L. W. Peterson and D. Artis, Intestinal epithelial cells: regulators of barrier function and immune homeostasis, Nat Rev Immunol, vol.14, pp.141-153, 2014.

Y. Goto, Epithelial cells as a transmitter of signals from commensal bacteria and host immune cells, Front Immunol, vol.10, p.2057, 2019.

J. M. Allaire, S. M. Crowley, H. T. Law, S. Chang, H. Ko et al., The intestinal epithelium: central coordinator of mucosal immunity, Trends Immunol, vol.39, pp.677-696, 2018.

N. Jain and W. A. Walker, Diet and host-microbial crosstalk in postnatal intestinal immune homeostasis, Nat Rev Gastroenterol Hepatol, vol.12, pp.14-25, 2015.

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. Rakoff-nahoum, Y. Kong, S. H. Kleinstein, S. Subramanian, P. P. Ahern et al., Analysis of gene-environment interactions in postnatal development of the mammalian intestine, PNAS, vol.112, pp.1929-1936, 2015.

M. Fulde, F. Sommer, B. Chassaing, K. Van-vorst, A. Dupont et al., Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition, Nature, vol.560, pp.489-493, 2018.

W. Pan, F. Sommer, M. Falk-paulsen, T. Ulas, P. Best et al., Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development, Genome Med, vol.10, p.27, 2018.

J. Pácha, Development of intestinal transport function in mammals, Physiol Rev, vol.80, pp.1633-1667, 2000.

A. Nabhani, Z. Dulauroy, S. Marques, R. Cousu, C. et al., A weaning reaction to microbiota is required for resistance to immunopathologies in the adult, Immunity, vol.50, pp.1276-1288, 2019.

F. Bäckhed, J. Roswall, Y. Peng, Q. Feng, H. Jia et al., Dynamics and stabilization of the human gut microbiome during the first year of life, Cell Host Microbe, vol.17, pp.690-703, 2015.

J. E. Koenig, A. Spor, N. Scalfone, A. D. Fricker, J. Stombaugh et al., Succession of microbial consortia in the developing infant gut microbiome, PNAS, vol.108, pp.4578-4585, 2011.

E. J. Muinck and P. De-trosvik, Individuality and convergence of the infant gut microbiota during the first year of life, Nat Commun, vol.9, p.2233, 2018.

N. Voreades, A. Kozil, and T. L. Weir, Diet and the development of the human intestinal microbiome, Front Microbiol, vol.5, p.494, 2014.

L. V. Hooper, Bacterial contributions to mammalian gut development, Trends Microbiol, vol.12, pp.129-134, 2004.

N. Torow and M. W. Hornef, The neonatal window of opportunity: setting the stage for life-long host-microbial interaction and immune homeostasis, J Immunol, vol.198, pp.557-563, 2017.

K. Oliphant and E. Allen-vercoe, Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

. Microbiome, , vol.7, p.91, 2019.

I. Rowland, G. Gibson, A. Heinken, K. Scott, J. Swann et al., Gut microbiota functions: metabolism of nutrients and other food components, Eur J Nutr, vol.57, pp.1-24, 2018.

T. Gidenne and F. Lebas, Feeding in domestic vertebrates: from structure to behaviour, pp.179-194, 2006.

Y. L. Dorokhov, A. V. Shindyapina, E. V. Sheshukova, and T. V. Komarova, Metabolic methanol: molecular pathways and physiological roles, Physiol Rev, vol.95, pp.603-644, 2015.

S. Mckeen, W. Young, J. Mullaney, K. Fraser, W. C. Mcnabb et al., Infant complementary feeding of prebiotics for the microbiome and immunity, Nutrients, vol.11, p.364, 2019.

M. R. Charbonneau, L. V. Blanton, D. B. Digiulio, D. A. Relman, C. B. Lebrilla et al., A microbial perspective of human developmental biology, Nature, vol.535, pp.48-55, 2016.

S. A. Frese, K. Parker, C. C. Calvert, and D. A. Mills, Diet shapes the gut microbiome of pigs during nursing and weaning, Microbiome, vol.3, p.28, 2015.

