E. Angelakis, F. Armougom, M. Million, and D. Raoult, The relationship between gut microbiota and weight gain in humans, Future Microbiology, vol.7, issue.1, pp.91-109, 2012.
DOI : 10.2217/fmb.11.142

E. Angelakis, V. Merhej, and D. Raoult, Related actions of probiotics and antibiotics on gut microbiota and weight modification, The Lancet Infectious Diseases, vol.13, issue.10, pp.889-899, 2013.
DOI : 10.1016/S1473-3099(13)70179-8

J. Aron-wisnewsky, J. Dore, and K. Clement, The importance of the gut microbiota after bariatric surgery, Nature Reviews Gastroenterology & Hepatology, vol.45, issue.10, p.22926153, 2012.
DOI : 10.1038/nrgastro.2012.161

P. Cotter, Small intestine and microbiota, Current Opinion in Gastroenterology, vol.27, issue.2, pp.99-105, 2011.
DOI : 10.1097/MOG.0b013e328341dc67

R. Krajmalnik-brown, Z. Ilhan, D. Kang, and J. Dibaise, Effects of Gut Microbes on Nutrient Absorption and Energy Regulation, Nutrition in Clinical Practice, vol.5, issue.2, pp.201-214, 2012.
DOI : 10.1111/j.1365-2362.2011.02590.x

K. El, F. Armougom, J. 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.

J. Lagier, M. Million, P. Hugon, F. Armougom, and D. Raoult, Human Gut Microbiota: Repertoire and Variations, Frontiers in Cellular and Infection Microbiology, vol.2, p.23130351, 2012.
DOI : 10.3389/fcimb.2012.00136

M. Yasir, E. Angelakis, F. Bibi, E. Azhar, D. Bachar et al., Comparison of the gut microbiota of people in France and Saudi Arabia, Nutrition & Diabetes, vol.486, issue.4, p.25915742, 2015.
DOI : 10.1038/ncomms4654

URL : https://hal.archives-ouvertes.fr/hal-01216407

M. Wang, S. Ahrne, B. Jeppsson, and G. Molin, Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes, FEMS Microbiology Ecology, vol.54, issue.2, pp.219-231, 2005.
DOI : 10.1016/j.femsec.2005.03.012

E. Zoetendal, J. Raes, B. Van-den-bogert, M. Arumugam, C. Booijink et al., The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates, The ISME Journal, vol.128, issue.7, pp.1415-1426, 2012.
DOI : 10.1136/gut.2007.133603

F. Carriere, C. Renou, S. Ransac, V. Lopez, D. Caro et al., Inhibition of gastrointestinal lipolysis by Orlistat during digestion of test meals in healthy volunteers, Am J Physiol Gastrointest Liver Physiol, vol.281, pp.16-28, 2001.

G. Dubourg, J. Lagier, F. Armougom, C. Robert, I. Hamad et al., The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics, European Journal of Clinical Microbiology & Infectious Diseases, vol.8, issue.Suppl 4, pp.637-645, 2013.
DOI : 10.1007/s10096-012-1787-3

G. Dubourg, J. Lagier, F. Armougom, C. Robert, G. Audoly et al., High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment, International Journal of Antimicrobial Agents, vol.41, issue.2, pp.149-155, 2013.
DOI : 10.1016/j.ijantimicag.2012.10.012

J. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. Bushman et al., QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

Q. Wang, G. Garrity, J. Tiedje, and J. Cole, Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, vol.73, issue.16, pp.5261-5267, 2007.
DOI : 10.1128/AEM.00062-07

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

A. Masella, A. Bartram, J. Truszkowski, D. Brown, and J. Neufeld, PANDAseq: paired-end assembler for illumina sequences, BMC Bioinformatics, vol.13, issue.1, pp.31-22333067, 2012.
DOI : 10.1093/bioinformatics/btl158

K. Grant, I. Belandia, N. Dekker, P. Richardson, and S. Park, Molecular characterization of pldA, the structural gene for a phospholipase A from Campylobacter coli, and its contribution to cell-associated hemolysis, Infect Immun, vol.65, pp.1172-1180, 1997.

N. Dorrell, M. Martino, R. Stabler, S. Ward, Z. Zhang et al., Characterization of Helicobacter pylori PldA, a phospholipase with a role in colonization of the gastric mucosa, Gastroenterology, vol.117, issue.5, pp.1098-1104, 1999.
DOI : 10.1016/S0016-5085(99)70394-X

P. Hugon, J. Lagier, C. Robert, C. Lepolard, L. Papazian et al., Molecular Studies Neglect Apparently Gram-Negative Populations in the Human Gut Microbiota, Journal of Clinical Microbiology, vol.51, issue.10, pp.3286-3293, 2013.
DOI : 10.1128/JCM.00473-13

URL : https://hal.archives-ouvertes.fr/hal-00964198

H. Zhang, J. Dibaise, A. Zuccolo, D. Kudrna, M. Braidotti et al., Human gut microbiota in obesity and after gastric bypass, Proceedings of the National Academy of Sciences, vol.106, issue.7, pp.2365-2370, 2009.
DOI : 10.1073/pnas.0812600106

