A. Hruby and F. B. Hu, The epidemiology of obesity: a big picture, Pharmacoeconomics, vol.33, issue.7, pp.673-89, 2015.

D. Nocca, M. Loureiro, and E. M. Skalli, Five-year results of laparoscopic sleeve gastrectomy for the treatment of severe obesity, Surg Endosc, vol.31, issue.8, pp.3251-3258, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01793377

J. L. Colquitt, K. Pickett, E. Loveman, and G. K. Frampton, Surgery for weight loss in adults, Cochrane Database Syst Rev, issue.8, p.3641, 2014.

R. Peterli, B. K. W?-olnerhanssen, and T. Peters, Effect of laparoscopic sleeve gastrectomy vs laparoscopic Roux-en-Y gastric bypass on weight loss in patients with morbid obesity: the SM-BOSS randomized clinical trial, JAMA, vol.319, issue.3, pp.255-65, 2018.

O. A. Baothman, M. A. Zamzami, I. Taher, J. Abubaker, and M. Abu-farha, The role of gut microbiota in the development of obesity and diabetes, Lipids Health Dis, vol.15, p.108, 2016.

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, issue.7122, pp.1027-1058, 2006.

P. J. Turnbaugh and J. I. Gordon, The core gut microbiome, energy balance and obesity, J Physiol, vol.587, pp.4153-4161, 2009.

L. Chatelier, E. Nielsen, T. Qin, and J. , Richness of human gut microbiome correlates with metabolic markers, Nature, vol.500, issue.7464, pp.541-547, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01190602

D. J. Morrison and T. Preston, Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism, Gut Microbes, vol.7, issue.3, pp.189-200, 2016.

M. C. Dao, E. A. Aron-wisnewsky, and J. , Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology, Gut, vol.65, issue.3, pp.426-462, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02639895

A. Everard, C. Belzer, and L. Geurts, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc Natl Acad Sci U S A, vol.110, issue.22, pp.9066-71, 2013.

H. Plovier, A. Everard, and C. Druart, A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice, Nat Med, vol.23, issue.1, pp.107-120, 2017.

A. Palleja, A. Kashani, and K. H. Allin, Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota, Genome Med, vol.8, issue.1, p.67, 2016.

A. P. Liou, M. Paziuk, J. Luevano, S. Machineni, P. J. Turnbaugh et al., Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity, Sci Transl Med, vol.5, issue.178, p.41, 2013.

L. Kong, J. Tap, A. , and J. , Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes, Am J Clin Nutr, vol.98, issue.1, pp.16-24, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02652440

J. Furet, L. Kong, and J. Tap, Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers, Diabetes, vol.59, issue.12, pp.3049-57, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668840

H. Zhang, J. K. Dibaise, and A. Zuccolo, Human gut microbiota in obesity and after gastric bypass, Proc Natl Acad Sci U S A, vol.106, issue.7, pp.2365-70, 2009.

D. A. Medina, J. P. Pedreros, and D. Turiel, Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients, PeerJ, vol.5, p.3443, 2017.

R. Murphy, P. Tsai, M. J?-ullig, A. Liu, L. Plank et al., Differential changes in gut microbiota after gastric bypass and sleeve gastrectomy bariatric surgery vary according to diabetes remission, Obes Surg, vol.27, issue.4, pp.917-942, 2017.

V. Tremaroli, F. Karlsson, and M. Werling, Roux-en-Y gastric bypass and vertical banded gastroplasty induce long-term changes on the human gut microbiome contributing to fat mass regulation, Cell Metab, vol.22, issue.2, pp.228-266, 2015.

J. V. Li, H. Ashrafian, and M. Bueter, Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk, Gut, vol.60, issue.9, pp.1214-1237, 2011.

R. Ranjan, A. Rani, A. Metwally, H. S. Mcgee, and D. L. Perkins, Analysis of the microbiome: advantages of whole genome shotgun versus 16 S amplicon sequencing, Biochem Biophys Res Commun, vol.469, issue.4, pp.967-77, 2016.

J. Graessler, Y. Qin, and H. Zhong, Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters, Pharmacogenomics J, vol.13, issue.6, pp.514-536, 2013.

Z. E. Ilhan, J. K. Dibaise, and N. G. Isern, Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding, ISME J, vol.11, issue.9, pp.2047-58, 2017.

D. A. Medina, T. Li, P. Thomson, A. Artacho, V. Brocal et al., Cross-regional view of functional and taxonomic microbiota composition in obesity and post-obesity treatment shows country specific microbial contribution, Front Microbiol, vol.10, 2019.

A. Damms-machado, M. S. Schollenberger, and A. E. , Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption, Biomed Res Int, p.806248, 2015.

