. Ishihara, T. Okubo et al., and butyrate-producing bacteria in the human large intestine, Beneficial Microbes, vol.6, issue.4, pp.451-455, 2015.
DOI : 10.3920/BM2014.0118

M. Begley, C. Hill, and C. G. Gahan, Bile Salt Hydrolase Activity in Probiotics, Bile Salt Hydrolase Activity in Probiotics Bile Salt Hydrolase Activity in Probiotics, pp.1729-1738, 2006.
DOI : 10.1128/AEM.72.3.1729-1738.2006
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1393245

D. Mudgil, S. Barak, and B. S. Khatkar, Guar gum: processing, properties and food applications?A Review, Journal of Food Science and Technology, vol.85, issue.3, pp.409-418, 2011.
DOI : 10.1002/jsfa.2308
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931889