, From day 3, water flasks were supplemented with ampicillin 1 g/liter and with an antibiotic concoction consisting of vancomycin 5 mg/ml, neomycin 10 mg/ml, metronidazole 10 mg/ml, and amphotericin B 0.1 mg/ml, administered by antibiotic gavage daily for 7 days. A gavage volume of 10 ml/kg of body weight was delivered with a stainless steel tube without prior sedation of the mice. From the day following the end of the microbiota-depleting treatment, Briefly, antibiotic treatment started with 3 days of amphotericin B 0.1 mg/ml, administered by gavage daily

F. Safe, 13% energy from fat) or HFD (235HF; SAFE, France) (45% energy from fat; cholesterol, 0.17 mg/g), both sterilized by gamma irradiation. The experiment was carried out twice. Mice were weighed weekly, and fresh stool samples were taken up. Mice were killed by cervical dislocation after 1 h of fasting, and blood, liver, and small intestine were recovered and immediately used for measurement of serum parameters (see the supplemental material), histological procedures (jejunum), RNA extraction

. Cells, The m-ICcl2 murine intestinal epithelial cell line was cultured as previously described (28) and seeded on Costar transwell plates with a 0.4-m-pore-size filter (Thermo Fisher) at a density of 3.10 5 /cm 2 . The medium was changed every 2 to 3 days until complete differentiation occurred

, Bacterial strains. L. paracasei ATCC 334 (formerly referred to as Lactobacillus casei ATCC 334) and a nonpathogenic murine E. coli isolate (13) were grown at 37°C in aerobic atmosphere in MRS medium and TS medium (Thermo Fisher), respectively. Bacteria in stationary-growth phase were harvested by centrifugation, washed with PBS, and resuspended in cell culture medium and water for cellular and animal experiments, respectively. To identify specific effectors, bacteria were incubated in m-ICcl2 medium for 16 h, and bacterial pellets were collected, subjected to heat treatment (110°C, 30 min), and resuspended. Culture supernatants (CS) were filtered (pore size, 0.22 m), Bacteria (multiplicity of infection of 100) were added in the upper compartment of the cell chamber, and, following 16 h of incubation, culture supernatants from the upper and lower compartments were collected and cells washed twice in phosphate-buffered saline (PBS) before lysis unless otherwise specified. Cell viability was monitored using the CytoTox 96 cytotoxicity assay (Promega)

T. Fisher, , vol.000, p.5

, RNA extractions from organs and cultured cells were performed using a NucleoSpin RNA II kit (Macherey-Nagel) before cDNA synthesis and RT-qPCR were performed with the primers listed in Table S6 in the supplemental material. Western blotting. Cells were lysed in 300 l of radioimmunoprecipitation assay (RIPA) buffer, and the lysate was heated in Laemmli buffer for 5 min at 90°C before migration in acrylamide SDS-PAGE. Proteins were transferred onto polyvinylidene difluoride (PVDF) membranes, incubated with the primary antibodies (see the supplemental material) overnight at 4°C in 5% bovine serum albumin (BSA)-PBS, washed in PBS-Tween 0.1%, incubated with a peroxidase-labeled secondary antibody (1:10,000) for 1 h, and revealed by the use of ECL chemiluminescence reagent (Thermo Fisher). Image acquisitions and quantifications were performed with an Amersham Imager 600 system (GE Healthcare), RNA isolation and quantitative real-time PCR (RT-qPCR). Distal jejunum and liver left lobe were homogenized in 2-ml and 7-ml tubes containing a mix of 1.4-diameter and 2.8-mm-diameter glass beads and 1 ml and 2 ml Trizol, respectively, using a Precellys system (Bertin Technologies)

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.
URL : https://hal.archives-ouvertes.fr/cea-00908974

V. K. Ridaura, J. J. Faith, F. E. Rey, J. Cheng, A. E. Duncan et al., Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, vol.341, p.1241214, 2013.

F. Sommer and F. Bäckhed, The gut microbiota-masters of host development and physiology, Nat Rev Microbiol, vol.11, pp.227-238, 2013.

V. Tremaroli and F. Bäckhed, Functional interactions between the gut microbiota and host metabolism, Nature, vol.489, pp.242-249, 2012.

F. Karlsson, V. Tremaroli, J. Nielsen, and F. Bäckhed, Assessing the human gut microbiota in metabolic diseases, Diabetes, vol.62, pp.3341-3349, 2013.

F. Bäckhed, 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 U S A, vol.101, pp.15718-15723, 2004.

Y. Wang, J. Viscarra, S. J. Kim, and H. S. Sul, Transcriptional regulation of hepatic lipogenesis, Nat Rev Mol Cell Biol, vol.16, pp.678-689, 2015.

