Z. M. Younossi, A. B. Koenig, D. Abdelatif, Y. Fazel, L. Henry et al., Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes, Hepatology, vol.64, pp.73-84, 2016.

B. Q. Starley, C. J. Calcagno, and S. A. Harrison, Nonalcoholic fatty liver disease and hepatocellular carcinoma: A weighty connection, Hepatology, vol.51, pp.1820-1832, 2010.

P. Gerard, Gut microbiota and obesity, Cell. Mol. Life Sci. CMLS, vol.73, pp.147-162, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01532527

Z. Safari and P. Gerard, The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD)

, Cell. Mol. Life Sci. CMLS, vol.76, pp.1541-1558, 2019.

J. H. Kreznar, M. P. Keller, L. L. Traeger, M. E. Rabaglia, K. L. Schueler et al., Host genotype and gut microbiome modulate insulin secretion and diet-induced metabolic phenotypes, vol.18, pp.1739-1750, 2017.

B. W. Parks, E. Nam, E. Org, E. Kostem, F. Norheim et al., Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice, Cell Metab, vol.17, pp.141-152, 2013.

H. Denk, P. M. Abuja, and K. Zatloukal, Animal models of NAFLD from the pathologist's point of view, Biochim. Biophys. Acta Mol. Basis Dis, 1865.

G. Kanuri and I. Bergheim, In vitro and in vivo models of non-alcoholic fatty liver disease (NAFLD), Int. J. Mol. Sci, vol.14, pp.11963-11980, 2013.

S. Collins, T. L. Martin, R. S. Surwit, and J. Robidoux, Genetic vulnerability to diet-induced obesity in the C57BL/6J mouse: Physiological and molecular characteristics, Physiol. Behav, vol.81, pp.243-248, 2004.

A. E. Hill-baskin, M. M. Markiewski, D. A. Buchner, H. Shao, D. Desantis et al., Diet-induced hepatocellular carcinoma in genetically predisposed mice, Hum. Mol. Genet, vol.18, pp.2975-2988, 2009.

M. N. Vansaun, I. K. Lee, M. K. Washington, L. Matrisian, and D. L. Gorden, High fat diet induced hepatic steatosis establishes a permissive microenvironment for colorectal metastases and promotes primary dysplasia in a murine model, Am. J. Pathol, vol.175, pp.355-364, 2009.

J. C. Fraulob, R. Ogg-diamantino, C. Fernandes-santos, M. B. Aguila, and C. A. Mandarim-de-lacerda, A mouse model of metabolic syndrome: Insulin resistance, fatty liver and non-alcoholic fatty pancreas disease (NAFPD) in C57BL/6 mice fed a high fat diet, J. Clin. Biochem. Nutr, vol.46, pp.212-223, 2010.

C. Gallou-kabani, A. Vigé, M. Gross, J. Rabès, C. Boileau et al., C57BL/6J and A/J mice fed a high-fat diet delineate components of metabolic syndrome, Obesity, vol.15, 1996.

C. D. Mills, K. Kincaid, J. M. Alt, M. J. Heilman, and A. M. Hill, M-1/M-2 macrophages and the Th1/Th2 paradigm, J. Immunol, vol.164, p.6166, 2000.

R. S. Surwit, M. N. Feinglos, J. Rodin, A. Sutherland, A. E. Petro et al., Differential effects of fat and sucrose on the development of obesity and diabetes in C57BL/6J and A/J mice, Metab. Clin. Exp, vol.44, pp.645-651, 1995.

R. S. Surwit, M. F. Seldin, C. M. Kuhn, C. Cochrane, and M. Feinglos, Control of expression of insulin resistance and hyperglycemia by different genetic factors in diabetic C57BL/6J mice, Diabetes, vol.40, 1991.

H. Kondo, Y. Minegishi, Y. Komine, T. Mori, I. Matsumoto et al., Differential regulation of intestinal lipid metabolism-related genes in obesity-resistant A/J vs. obesity-prone C57BL/6J mice, Am. J. Physiol. Endocrinol. Metab, vol.291, pp.1092-1099, 2006.