F. Armougom, M. Henry, B. Vialettes, D. Raccah, and D. Raoult, Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients, PLoS ONE, vol.105, issue.9, 2009.
DOI : 10.1371/journal.pone.0007125.s001

M. Hattori and T. Taylor, The Human Intestinal Microbiome: A New Frontier of Human Biology, DNA Research, vol.16, issue.1, 2009.
DOI : 10.1093/dnares/dsn033

J. Qin, R. Li, J. Raes, M. Arumugam, K. Burgdorf et al., A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.59-65, 2010.
DOI : 10.1038/nature08821

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

L. Roesch, G. Casella, O. Simell, J. Krischer, C. Wasserfall et al., Influence of Fecal Sample Storage on Bacterial Community Diversity, The Open Microbiology Journal, vol.3, issue.1, pp.40-46, 2009.
DOI : 10.2174/1874285800903010040

C. Lauber, N. Zhou, J. Gordon, R. Knight, and N. Fierer, Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples, FEMS Microbiology Letters, vol.307, issue.1, pp.80-86, 2010.
DOI : 10.1111/j.1574-6968.2010.01965.x

I. Carroll, T. Ringel-kulka, J. Siddle, T. Klaenhammer, and Y. Ringel, Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage, PLoS ONE, vol.7, issue.10, p.23071673, 2012.
DOI : 10.1371/journal.pone.0046953.t001

M. Derrien, M. Van-passel, J. Van-de-bovenkamp, R. Schipper, W. De-vos et al., Mucin-bacterial interactions in the human oral cavity and digestive tract, Gut Microbes, vol.56, issue.4, pp.254-268, 2010.
DOI : 10.4161/gmic.1.4.12778

E. Barrett, C. Guinane, C. Ryan, E. Dempsey, B. Murphy et al., Microbiota diversity and stability of the preterm neonatal ileum and colon of two infants, MicrobiologyOpen, vol.1, issue.2, pp.215-225, 2013.
DOI : 10.1002/mbo3.64

P. Turnbaugh, M. Hamady, T. Yatsunenko, B. Cantarel, A. Duncan et al., A core gut microbiome in obese and lean twins, Nature, vol.8, issue.7228, pp.480-484, 2009.
DOI : 10.1038/nature07540

R. Ley, P. Turnbaugh, S. Klein, and J. Gordon, Microbial ecology: Human gut microbes associated with obesity, Nature, vol.308, issue.7122, pp.1022-1023, 2006.
DOI : 10.1038/4441022a

R. Ley, F. Backhed, P. Turnbaugh, C. Lozupone, R. Knight et al., Obesity alters gut microbial ecology, Proceedings of the National Academy of Sciences, vol.102, issue.31, pp.11070-11075, 2005.
DOI : 10.1073/pnas.0504978102

M. Murri, I. Leiva, J. Gomez-zumaquero, F. Tinahones, F. Cardona et al., Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study, BMC Medicine, vol.60, issue.1, p.23433344, 2013.
DOI : 10.1371/journal.pone.0035240

A. Audet, G. Nantel, and P. Proulx, Phospholipase a activity in growing Eacherichia coli cells, Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, vol.348, issue.3, pp.334-343, 1974.
DOI : 10.1016/0005-2760(74)90213-6

N. Bakala, J. Goma, S. Amara, K. Dridi, V. Jannin et al., Understanding the lipid-digestion processes in the GI tract before designing lipid-based drug-delivery systems, Ther Deliv, vol.3, pp.105-124, 2012.

F. Laugerette, M. Alligier, J. Bastard, J. Drai, E. Chanseaume et al., Overfeeding increases postprandial endotoxemia in men: Inflammatory outcome may depend on LPS transporters LBP and sCD14, Molecular Nutrition & Food Research, vol.9, issue.7, pp.1513-1518, 2014.
DOI : 10.1002/mnfr.201400044

M. Herieka and C. Erridge, High-fat meal induced postprandial inflammation, Molecular Nutrition & Food Research, vol.53, issue.1, pp.136-146, 2014.
DOI : 10.1002/mnfr.201300104

A. Moreira, T. Texeira, A. Ferreira, M. Peluzio, and R. Alfenas, Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia, British Journal of Nutrition, vol.81, issue.05, pp.801-809, 2012.
DOI : 10.1023/B:DDAS.0000026302.92898.ae

P. Hildebrand, C. Petrig, B. Burckhardt, S. Ketterer, H. Lengsfeld et al., Hydrolysis of dietary fat by pancreatic lipase stimulates cholecystokinin release, Gastroenterology, vol.114, issue.1, pp.123-129, 1998.
DOI : 10.1016/S0016-5085(98)70640-7

D. Cummings and J. Overduin, Gastrointestinal regulation of food intake, Journal of Clinical Investigation, vol.117, issue.1, pp.13-23, 2007.
DOI : 10.1172/JCI30227

D. Breen, B. Rasmussen, C. Cote, V. Jackson, and T. Lam, Nutrient-Sensing Mechanisms in the Gut as Therapeutic Targets for Diabetes, Diabetes, vol.62, issue.9, pp.3005-3013, 2013.
DOI : 10.2337/db13-0523

T. Lam, Neuronal regulation of homeostasis by nutrient sensing, Nature Medicine, vol.13, issue.4, pp.392-395, 2010.
DOI : 10.1038/nm0410-392