M. Blaut, M. D. Collins, G. W. Welling, J. Dore, J. Van-loo et al., Molecular biological methods for studying the gut microbiota: the EU human gut flora project, Br J Nutr, vol.87, issue.2, pp.203-214, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02675095

D. C. Savage, Microbial ecology of the gastrointestinal tract, Annu Rev Microbiol, vol.31, pp.107-133, 1977.

E. G. Zoetendal, C. T. Collier, S. Koike, R. I. Mackie, and H. R. Gaskins, Molecular ecological analysis of the gastrointestinal microbiota: a review, J Nutr, vol.134, pp.465-472, 2004.

P. B. Eckburg, E. M. Bik, C. N. Berstein, E. Purdom, L. Dethlefsen et al., Diversity of the human intestinal microbial flora, Science, vol.308, pp.1635-1638, 2005.

C. Manichanh, L. Rigottier-gois, E. Bonnaud, K. Gloux, E. Pelletier et al., Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach, Gut, vol.55, pp.205-211, 2006.

C. Lay, M. Sutren, V. Rochet, K. Saunier, J. Doré et al., Design and validation of 16S rDNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota, Environ Microbiol, vol.7, pp.933-946, 2005.

R. E. Ley, P. Turnbaugh, S. Klein, and J. I. Gordon, Microbial ecology: human gut microbes associated with obesity, Nature, vol.444, pp.1022-1023, 2006.

H. J. Harmsen, G. C. Raangs, T. He, J. F. Degener, and G. W. Welling, Extensive set of 16S rRNA-based probes for detection of bacteria in human feces, Appl Environ Microbiol, vol.68, pp.2982-2990, 2002.

C. Palmer, E. M. Bik, D. B. Digiulio, D. A. Relman, and P. O. Brown, Development of the human infant intestinal microbiota, PLoS Biol, vol.5, issue.7, p.117, 2007.

F. Bäckhed, R. E. Ley, J. L. Sonnenburg, D. A. Peterson, and J. L. Gordon, Hostbacterial mutualism in the human intestine, Science, vol.307, pp.1915-1920, 2005.

A. J. Macpherson and N. L. Harris, Interactions between commensal intestinal bacteria and the immune system, Nat Rev Immunol, vol.4, pp.478-485, 2004.

A. M. Mowat, Anatomical basis of tolerance and immunity to intestinal antigens, Nat Rev Immunol, vol.3, issue.4, pp.331-372, 2003.

A. H. Franks, H. J. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut et al., Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes, Appl Environ Microbiol, vol.64, pp.3336-3345, 1998.

X. Hébuterne, Gut changes attributed to ageing: effects on intestinal microflora, Curr Opin Clin Nutr Metab Care, vol.6, pp.49-54, 2003.

M. J. Hopkins and G. T. Macfarlane, Changes in predominant bacterial populations in human faeces with age and with Clostridium difficile infection, J Med Microbiol, vol.51, pp.448-454, 2002.

S. P. Van-tongeren, J. Slaets, H. Harmsen, and G. W. Welling, Fecal microbiota composition and frailty, Appl Environ Microbiol, vol.71, pp.6438-6442, 2005.

E. J. Woodmansey, Intestinal bacteria and ageing, J Appl Microbiol, vol.102, pp.1178-1186, 2007.

K. Saunier and J. Doré, Gastrointestinal tract and the elderly: functional foods, gut microflora and healthy ageing. Dig Liver Dis, vol.34, pp.19-24, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02671454

M. J. Hopkins, R. Sharp, and G. T. Macfarlane, Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles, Gut, vol.48, pp.198-205, 2001.

J. P. Furet, O. Firmesse, M. Gourmelon, C. Bridonneau, J. Tap et al., Comparative assessment of human and farm animal fecal microbiota using real-time quantitative PCR, FEMS Microbiol Ecol, vol.68, pp.351-362, 2009.

L. Rigottier-gois, A. Bourhis, G. Gramet, V. Rochet, and J. Doré, Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes, FEMS Microbiol Ecol, vol.43, pp.237-245, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02675094

H. Hayashi, M. Sakamoto, and Y. Benno, Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods, Microbiol Immunol, vol.46, pp.535-548, 2002.

S. Salminen and E. Isolauri, Intestinal colonization, microbiota and probiotics, J Pediatr, vol.149, pp.115-120, 2006.

M. Haarman and J. Knol, Quantitative real-time PCR analysis of fecal Lactobacillus species in infants receiving a prebiotic infant formula, Appl Environ Microbiol, vol.72, issue.4, pp.2359-65, 2006.

H. J. Harmsen, A. C. Wildeboer-veloo, G. C. Raangs, A. A. Wagendorp, N. Klijn et al., Analysis of intestinal microflora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J Pediatr Gastroenterol Nutr, vol.30, issue.1, pp.61-68, 2000.

S. Bartosch, A. Fite, G. T. Macfarlane, and M. E. Mcmurdo, Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota, Appl Environ Microbiol, vol.70, pp.3575-3581, 2004.

H. Hayashi, M. Sakamoto, M. Kitahara, and Y. Benno, Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP, Microbiol Immunol, vol.47, pp.557-570, 2003.

F. He, A. C. Ouwehand, E. Isolauri, M. Hosoda, Y. Benno et al., Differences in composition and mucosal adhesion of bifidobacteria isolated from healthy adults and healthy seniors, Curr Microbiol, vol.43, pp.351-354, 2001.

J. J. Godon, E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta, Molecular microbial diversity of an anaerobic digestor as determined by small-unit rDNA sequence analysis, Appl Environ Microbiol, vol.63, pp.2802-2813, 1997.

C. Lay, L. Rigottier-gois, K. Holmstrom, M. Rajilic, E. E. Vaughan et al., Colonic microbiota signatures across five northern European countries, Appl Environ Microbiol, vol.71, issue.7, pp.4153-4158, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682963

O. A. Firmesse, A. Mogenet, J. Bresson, G. Corthier, and J. P. Furet, Lactobacillus rhamnosus R11 consumed in a food supplement survived human digestive transist without modifying microbiota equilibrium as assessed by real time Polymerase Chain Reaction, J Mol Microbiol Biotechnol, vol.14, pp.90-99, 2008.

S. R. Lyons, A. L. Griffen, and E. J. Leys, Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria, J Clin Microbiol, vol.38, issue.6, pp.2362-2367, 2000.