N. Mach, M. Berri, J. Estellé, F. Levenez, G. Lemonnier et al., Early-life establishment of the swine gut microbiome and impact on host phenotypes: role of early-life gut microbiome on pigs' health, Environ Microbiol Rep, vol.7, pp.554-569, 2015.

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

L. Pinotti, A. Baldi, and V. Dell'orto, Comparative mammalian choline metabolism with emphasis on the high-yielding dairy cow, Nutr Res Rev, vol.15, pp.315-332, 2002.

S. H. Zeisel, J. S. Wishnok, and J. K. Blusztajn, Formation of methylamines from ingested choline and lecithin, J Pharmacol Exp Ther, vol.225, pp.320-324, 1983.

D. Fennema, I. R. Phillips, and E. A. Shephard, Trimethylamine and trimethylamine N-Oxide, a flavin-containing monooxygenase 3 (FMO3)-mediated host-microbiome metabolic axis implicated in health and disease, Drug Metab Dispos, vol.44, pp.1839-1850, 2016.

A. M. Campo, S. Bodea, H. A. Hamer, J. A. Marks, H. J. Haiser et al., Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria, mBio, vol.6, pp.42-57, 2015.

T. Read, L. Fortun-lamothe, G. Pascal, L. Boulch, M. Cauquil et al., Diversity and co-occurrence pattern analysis of cecal microbiota establishment at the onset of solid feeding in young rabbits, Front Microbiol, vol.10, p.973, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02154596

A. L. Thompson, A. Monteagudo-mera, M. B. Cadenas, and M. L. Lampl, Azcarate-Peril MA. Milk-and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome, Front Cell Infect Microbiol, vol.5, p.3, 2015.

L. Reau, A. J. Suen, and G. , The Ruminococci: key symbionts of the gut ecosystem, J Microbiol, vol.56, pp.199-208, 2018.

S. Moco, F. Martin, and S. Rezzi, Metabolomics view on gut microbiome modulation by polyphenol-rich foods, J Proteome Res, vol.11, pp.4781-4790, 2012.

H. Gehart and H. Clevers, Tales from the crypt: new insights into intestinal stem cells, Nat Rev Gastroenterol Hepatol, vol.16, pp.19-34, 2019.

J. L. Holmes, C. M. Van-itallie, J. E. Rasmussen, and J. M. Anderson, Claudin profiling in the mouse during postnatal intestinal development and along the gastrointestinal tract reveals complex expression patterns, Gene Expr Patterns, vol.6, pp.581-588, 2006.

R. M. Patel, L. S. Myers, A. R. Kurundkar, A. Maheshwari, A. Nusrat et al., Probiotic bacteria induce maturation of intestinal claudin 3 expression and barrier function, Am J Pathol, vol.180, pp.626-635, 2012.

J. N. Udall, K. Pang, L. Fritze, R. Kleinman, and W. A. Walker, Development of gastrointestinal mucosal barrier. I. The effect of age on intestinal permeability to macromolecules, Pediatr Res, vol.15, pp.241-244, 1981.

V. Garcia-hernandez, M. Quiros, and A. Nusrat, Intestinal epithelial claudins: expression and regulation in homeostasis and inflammation, Ann N Y Acad Sci, vol.1397, pp.66-79, 2017.

J. D. Schulzke, A. H. Gitter, J. Mankertz, S. Spiegel, U. Seidler et al., Epithelial transport and barrier function in occludin-deficient mice, Biochim Biophys Acta, vol.1669, pp.34-42, 2005.

M. A. Odenwald and J. R. Turner, The intestinal epithelial barrier: a therapeutic target, Nat Rev Gastroenterol Hepatol, vol.14, pp.9-21, 2017.

L. R. Muniz, C. Knosp, and G. Yeretssian, Intestinal antimicrobial peptides during homeostasis, infection, and disease, Front Immunol, vol.3, p.310, 2012.

S. Mukherjee and L. V. Hooper, Antimicrobial defense of the intestine, Immunity, vol.42, pp.28-39, 2015.

S. Ménard, V. Förster, M. Lotz, D. Gütle, C. U. Duerr et al., Developmental switch of intestinal antimicrobial peptide expression, J Exp Med, vol.205, pp.183-193, 2008.

