E. Angelakis, F. Armougom, M. Million, and D. Raoult, The relationship between gut microbiota and weight gain in humans, Future Microbiology, vol.299, issue.1, pp.91-109, 2012.
DOI : 10.1002/9780470743386

M. Million, E. Angelakis, F. Drissi, and D. Raoult, Occam's razor and probiotics activity on Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.109, issue.38, p.1, 2013.
DOI : 10.1073/pnas.1205147109

URL : http://www.pnas.org/content/110/1/E1.full.pdf

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

D. Raoult, Human microbiome: take-home lesson on growth promoters?, Nature, vol.453, issue.7205, pp.690-691, 2008.
DOI : 10.1038/454690c

URL : http://www.nature.com/nature/journal/v454/n7205/pdf/454690c.pdf

I. Trehan, H. Goldbach, L. Lagrone, G. Meuli, R. Wang et al., Antibiotics as Part of the Management of Severe Acute Malnutrition, New England Journal of Medicine, vol.368, issue.5, pp.425-435, 2013.
DOI : 10.1056/NEJMoa1202851

T. Ajslev, C. Andersen, M. Gamborg, T. Sorensen, and J. T. , Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics, International Journal of Obesity, vol.64, issue.4, pp.522-529, 2011.
DOI : 10.1016/j.jaci.2006.12.608

K. Ray, Adding weight to the microbiota's role in obesity???exposure to antibiotics early in life can lead to increased adiposity, Nature Reviews Gastroenterology & Hepatology, vol.9, issue.11, p.615, 2012.
DOI : 10.1038/nrgastro.2012.175

F. Thuny, H. Richet, J. Casalta, E. Angelakis, G. Habib et al., Vancomycin Treatment of Infective Endocarditis Is Linked with Recently Acquired Obesity, PLoS ONE, vol.5, issue.2, p.9074, 2010.
DOI : 10.1371/journal.pone.0009074.t003

I. Cho, S. Yamanishi, L. Cox, B. Methe, J. Zavadil et al., Antibiotics in early life alter the murine colonic microbiome and adiposity, Nature, vol.20, issue.7413, pp.621-626, 2012.
DOI : 10.1002/bmc.580

E. Stokstad, Antibiotics in Animal Nutrition, Physiological Reviews, vol.34, issue.1, pp.25-51, 1954.
DOI : 10.1152/physrev.1954.34.1.25

M. Smith, T. Yatsunenko, M. Manary, I. Trehan, R. Mkakosya et al., Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor, Science, vol.6, issue.2, pp.548-554, 2013.
DOI : 10.1159/000198931

E. Angelakis, D. Bastelica, A. Ben, F. El, 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

M. Miyoshi, A. Ogawa, S. Higurashi, and Y. Kadooka, Anti-obesity effect of Lactobacillus gasseri SBT2055 accompanied by inhibition of pro-inflammatory gene expression in the visceral adipose tissue in diet-induced obese mice, European Journal of Nutrition, vol.66, issue.Suppl 3, 2013.
DOI : 10.1203/PDR.0b013e3181aabd4f

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

M. Million, E. Angelakis, M. Paul, F. Armougom, L. Leibovici et al., Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals, Microbial Pathogenesis, vol.53, issue.2, pp.100-108, 2012.
DOI : 10.1016/j.micpath.2012.05.007

URL : https://hal.archives-ouvertes.fr/hal-01773004

J. Stsepetova, E. Sepp, H. Kolk, K. Loivukene, E. Songisepp et al., Diversity and metabolic impact of intestinal Lactobacillus species in healthy adults and the elderly, British Journal of Nutrition, vol.47, issue.08, pp.1235-1244, 2011.
DOI : 10.1016/j.nut.2006.09.002

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.77, issue.3, pp.201-214, 2012.
DOI : 10.1038/ismej.2010.118

H. Flint, K. Scott, P. Louis, and S. Duncan, The role of the gut microbiota in nutrition and health, Nature Reviews Gastroenterology & Hepatology, vol.1, issue.10, pp.577-589, 2012.
DOI : 10.3920/BM2009.0027

E. Kaoutari, A. Armougom, F. Gordon, J. Raoult, D. Henrissat et al., The abundance and variety of carbohydrate-active enzymes in the human gut microbiota, Nature Reviews Microbiology, vol.6, issue.7, pp.497-504, 2013.
DOI : 10.1038/ismej.2012.4

C. Canchaya, M. Claesson, G. Fitzgerald, D. Van-sinderen, O. Toole et al., Diversity of the genus Lactobacillus revealed by comparative genomics of five species, Microbiology, vol.152, issue.11, pp.3185-3196, 2006.
DOI : 10.1099/mic.0.29140-0

O. Lukjancenko, D. Ussery, and T. Wassenaar, Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera, Microbial Ecology, vol.59, issue.Suppl 2, pp.651-673, 2012.
DOI : 10.1007/s00248-009-9596-7

A. Darling, B. Mau, and N. Perna, progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement, PLoS ONE, vol.15, issue.6, p.11147, 2010.
DOI : 10.1371/journal.pone.0011147.s005

URL : https://doi.org/10.1371/journal.pone.0011147

R. Aziz, D. Bartels, A. Best, M. Dejongh, T. Disz et al., The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, issue.1, p.75, 2008.
DOI : 10.1186/1471-2164-9-75

M. Ashburner, C. Ball, J. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1091/mbc.9.12.3273

H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono et al., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.26, issue.1, pp.29-34, 1999.
DOI : 10.1093/nar/26.1.38

L. Johnson, S. Eddy, and E. Portugaly, Hidden Markov model speed heuristic and iterative HMM search procedure, BMC Bioinformatics, vol.11, issue.1, p.431, 2010.
DOI : 10.1186/1471-2105-11-431

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-431?site=bmcbioinformatics.biomedcentral.com

T. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98NT, Nucleic Acids Symp Ser, vol.41, pp.95-98, 1999.