M. A. Hildebrandt, C. Hoffmann, S. A. Sherrill-mix, S. A. Keilbaugh, M. Hamady et al., High-fat diet determines the composition of the murine gut microbiome independently of obesity, Gastroenterology, vol.137, pp.1716-1724, 2009.

C. Zhang, M. Zhang, X. Pang, Y. Zhao, L. Wang et al., Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations, ISME J, vol.6, pp.1848-1857, 2012.

M. Serino, E. Luche, S. Gres, A. Baylac, M. Berge et al., Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota, Gut, vol.61, pp.543-553, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-00726182

L. Roy, T. Llopis, M. Lepage, P. Bruneau, A. Rabot et al., Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice, Gut, vol.62, pp.1787-1794, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01193804

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, vol.103, pp.12511-12516, 2006.

M. Lemaire, S. Dou, A. Cahu, M. Formal, L. Le-normand et al., Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs, Sci. Rep, vol.8, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01858523

F. Escudie, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al., FROGS: Find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01886389

N. A. Bokulich, S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon et al., Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing, Nat. Methods, vol.10, pp.57-59, 2013.

B. O. Schroeder and F. Backhed, Signals from the gut microbiota to distant organs in physiology and disease, Nat. Med, vol.22, pp.1079-1089, 2016.

S. Tamburini, N. Shen, H. C. Wu, and J. C. Clemente, The microbiome in early life: Implications for health outcomes, Nat. Med, vol.22, pp.713-722, 2016.

S. Ussar, N. W. Griffin, O. Bezy, S. Fujisaka, S. Vienberg et al., Interactions between gut microbiota, host genetics and diet modulate the predisposition to obesity and metabolic syndrome, Cell Metab, vol.22, pp.516-530, 2015.

B. W. Parks, T. Sallam, M. Mehrabian, N. Psychogios, S. T. Hui et al., Genetic architecture of insulin resistance in the mouse, Cell Metab, vol.21, pp.334-347, 2015.

R. S. Surwit, C. M. Kuhn, C. Cochrane, J. A. Mccubbin, and M. N. Feinglos, Diet-induced type II diabetes in C57BL/6J mice, Diabetes, vol.37, pp.1163-1167, 1988.

S. Rabot, M. Membrez, A. Bruneau, P. Gerard, T. Harach et al., Germ-free C57BL/6J mice are resistant to high-fat-diet-induced insulin resistance and have altered cholesterol metabolism, FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol, vol.24, pp.4948-4959, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01204268

S. Fujisaka, S. Ussar, C. Clish, S. Devkota, J. M. Dreyfuss et al., Antibiotic effects on gut microbiota and metabolism are host dependent, J. Clin. Investig, vol.126, pp.4430-4443, 2016.

M. Ellekilde, E. Selfjord, C. S. Larsen, M. Jakesevic, I. Rune et al., Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice

D. Alexander, A. Orcutt, R. P. Henry, J. C. Baker, J. Jr et al., Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment, Mamm. Genome Off. J. Int. Mamm. Genome Soc, vol.17, pp.1093-1104, 2006.

A. Kovacs, N. Ben-jacob, H. Tayem, E. Halperin, F. A. Iraqi et al., Genotype is a stronger determinant than sex of the mouse gut microbiota, Microb. Ecol, vol.61, pp.423-428, 2011.

T. Jost, C. Lacroix, C. P. Braegger, and C. Chassard, New insights in gut microbiota establishment in healthy breast fed neonates, PLoS ONE, vol.7, 2012.

R. S. Kootte, E. Levin, J. Salojarvi, L. P. Smits, A. V. Hartstra et al., Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition, Cell Metab, vol.26, pp.611-619, 2017.

C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, Diversity, stability and resilience of the human gut microbiota, Nature, vol.489, pp.220-230, 2012.

A. C. Ericsson, J. W. Davis, W. Spollen, N. Bivens, S. Givan et al., Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice, PLoS ONE, vol.10, 2015.

