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

M. Dalamaga, Obesity, insulin resistance, adipocytokines and breast cancer: New biomarkers and attractive therapeutic targets, World J Exp Med, vol.3, pp.34-42, 2013.

C. Apovian, The clinical and economic consequences of obesity, Am J Manag Care, vol.19, pp.219-228, 2013.

L. David, C. Maurice, R. Carmody, D. Gootenberg, J. Button et al., Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.24, issue.7484, pp.559-563, 2014.
DOI : 10.1111/j.1365-294X.1993.tb00005.x

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

A. Cotillard, S. Kennedy, L. Kong, E. Prifti, N. Pons et al., Dietary intervention impact on gut microbial gene richness, Nature, vol.27, issue.7464, pp.585-588, 2013.
DOI : 10.1038/nature12480

URL : https://hal.archives-ouvertes.fr/hal-01001543

M. Million, F. Thuny, E. Angelakis, J. Casalta, R. Giorgi et al., Lactobacillus reuteri and Escherichia coli in the human gut microbiota may predict weight gain associated with vancomycin treatment, Nutrition & Diabetes, vol.65, issue.9, p.87, 2013.
DOI : 10.1126/science.1233521

L. Chatelier, E. Nielsen, T. Qin, J. Prifti, E. Hildebrand et al., Richness of human gut microbiome correlates with metabolic markers, Nature, vol.40, issue.7464, pp.541-546, 2013.
DOI : 10.1038/nature12506

URL : https://hal.archives-ouvertes.fr/hal-01190602

D. Filippo, C. Cavalieri, D. Di, P. Ramazzotti, M. Poullet et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proceedings of the National Academy of Sciences, vol.107, issue.33, pp.14691-14696, 2010.
DOI : 10.1073/pnas.1005963107

C. Lozupone, J. Stombaugh, A. Gonzalez, G. Ackermann, D. Wendel et al., Meta-analyses of studies of the human microbiota, Genome Research, vol.23, issue.10, pp.1704-1714, 2013.
DOI : 10.1101/gr.151803.112

M. Arumugam, J. Raes, E. Pelletier, L. Paslier, D. Yamada et al., Enterotypes of the human gut microbiome, Nature, vol.106, issue.7346, pp.174-180, 2011.
DOI : 10.1038/nature09944

URL : https://hal.archives-ouvertes.fr/cea-00903625

A. Al-othaimeen, M. Nozha, and A. Osman, Obesity: an emerging problem in Saudi Arabia Analysis of data from the National Nutrition Survey, East Mediterr Health J, vol.13, pp.441-448, 2007.

M. Alokail, N. Daghri, O. Al-attas, and T. Hussain, Combined effects of obesity and type 2 diabetes contribute to increased breast cancer risk in premenopausal women, Cardiovascular Diabetology, vol.8, issue.1, p.33, 2009.
DOI : 10.1186/1475-2840-8-33

I. Diouf, M. Charles, P. Ducimetiere, A. Basdevant, E. Eschwege et al., Evolution of Obesity Prevalence in France, Epidemiology, vol.21, issue.3, pp.360-365, 2010.
DOI : 10.1097/EDE.0b013e3181d5bff5

URL : https://hal.archives-ouvertes.fr/inserm-00559257

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

E. Zoetendal, C. Booijink, E. Klaassens, H. Heilig, M. Kleerebezem et al., Isolation of RNA from bacterial samples of the human gastrointestinal tract, Nature Protocols, vol.33, issue.2, pp.954-959, 2006.
DOI : 10.1016/S0167-7012(03)00121-0

A. Masella, A. Bartram, J. Truszkowski, D. Brown, J. Neufeld et al., PANDAseq: paired-end assembler for illumina sequences, BMC Bioinformatics, vol.13, issue.1, pp.31-1002742, 2012.
DOI : 10.1093/bioinformatics/btl158

T. Stoeck, A. Behnke, R. Christen, L. Amaral-zettler, M. Rodriguez-mora et al., Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities, BMC Biology, vol.7, issue.1, p.72, 2009.
DOI : 10.1186/1741-7007-7-72

URL : https://hal.archives-ouvertes.fr/hal-00484166

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 Research, vol.41, issue.D1, pp.590-596, 2013.
DOI : 10.1093/nar/gks1219

A. Chao and T. Shen, Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample, Environmental and Ecological Statistics, vol.10, issue.4, pp.429-443, 2003.
DOI : 10.1023/A:1026096204727

J. Escobar, B. Klotz, B. Valdes, and G. Agudelo, The gut microbiota of Colombians differs from that of Americans, Europeans and Asians, BMC Microbiology, vol.63, issue.1, p.311, 2014.
DOI : 10.1186/s12866-014-0311-6

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

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, p.7125, 2009.
DOI : 10.1371/journal.pone.0007125.s001

H. Zuo, Z. Xie, W. Zhang, Y. Li, W. Wang et al., Gut bacteria alteration in obese people and its relationship with gene polymorphism, World Journal of Gastroenterology, vol.17, issue.8, pp.1076-1081, 2011.
DOI : 10.3748/wjg.v17.i8.1076

M. Smith, T. Yatsunenko, M. Manary, I. Trehan, R. Mkakosya et al., Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor, Science, vol.339, issue.6119, pp.548-554, 2013.
DOI : 10.1126/science.1229000

M. Collado, E. Isolauri, K. Laitinen, and S. Salminen, Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women, Am J Clin Nutr, vol.88, pp.894-899, 2008.