R. Liu, J. Hong, and X. Xu, Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention, Nat Med, vol.23, issue.7, pp.859-68, 2017.

F. Plaza-oñate, L. Chatelier, E. Almeida, and M. , MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data, Bioinformatics, vol.35, issue.9, pp.1544-52, 2019.

, International Human Microbiome Standards; c2015 [, vol.5, p.292, 2009.

. Sops07, International Human Microbiome Standards; c2015 [, vol.5, p.254, 2009.

N. Pons, J. Batto, and S. Kennedy, A platform for quantitative metagenomic profiling of complex system

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memoryefficient alignment of short DNA sequences to the human genome

, Genome Biol, vol.10, issue.3, p.25, 2009.

J. Li, H. Jia, and X. Cai, An integrated catalog of reference genes in the human gut microbiome, Nat Biotechnol, vol.32, issue.8, pp.834-875, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01195478

M. Kanehisa, S. Goto, Y. Sato, M. Kawashima, M. Furumichi et al., Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res, vol.42, pp.199-205, 2014.

T. Tatusova, S. Ciufo, B. Fedorov, K. O'neill, and I. Tolstoy, RefSeq microbial genomes database: new representation and annotation strategy, Nucleic Acids Res, vol.42, pp.553-562, 2014.

L. I. Lin, A concordance correlation coefficient to evaluate reproducibility, Biometrics, vol.45, issue.1, pp.255-68, 1989.

Y. Darzi, G. Falony, S. Vieira-silva, and J. Raes, Towards biome-specific analysis of meta-omics data, ISME J, vol.10, issue.5, pp.1025-1033, 2016.

L. W. Hugerth and A. F. Andersson, Analysing microbial community composition through amplicon sequencing: from sampling to hypothesis testing, Front Microbiol, vol.8, p.1561, 2017.

J. Oksanen, F. Blanchet, and M. Friendly, Community Ecology Package. R package version 2.5-6, 2019.

Y. Xia, J. Sun, and D. Chen, Statistical analysis of microbiome data with R, 2018.

W. Haynes, W. Benjamini-hochberg-method-;-dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Encyclopedia of systems biology, p.78, 2013.

I. Quercia, R. Dutia, D. P. Kotler, S. Belsley, and . Laferr, Gastrointestinal changes after bariatric surgery, Diabetes Metab, vol.40, issue.2, pp.87-94, 2014.

F. L. Paganelli, M. Luyer, and C. M. Hazelbag, Roux-Y gastric bypass and sleeve gastrectomy directly change gut microbiota composition independent of surgery type, Sci Rep, vol.9, issue.1, p.10979, 2019.

E. H. Crost, L. E. Tailford, and M. Monestier, The mucin-degradation strategy of Ruminococcus gnavus: the importance of intramolecular trans-sialidases, Gut Microbes, vol.7, issue.4, pp.302-314, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01439896

H. Celiker, A new proposed mechanism of action for gastric bypass surgery: air hypothesis, Med Hypotheses, vol.107, pp.81-90, 2017.

A. L. Hartman, D. M. Lough, and D. K. Barupal, Human gut microbiome adopts an alternative state following small bowel transplantation, Proc Natl Acad U S A, vol.106, issue.40, pp.17187-92, 2009.

M. Tiso and A. N. Schechter, Nitrate reduction to nitrite, nitric oxide and ammonia by gut bacteria under physiological conditions, PLoS One, vol.10, issue.3, p.119712, 2015.

S. E. Winter, M. G. Winter, and M. N. Xavier, Host-derived nitrate boosts growth of E. coli in the inflamed gut, Science, vol.339, issue.6120, pp.708-719, 2013.

L. Hoyles, J. Enez-pranteda, M. L. Chilloux, and J. , Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota, Microbiome, vol.6, issue.1, p.73, 2018.

H. V. Lin, A. Frassetto, K. Jr, and E. J. , Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms, PLoS One, vol.7, issue.4, p.35240, 2012.

P. Jirapinyo, D. X. Jin, T. Qazi, N. Mishra, and C. C. Thompson, A Meta-analysis of GLP-1 after Roux-en-Y gastric bypass: impact of surgical technique and measurement strategy, Obes Surg, vol.28, issue.3, pp.615-641, 2018.

E. S. Chambers, A. Viardot, and A. Psichas, Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults, Gut, vol.64, issue.11, pp.1744-54, 2015.

J. Breton, N. Tennoune, and N. Lucas, Gut commensal E. coli proteins activate host satiety pathways following nutrient-induced bacterial growth, Cell Metab, vol.23, issue.2, pp.324-358, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01397996