J. P. Furet, O. Firmesse, M. Gourmelon, and C. Bridonneau, Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR, FEMS microbiology ecology, vol.68, pp.351-362, 2009.

B. Dridi, M. Henry, A. El-khechine, D. Raoult, and M. Drancourt, High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol, PloS one, vol.4, p.7063, 2009.

S. R. Lyons, A. L. Griffen, and E. J. Leys, Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria, Journal of clinical microbiology, vol.38, pp.2362-2365, 2000.

J. J. Kozich, S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss, Development of a dualindex sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform, Applied and environmental microbiology, vol.79, pp.5112-5120, 2013.

T. Magoc and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011.

J. G. Caporaso, J. Kuczynski, J. Stombaugh, and K. Bittinger, QIIME allows analysis of highthroughput community sequencing data, Nature methods, vol.7, pp.335-336, 2010.

T. D. Schmittgen and K. J. Livak, Analyzing real-time PCR data by the comparative C(T) method, Nature protocols, vol.3, pp.1101-1108, 2008.

P. J. Mcmurdie and S. Holmes, Waste not, want not: why rarefying microbiome data is inadmissible, PLoS computational biology, vol.10, p.1003531, 2014.

S. Tanabe, T. Suzuki, Y. Wasano, and F. Nakajima, Anti-inflammatory and Intestinal Barrierprotective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds, Journal of equine science, vol.25, pp.37-43, 2014.

W. R. Russell, S. W. Gratz, S. H. Duncan, and G. Holtrop, High-protein, reducedcarbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health, The American journal of clinical nutrition, vol.93, pp.1062-1072, 2011.

L. Zhou, L. Fang, Y. Sun, Y. Su, and W. Zhu, Effects of the dietary protein level on the microbial composition and metabolomic profile in the hindgut of the pig, Anaerobe, vol.38, pp.61-69, 2016.

C. Mu, Y. Yang, Z. Luo, L. Guan, and W. Zhu, The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet, The Journal of nutrition, vol.146, pp.474-483, 2016.

K. Windey, V. De-preter, and K. Verbeke, Relevance of protein fermentation to gut health. Molecular nutrition & food research, vol.56, pp.184-196, 2012.

A. M. Davila, F. Blachier, M. Gotteland, and M. Andriamihaja, Intestinal luminal nitrogen metabolism: role of the gut microbiota and consequences for the host, Pharmacological research : the official journal of the Italian Pharmacological Society, vol.68, pp.95-107, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01001597

K. Windey, V. De-preter, T. Louat, and F. Schuit, Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects, PloS one, vol.7, p.52387, 2012.

J. H. Cummings, The large intestine in nutrition and diseases, Danone Institute, pp.15-47, 1997.

F. Blachier, F. Mariotti, J. F. Huneau, and D. Tome, Effects of amino acid-derived luminal metabolites on the colonic epithelium and physiopathological consequences, Amino acids, vol.33, pp.547-562, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01186779

G. T. Macfarlane and J. H. Cummings, The control and consequences of bacterial fermentation in the human colon, J appl Bacteriol, vol.6, pp.443-459, 1991.

K. P. Scott, S. W. Gratz, P. O. Sheridan, H. J. Flint, and S. H. Duncan, The influence of diet on the gut microbiota, Pharmacological research : the official journal of the Italian Pharmacological Society, vol.69, pp.52-60, 2013.

L. A. David, C. F. Maurice, R. N. Carmody, and D. B. Gootenberg, Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.505, pp.559-563, 2014.

G. D. Wu, J. Chen, C. Hoffmann, and K. Bittinger, Linking long-term dietary patterns with gut microbial enterotypes, Science, vol.334, pp.105-108, 2011.

M. E. Handlogten, S. P. Hong, C. M. Westhoff, and I. D. Weiner, Apical ammonia transport by the mouse inner medullary collecting duct cell (mIMCD-3), American journal of physiology. Renal physiology, vol.289, pp.347-358, 2005.

M. Eklou-lawson, F. Bernard, N. Neveux, and C. Chaumontet, Colonic luminal ammonia and portal blood L-glutamine and L-arginine concentrations: a possible link between colon mucosa and liver ureagenesis, Amino acids, vol.37, pp.751-760, 2009.

F. Blachier, A. M. Davila, S. Mimoun, and P. H. Benetti, Luminal sulfide and large intestine mucosa: friend or foe? Amino acids, vol.39, pp.335-347, 2010.

P. D. Cani and M. Van-hul, Novel opportunities for next-generation probiotics targeting metabolic syndrome. Current opinion in biotechnology, vol.32, pp.21-27, 2015.

D. Gevers, S. Kugathasan, L. A. Denson, and Y. Vazquez-baeza, The treatment-naive microbiome in new-onset Crohn's disease. Cell host & microbe, vol.15, pp.382-392, 2014.

C. L. Garcia-rodenas, M. Lepage, C. Ngom-bru, and A. Fotiou, Effect of Formula Containing Lactobacillus reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section, vol.63, pp.681-687, 2016.