S. Rabot, M. Membrez, A. Bruneau, P. Gérard, 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, vol.24, pp.4948-4959, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01204268

I. Semova, J. D. Carten, J. Stombaugh, L. C. Mackey, R. Knight et al., Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish, Cell Host Microbe, vol.12, pp.277-288, 2012.

S. El-aidy, C. A. Merrifield, M. Derrien, P. Van-baarlen, G. Hooiveld et al., The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation, Gut, vol.62, pp.1306-1314, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01003332

E. Larsson, V. Tremaroli, Y. S. Lee, O. Koren, I. Nookaew et al., Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88, Gut, vol.61, pp.1124-1131, 2012.

F. Sommer, I. Nookaew, N. Sommer, P. Fogelstrand, and F. Bäckhed, Site-specific programming of the host epithelial transcriptome by the gut microbiota, Genome Biol, vol.16, p.62, 2015.

J. Amar, C. Chabo, A. Waget, P. Klopp, C. Vachoux et al., Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: molecular mechanisms and probiotic treatment, EMBO Mol Med, vol.3, pp.559-572, 2011.
URL : https://hal.archives-ouvertes.fr/inserm-00801348

E. Naito, Y. Yoshida, K. Makino, Y. Kounoshi, S. Kunihiro et al., Beneficial effect of oral administration of Lactobacillus casei strain Shirota on insulin resistance in diet-induced obesity mice, J Appl Microbiol, vol.110, pp.650-657, 2011.

Ö. Öner, B. Aslim, and S. B. Ayda?, Mechanisms of cholesterol-lowering effects of lactobacilli and bifidobacteria strains as potential probiotics with their bsh gene analysis, J Mol Microbiol Biotechnol, vol.24, pp.12-18, 2014.

S. Park, Y. Ji, H. Jung, H. Park, J. Kang et al., Lactobacillus plantarum HAC01 regulates gut microbiota and adipose tissue accumulation in a diet-induced obesity murine model, Appl Microbiol Biotechnol, vol.101, pp.1605-1614, 2017.

R. Martin, H. Makino, C. Yavuz, A. Ben-amor, K. Roelofs et al., Early-life events, including mode of delivery and type of feeding, siblings and gender, shape the developing gut microbiota, PLoS One, vol.11, 2016.

T. Secher, C. Brehin, and E. Oswald, Early settlers: which E. coli strains do you not want at birth?, Am J Physiol Gastrointest Liver Physiol, vol.311, pp.123-129, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01602829

L. Aronsson, Y. Huang, P. Parini, M. Korach-andré, J. Håkansson et al., Decreased fat storage by Lactobacillus paracasei is associated with increased levels of angiopoietin-like 4 protein (ANGPTL4), PLoS One, vol.5, 2010.

M. Tanida, J. Shen, K. Maeda, Y. Horii, T. Yamano et al., High-fat diet-induced obesity is attenuated by probiotic strain Lactobacillus paracasei ST11 (NCC2461) in rats, Obes Res Clin Pract, vol.2, 2008.

A. Zadjali and F. , Use of germ-free animal models in microbiota-related research, J Microbiol Biotechnol, vol.25, pp.1583-1588, 2015.

D. H. Reikvam, A. Erofeev, A. Sandvik, V. Grcic, F. L. Jahnsen et al., Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression, PLoS One, vol.6, 2011.

J. Iqbal and M. M. Hussain, Intestinal lipid absorption, Am J Physiol Endocrinol Metab, vol.296, pp.1183-1194, 2008.

K. Nakajima, T. Nagamine, M. Q. Fujita, A. M. Tanaka, A. Schaefer et al., Apolipoprotein B-48: a unique marker of chylomicron metabolism, Adv Clin Chem, vol.64, pp.117-177, 2014.

A. S. Laganà, S. G. Vitale, A. Nigro, V. Sofo, F. M. Salmeri et al., Pleiotropic actions of peroxisome proliferator-activated receptors (PPARs) in dysregulated metabolic homeostasis, inflammation and cancer: current evidence and future perspectives, Int J Mol Sci, vol.17, p.999, 2016.

A. Caron, D. Richard, and M. Laplante, The roles of mTOR complexes in lipid metabolism, Annu Rev Nutr, vol.35, pp.321-348, 2015.

Y. J. Lee, E. H. Ko, J. E. Kim, E. Kim, H. Lee et al., Nuclear receptor PPAR?-regulated monoacylglycerol O-acyltransferase 1 (MGAT1) expression is responsible for the lipid accumulation in diet-induced hepatic steatosis, Proc Natl Acad Sci U S A, vol.109, pp.13656-13661, 2012.

M. Bens, A. Bogdanova, F. Cluzeaud, L. Miquerol, S. Kerneis et al., Transimmortalized mouse intestinal cells (m-ICc12) that maintain a crypt phenotype, Am J Physiol, vol.270, pp.1666-1674, 1996.