J. Wehkamp, H. Chu, B. Shen, R. W. Feathers, R. J. Kays et al., Paneth cell antimicrobial peptides: topographical distribution and quantification in human gastrointestinal tissues, FEBS Lett, vol.580, pp.5344-5350, 2006.

S. Pérez, R. Taléns-visconti, S. Rius-pérez, I. Finamor, and J. Sastre, Redox signaling in the gastrointestinal tract, Free Radical Biol Med, vol.104, pp.75-103, 2017.

S. L. Jenkins, J. Wang, M. Vazir, J. Vela, O. Sahagun et al., Role of passive and adaptive immunity in influencing enterocyte-specific gene expression, Am J Physiol-Gastrointestinal Liver Physiol, vol.285, pp.714-739, 2003.

L. Peng, Z. He, W. Chen, I. R. Holzman, and J. Lin, Effects of butyrate on intestinal barrier function in a Caco-2 cell monolayer model of intestinal barrier, Pediatr Res, vol.61, pp.37-41, 2007.

L. Zheng, C. J. Kelly, K. D. Battista, R. Schaefer, J. M. Lanis et al., Microbial-derived butyrate promotes epithelial barrier function through IL-10 Receptordependent repression of claudin-2, J Immunol, vol.199, pp.2976-2984, 2017.

M. C. Valenzano, K. Diguilio, J. Mercado, M. Teter, J. To et al., Remodeling of tight junctions and enhancement of barrier integrity of the CACO-2 intestinal epithelial cell layer by micronutrients, PLoS One, vol.10, p.133926, 2015.

D. Yu, M. Gadkari, Q. Zhou, S. Yu, N. Gao et al., Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome, Genome Biol, vol.16, p.211, 2015.

K. A. Romano, A. Martinez-del-campo, K. Kasahara, C. L. Chittim, E. I. Vivas et al., Metabolic, epigenetic, and transgenerational effects of gut bacterial choline consumption, Cell Host Microbe, vol.22, pp.279-290, 2017.

K. A. Krautkramer, R. S. Dhillon, J. M. Denu, and H. V. Carey, Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin, Transl Res, vol.189, pp.30-50, 2017.

M. Natoli, B. D. Leoni, D. 'agnano, I. Zucco, F. Felsani et al., Good Caco-2 cell culture practices, Toxicol in Vitro, vol.26, pp.1243-1246, 2012.

Y. Li, Y. Liu, B. Liu, J. Wang, S. Wei et al., A growth factor-free culture system underscores the coordination between Wnt and BMP signaling in Lgr5+ intestinal stem cell maintenance, Cell Discovery, vol.4, p.49, 2018.

L. Verschuren, M. Calus, A. Jansman, R. Bergsma, E. F. Knol et al., Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex, J Anim Sci, vol.96, pp.1405-1418, 2018.

F. Escudié, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil et al., FROGS: find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2018.

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2012.

G. M. Douglas, V. J. Maffei, J. Zaneveld, S. N. Yurgel, J. R. Brown et al., PICRUSt2: an improved and extensible approach for metagenome inference, bioRxiv, 2019.

F. Giacomoni, L. Corguillé, G. Monsoor, M. Landi, M. Pericard et al., Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics, Bioinformatics, vol.31, pp.1493-1495, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01214152

K. J. Livak and T. D. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2 ???CT method, Methods, vol.25, pp.402-408, 2001.

P. J. Mcmurdie, S. Holmes, and M. Watson, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, p.61217, 2013.

F. Rohart, B. Gautier, A. Singh, K. Cao, and D. Schneidman, mixOmics: an R package for 'omics feature selection and multiple data integration, PLoS Comput Biol, vol.13, p.1005752, 2017.

L. Maertens, J. M. Pérez, M. Villamide, C. Cervera, T. Gidenne et al., Nutritive value of raw materials for rabbits: egran tables 2002, World Rabbit Sci, vol.10, pp.157-166, 2010.