A. Schwiertz, D. Taras, K. Schafer, S. Beijer, N. Bos et al., Microbiota and SCFA in Lean and Overweight Healthy Subjects, Obesity, vol.57, issue.1 Suppl, pp.190-195, 2010.
DOI : 10.1038/oby.2009.167

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

I. Nadal, A. Santacruz, M. A. Warnberg, J. Garagorri, M. Moreno et al., Shifts in clostridia, bacteroides and immunoglobulin-coating fecal bacteria associated with weight loss in obese adolescents, International Journal of Obesity, vol.61, issue.7, pp.758-767, 2009.
DOI : 10.1079/BJN20041114

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

S. Macfarlane and G. Macfarlane, Bacterial Diversity in the Human Gut, Adv Appl Microbiol, vol.54, pp.261-289, 2004.
DOI : 10.1016/S0065-2164(04)54010-8

A. Scupham, Succession in the intestinal microbiota of preadolescent turkeys, FEMS Microbiology Ecology, vol.60, issue.1, pp.136-147, 2007.
DOI : 10.1111/j.1574-6941.2006.00245.x

G. Henderson, F. Cox, S. Kittelmann, V. Miri, M. Zethof et al., Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities, PLoS ONE, vol.6, issue.9, p.74787, 2013.
DOI : 10.1371/journal.pone.0074787.s009

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

D. Saulnier, J. Spinler, G. Gibson, and J. Versalovic, Mechanisms of probiosis and prebiosis: considerations for enhanced functional foods, Current Opinion in Biotechnology, vol.20, issue.2, pp.135-141, 2009.
DOI : 10.1016/j.copbio.2009.01.002

E. Angelakis, M. Million, M. Henry, and D. Raoult, Rapid and Accurate Bacterial Identification in Probiotics and Yoghurts by MALDI-TOF Mass Spectrometry, Journal of Food Science, vol.85, issue.Suppl 2, pp.568-572, 2011.
DOI : 10.1111/j.1750-3841.2011.02369.x

E. Angelakis, D. Bastelica, B. Amara, A. Filali, A. Dutour et al., An evaluation of the effects of Lactobacillus ingluviei on body weight, the intestinal microbiome and metabolism in mice, Microbial Pathogenesis, vol.52, issue.1, pp.61-68, 2012.
DOI : 10.1016/j.micpath.2011.10.004

F. Drissi, V. Merhej, E. Angelakis, E. Kaoutari, A. Carriere et al., Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection, Nutrition & Diabetes, vol.136, issue.2, p.109, 2014.
DOI : 10.1111/j.1750-3841.2011.02369.x

F. Fak and F. Backhed, Lactobacillus reuteri Prevents Diet-Induced Obesity, but not Atherosclerosis, in a Strain Dependent Fashion in Apoe???/??? Mice, PLoS ONE, vol.7, issue.10, p.46837, 2012.
DOI : 10.1371/journal.pone.0046837.t002

F. Karlsson, V. Tremaroli, I. Nookaew, G. Bergstrom, C. Behre et al., Gut metagenome in European women with normal, impaired and diabetic glucose control, Nature, vol.35, issue.7452, pp.99-103, 2013.
DOI : 10.1038/nature12198

A. Al-rethaiaa, A. Fahmy, and N. Shwaiyat, Obesity and eating habits among college students in Saudi Arabia: a cross sectional study, Nutrition Journal, vol.50, issue.Suppl 1, p.39, 2010.
DOI : 10.1016/j.appet.2007.09.014

S. Washi and M. Ageib, Poor diet quality and food habits are related to impaired nutritional status in 13- to 18-year-old adolescents in Jeddah, Nutrition Research, vol.30, issue.8, pp.527-534, 2010.
DOI : 10.1016/j.nutres.2010.07.002

P. Turnbaugh, V. Ridaura, J. Faith, F. Rey, R. Knight et al., The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice, Science Translational Medicine, vol.1, issue.6, pp.6-14, 2009.
DOI : 10.1126/scitranslmed.3000322

R. Ley, M. Hamady, C. Lozupone, P. Turnbaugh, R. Ramey et al., Evolution of Mammals and Their Gut Microbes, Science, vol.320, issue.5883, pp.1647-1651, 2008.
DOI : 10.1126/science.1155725

T. Yatsunenko, F. Rey, M. Manary, I. Trehan, M. Dominguez-bello et al., Human gut microbiome viewed across age and geography, Nature, vol.2, pp.222-227, 2012.
DOI : 10.1038/nature11053

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376388

S. Schnorr, M. Candela, S. Rampelli, M. Centanni, C. Consolandi et al., Gut microbiome of the Hadza hunter-gatherers, Nature Communications, vol.26, p.3654, 2014.
DOI : 10.1002/ajpa.21040