R. N. Carmody, G. K. Gerber, J. M. Luevano, . Jr, D. M. Gatti et al., Diet dominates host genotype in shaping the murine gut microbiota, Cell Host Microbe, vol.17, pp.72-84, 2015.

C. De-filippo, D. Cavalieri, M. Di-paola, M. Ramazzotti, J. B. Poullet et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc. Natl. Acad. Sci, vol.107, pp.14691-14696, 2010.

Z. Safari, M. Monnoye, P. M. Abuja, M. Mariadassou, K. Kashofer et al., Steatosis and gut microbiota dysbiosis induced by high-fat diet are reversed by 1-week chow diet administration, Nutr. Res, vol.71, pp.72-88, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02503316

F. Hildebrand, T. L. Nguyen, B. Brinkman, R. G. Yunta, B. Cauwe et al., Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice, Genome Biol, vol.14, 2013.

N. R. Shin, T. W. Whon, and J. W. Bae, Proteobacteria: Microbial signature of dysbiosis in gut microbiota, Trends Biotechnol, vol.33, pp.496-503, 2015.

C. K. Fleissner, N. Huebel, M. M. El-bary, G. Loh, S. Klaus et al., Absence of intestinal microbiota does not protect mice from diet-induced obesity, Br. J. Nutr, vol.104, pp.919-929, 2010.

C. Zhang, M. Zhang, S. Wang, R. Han, Y. Cao et al., Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice, ISME J, vol.4, pp.232-241, 2010.

M. D. Spencer, T. J. Hamp, R. W. Reid, L. M. Fischer, S. H. Zeisel et al., Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency, Gastroenterology, vol.140, pp.976-986, 2011.

I. Martinez, G. Wallace, C. Zhang, R. Legge, A. K. Benson et al., Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota, Appl. Environ. Microbiol, vol.75, pp.4175-4184, 2009.

L. Zhu, S. S. Baker, C. Gill, W. Liu, R. Alkhouri et al., Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH, Hepatology, vol.57, pp.601-609, 2013.

J. Vaahtovuo, P. Toivanen, and E. Eerola, Bacterial composition of murine fecal microflora is indigenous and genetically guided, FEMS Microbiol. Ecol, vol.44, pp.131-136, 2003.

S. F. Clarke, E. F. Murphy, O. O'sullivan, R. P. Ross, P. W. O'toole et al., Targeting the microbiota to address diet-induced obesity: A time dependent challenge, PLoS ONE, vol.8, 2013.

B. M. Carvalho, D. Guadagnini, D. M. Tsukumo, A. A. Schenka, P. Latuf-filho et al., Modulation of gut microbiota by antibiotics improves insulin signalling in high-fat fed mice, Diabetologia, vol.55, pp.2823-2834, 2012.

K. M. Keeney, S. Yurist-doutsch, M. C. Arrieta, and B. B. Finlay, Effects of antibiotics on human microbiota and subsequent disease, Annu. Rev. Microbiol, vol.68, pp.217-235, 2014.

L. M. Cox, S. Yamanishi, J. Sohn, A. V. Alekseyenko, J. M. Leung et al., Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences, Cell, vol.158, pp.705-721, 2014.

A. Vrieze, C. Out, S. Fuentes, L. Jonker, I. Reuling et al., Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity, J. Hepatol, vol.60, pp.824-831, 2014.

F. Backhed, H. Ding, T. Wang, L. V. Hooper, G. Y. Koh et al., The gut microbiota as an environmental factor that regulates fat storage, Proc. Natl. Acad. Sci, vol.101, pp.15718-15723, 2004.

P. J. Turnbaugh, R. E. Ley, M. A. Mahowald, V. Magrini, E. R. Mardis et al., An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, vol.444, pp.1027-1031, 2006.

P. J. Turnbaugh, F. Backhed, L. Fulton, and J. I. Gordon, Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome, Cell Host Microbe, vol.3, pp.213-223, 2008.