N. Reichardt, S. H. Duncan, P. Young, and A. Belenguer, Phylogenetic distribution of three pathways for propionate production within the human gut microbiota, The ISME journal, vol.8, pp.1323-1335, 2014.

W. E. Moore and L. V. Holdeman, Human fecal flora: the normal flora of 20 Japanese-Hawaiians, Applied microbiology, vol.27, pp.961-979, 1974.

H. M. Roager, L. B. Hansen, M. I. Bahl, and H. L. Frandsen, Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut, Nature microbiology, vol.1, p.16093, 2016.

M. Derrien, C. Belzer, and W. M. De-vos, Akkermansia muciniphila and its role in regulating host functions, 2016.

M. C. Dao, A. Everard, J. Aron-wisnewsky, and N. Sokolovska, Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology, Gut, vol.65, pp.426-436, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02639895

A. Everard, C. Belzer, L. Geurts, and J. P. Ouwerkerk, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proceedings of the National Academy of Sciences of the United States of America, vol.110, pp.9066-9071, 2013.

M. Derrien, E. E. Vaughan, C. M. Plugge, and W. M. De-vos, Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium, International journal of systematic and evolutionary microbiology, vol.54, pp.1469-1476, 2004.

D. Vandeputte, G. Falony, S. Vieira-silva, and R. Y. Tito, Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates, Gut, vol.65, pp.57-62, 2016.

S. Zhang, M. Ren, X. Zeng, and P. He, Leucine stimulates ASCT2 amino acid transporter expression in porcine jejunal epithelial cell line (IPEC-J2) through PI3K/Akt/mTOR and ERK signaling pathways, Amino acids, vol.46, pp.2633-2642, 2014.

J. H. Cummings, M. J. Hill, E. S. Bone, W. J. Branch, and D. J. Jenkins, The effect of meat protein and dietary fiber on colonic function and metabolism. II. Bacterial metabolites in feces and urine. The American journal of clinical nutrition, vol.32, pp.2094-2101, 1979.

T. Terada, Y. Shimada, X. Pan, and K. Kishimoto, Expression profiles of various transporters for oligopeptides, amino acids and organic ions along the human digestive tract, Biochemical pharmacology, vol.70, pp.1756-1763, 2005.

B. H. Hirst, Dietary regulation of intestinal nutrient carriers, The Proceedings of the Nutrition Society, vol.52, pp.315-324, 1993.

J. R. Greenfield, I. S. Farooqi, J. M. Keogh, and E. Henning, Oral glutamine increases circulating glucagon-like peptide 1, glucagon, and insulin concentrations in lean, obese, and type 2 diabetic subjects. The American journal of clinical nutrition, vol.89, pp.106-113, 2009.

A. Gameiro, F. Reimann, A. M. Habib, and D. O'malley, The neurotransmitters glycine and GABA stimulate glucagon-like peptide-1 release from the GLUTag cell line, The Journal of physiology, vol.569, pp.761-772, 2005.

Y. Jiang, A. J. Rose, T. P. Sijmonsma, and A. Broer, Mice lacking neutral amino acid transporter B(0)AT1 (Slc6a19) have elevated levels of FGF21 and GLP-1 and improved glycaemic control, Molecular metabolism, vol.4, pp.406-417, 2015.

R. Rasoamanana, N. Darcel, G. Fromentin, and D. Tome, Nutrient sensing and signalling by the gut, The Proceedings of the Nutrition Society, vol.71, pp.446-455, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01003350

J. J. Meier, A. Gethmann, O. Gotze, and B. Gallwitz, Glucagon-like peptide 1 abolishes the postprandial rise in triglyceride concentrations and lowers levels of non-esterified fatty acids in humans, Diabetologia, vol.49, pp.452-458, 2006.

M. B. , D. J. , and V. , D: experiments, data acquirement and analysis and manuscript writing

K. , B. G. , C. M. , C. C. , A. D. et al.,

S. M. , 16S rDNA libraries and high throughput sequencing. D. T.: Study design I. S

G. F. , F. B. , and M. L. , ACKNOWLEDGMENTS This work was funded by a French governmental ANR grant through the Idex Alias program ANR-11-IDEX-0003-02, which also covered Daphné Jaoui, Martin Beaumont and Damien Mat PhD fellowships. The authors are grateful to D. Rousseau-Ralliard (UMR Biologie De la Reproduction, INRA) for the technical support for fatty acid composition analysis, to the INRA MIGALE bioinformatics platform

M. Beaumont, D. Jaoui, V. Douard, D. Mat, F. Koeth et al., Structure of protein emulsion in food impacts intestinal microbiota, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01598952

M. Beaumont, D. Jaoui, V. Douard, D. Mat, F. Koeth et al., Structure of protein emulsion in food impacts intestinal microbiota, caecal luminal content composition and distal intestine www.mnf-journal, 2017.

M. Beaumont, D. Jaoui, V. Douard, D. Mat, F. Koeth et al., Structure of protein emulsion in food impacts intestinal microbiota, caecal luminal content composition and distal intestine www.mnf-journal, 2017.