D. Ge, L. Han, S. Huang, N. Peng, P. Wang et al., Identification of a novel mTOR activator and discovery of a competing endogenous RNA regulating autophagy in vascular endothelial cells, Autophagy, vol.10, pp.957-971, 2014.

E. Levy, D. Ménard, E. Delvin, A. Montoudis, J. F. Beaulieu et al., Localization, function and regulation of the two intestinal fatty acid-binding protein types, Histochem Cell Biol, vol.132, pp.351-367, 2009.

H. Jamil, C. H. Chu, J. K. Dickson, Y. Chen, M. Yan et al., Evidence that microsomal triglyceride transfer protein is limiting in the production of apolipoprotein B-containing lipoproteins in hepatic cells, J Lipid Res, vol.39, pp.1448-1454, 1998.

I. Sekirov, S. L. Russell, L. Antunes, and B. B. Finlay, Gut microbiota in health and disease, Physiol Rev, vol.90, pp.859-904, 2009.

L. Poquet and T. J. Wooster, Infant digestion physiology and the relevance of in vitro biochemical models to test infant formula lipid digestion, Mol Nutr Food Res, vol.60, pp.1876-1895, 2016.

A. Swidsinski, V. Loening-baucke, H. Lochs, and L. P. Hale, Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice, World J Gastroenterol, vol.11, pp.1131-1140, 2005.

R. Dubos, R. W. Schaedler, R. Costello, and P. Hoet, Indigenous, normal, and autochtonous flora of the gastrointestinal tract, J Exp Med, vol.122, pp.67-76, 1965.

S. Gu, D. Chen, J. N. Zhang, X. Lv, K. Wang et al., Bacterial community mapping of the mouse gastrointestinal tract, PLoS One, vol.8, 2013.

C. Porter, N. L. Trevaskis, and W. N. Charman, Lipids and lipid-based formulations: optimizing the oral delivery of lipophilic drugs, Nat Rev Drug Discov, vol.6, pp.231-248, 2007.

T. Matsuki, T. Pédron, B. Regnault, C. Mulet, T. Hara et al., Epithelial cell proliferation arrest induced by lactate and acetate from Lactobacillus casei and Bifidobacterium breve, PLoS One, vol.8, 2013.

T. Conway and P. S. Cohen, Commensal and pathogenic Escherichia coli metabolism in the gut, Microbiol Spectr, vol.3, 2015.

A. El-kaoutari, F. Armougom, J. I. Gordon, D. Raoult, and B. Henrissat, The abundance and variety of carbohydrate-active enzymes in the human gut microbiota, Nat Rev Microbiol, vol.11, pp.497-504, 2013.

R. Oozeer, J. P. Furet, N. Goupil-feuillerat, J. Anba, J. Mengaud et al., Differential activities of four Lactobacillus casei promoters during bacterial transit through the gastrointestinal tracts of humanmicrobiota-associated mice, Appl Environ Microbiol, vol.71, pp.1356-1363, 2005.

U. Axling, C. Olsson, J. Xu, C. Fernandez, S. Larsson et al., Green tea powder and Lactobacillus plantarum affect gut microbiota, lipid metabolism and inflammation in highfat fed C57BL/6J mice, Nutr Metab, vol.9, p.105, 2012.

B. Kim, K. Y. Park, J. Y. Park, S. Holzapfel, W. Hyun et al., Protective effects of Lactobacillus rhamnosus GG against dyslipidemia in high-fat dietinduced obese mice, Biochem Biophys Res Commun, vol.473, pp.530-536, 2016.

E. Catry, B. D. Pachikian, N. Salazar, A. M. Neyrinck, P. D. Cani et al., Ezetimibe and simvastatin modulate gut microbiota and expression of genes related to cholesterol metabolism, Life Sci, vol.132, pp.77-84, 2015.

E. M. Hamad, M. Sato, K. Uzu, T. Yoshida, S. Higashi et al., Milk fermented by Lactobacillus gasseri SBT2055 influences adipocyte size via inhibition of dietary fat absorption in Zucker rats, Br J Nutr, vol.101, pp.716-724, 2009.

S. A. Joyce, J. Macsharry, P. G. Casey, M. Kinsella, E. F. Murphy et al., Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut, Proc Natl Acad Sci U S A, vol.111, pp.7421-7426, 2014.

M. X. Byndloss, E. E. Olsan, F. Rivera-chávez, C. R. Tiffany, S. A. Cevallos et al., Microbiota-activated PPAR-? signaling inhibits dysbiotic Enterobacteriaceae expansion, Science, vol.357, pp.570-575, 2017.

T. Pauquai, J. Bouchoux, D. Chateau, R. Vidal, M. Rousset et al., Adaptation of enterocytic Caco-2 cells to glucose modulates triacylglycerol-rich lipoprotein secretion through triacylglycerol targeting into the endoplasmic reticulum lumen, Biochem J, vol.395, pp.393-403, 2006.

. Tazi,