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.141, issue.3, pp.2731-2739, 2011.
DOI : 10.1007/BF00160154

V. Merhej, F. Armougom, C. Robert, and D. Raoult, Genome Sequence of Lactobacillus ingluviei, a Bacterium Associated with Weight Gain in Animals, Journal of Bacteriology, vol.194, issue.20, p.5697, 2012.
DOI : 10.1128/JB.01205-12

P. Hoffee and E. Englesberg, EFFECT OF METABOLIC ACTIVITY OF THE GLUCOSE PERMEASE OF BACTERIAL CELLS, Proceedings of the National Academy of Sciences, vol.48, issue.10, pp.1759-1765, 1962.
DOI : 10.1073/pnas.48.10.1759

D. Ollis, E. Cheah, M. Cygler, B. Dijkstra, F. Frolow et al., hydrolase fold, "Protein Engineering, Design and Selection", vol.5, issue.3, pp.197-211, 1992.
DOI : 10.1093/protein/5.3.197

URL : https://www.rug.nl/research/portal/files/3321987/1992ProteinEngOllis.pdf

K. Makarova, A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin et al., Comparative genomics of the lactic acid bacteria, Proceedings of the National Academy of Sciences, vol.29, issue.1, pp.15611-15616, 2006.
DOI : 10.1093/nar/29.1.22

T. Smokvina, M. Wels, J. Polka, C. Chervaux, S. Brisse et al., Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity, PLoS ONE, vol.1694, issue.7, p.68731, 2013.
DOI : 10.1371/journal.pone.0068731.s008

F. Douillard, A. Ribbera, R. Kant, T. Pietila, H. Jarvinen et al., Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG, PLoS Genetics, vol.42, issue.1, p.1003683, 2013.
DOI : 10.1371/journal.pgen.1003683.s010

S. Tomita, T. Irisawa, N. Tanaka, T. Nukada, E. Satoh et al., Strains, Bioscience, Biotechnology, and Biochemistry, vol.74, issue.5, pp.928-933, 2010.
DOI : 10.1271/bbb.90736

URL : https://hal.archives-ouvertes.fr/hal-00790870

S. Wakabayashi and Y. Hashii, Food and sugar preparation containing indigestable dextrin, Japanese Patent EP0582518 A2, 1994.

J. Vogt, K. Ishii-schrade, P. Pencharz, P. Jones, and T. Wolever, L-Rhamnose and Lactulose Decrease Serum Triacylglycerols and Their Rates of Synthesis, but Do Not Affect Serum Cholesterol Concentrations in Men, The Journal of Nutrition, vol.31, issue.8, pp.2160-2166, 2006.
DOI : 10.1139/y91-242

H. Yamashita, K. Fujisawa, E. Ito, S. Idei, N. Kawaguchi et al., Improvement of Obesity and Glucose Tolerance by Acetate in Type 2 Diabetic Otsuka Long-Evans Tokushima Fatty (OLETF) Rats, Bioscience, Biotechnology, and Biochemistry, vol.71, issue.5, pp.1236-1243, 2007.
DOI : 10.1271/bbb.60668

A. Fernandez-sanchez, E. Madrigal-santillan, M. Bautista, J. Esquivel-soto, A. Morales-gonzalez et al., Inflammation, Oxidative Stress, and Obesity, International Journal of Molecular Sciences, vol.292, issue.Suppl., pp.3117-3132, 2011.
DOI : 10.1152/ajpheart.00628.2006

A. Haapalainen, G. Merilainen, and R. Wierenga, The thiolase superfamily: condensing enzymes with diverse reaction specificities, Trends in Biochemical Sciences, vol.31, issue.1, pp.64-71, 2006.
DOI : 10.1016/j.tibs.2005.11.011

P. Maljaars, H. Peters, D. Mela, and A. Masclee, Ileal brake: A sensible food target for appetite control. A review, Physiology & Behavior, vol.95, issue.3, pp.271-281, 2008.
DOI : 10.1016/j.physbeh.2008.07.018

A. Servin, Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens, FEMS Microbiology Reviews, vol.28, issue.4, pp.405-440, 2004.
DOI : 10.1271/bbb.64.2706

C. Archambaud, M. Nahori, G. Soubigou, C. Becavin, L. Laval et al., Impact of lactobacilli on orally acquired listeriosis, Proceedings of the National Academy of Sciences, vol.19, issue.2, pp.16684-16689, 2012.
DOI : 10.1093/bioinformatics/19.2.185

URL : https://hal.archives-ouvertes.fr/hal-01003361

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 : 10.4319/lo.1997.42.3.0487

G. Musso, R. Gambino, and M. Cassader, Obesity, Diabetes, and Gut Microbiota: The hygiene hypothesis expanded?, Diabetes Care, vol.33, issue.10, pp.2277-2284, 2010.
DOI : 10.2337/dc10-0556

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.5, issue.10, pp.11070-11075, 2005.
DOI : 10.1016/S1074-5521(98)90108-9

URL : http://www.pnas.org/content/102/31/11070.full.pdf

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 : 10.3168/jds.S0022-0302(02)74164-7