F. Backhed, R. Ley, J. Sonnenburg, D. Peterson, and J. Gordon, Host-Bacterial Mutualism in the Human Intestine, Science, vol.307, issue.5717, pp.1915-1920, 2005.
DOI : 10.1126/science.1104816

I. Ivanov, K. Atarashi, N. Manel, E. Brodie, and T. Shima, Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria, Cell, vol.139, issue.3, pp.485-498, 2009.
DOI : 10.1016/j.cell.2009.09.033

D. Van-der-waaij, J. Berghuis-de-vries, and L. Lekkerkerk, SUMMARY, Journal of Hygiene, vol.111, issue.03, pp.405-411, 1971.
DOI : 10.1084/jem.128.1.97

E. Vollaard and H. Clasener, Colonization resistance., Antimicrobial Agents and Chemotherapy, vol.38, issue.3, pp.409-414, 1994.
DOI : 10.1128/AAC.38.3.409

B. Stecher and W. Hardt, The role of microbiota in infectious disease, Trends in Microbiology, vol.16, issue.3, pp.107-114, 2008.
DOI : 10.1016/j.tim.2007.12.008

M. Barthel, S. Hapfelmeier, L. Quintanilla-martinez, M. Kremer, and M. Rohde, Pretreatment of Mice with Streptomycin Provides a Salmonella enterica Serovar Typhimurium Colitis Model That Allows Analysis of Both Pathogen and Host, Infection and Immunity, vol.71, issue.5, pp.2839-2858, 2003.
DOI : 10.1128/IAI.71.5.2839-2858.2003

M. Barman, D. Unold, K. Shifley, E. Amir, and K. Hung, Enteric Salmonellosis Disrupts the Microbial Ecology of the Murine Gastrointestinal Tract, Infection and Immunity, vol.76, issue.3, pp.907-915, 2008.
DOI : 10.1128/IAI.01432-07

E. Hohmann, Nontyphoidal salmonellosis, Clin Infect Dis, vol.32, pp.263-269, 2001.

L. Dethlefsen, S. Huse, M. Sogin, and D. Relman, The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing, PLoS Biology, vol.72, issue.11, p.280, 2008.
DOI : 10.1371/journal.pbio.0060280.sd008

K. Dore, J. Buxton, B. Henry, F. Pollari, and D. Middleton, Risk factors for Salmonella Typhimurium DT104 and non-DT104 infection: a Canadian multi-provincial case-control study, Epidemiology and Infection, vol.132, issue.3, pp.485-493, 2004.
DOI : 10.1017/S0950268803001924

D. Buchwald and M. Blaser, A Review of Human Salmonellosis: II. Duration of Excretion Following Infection with Nontyphi Salmonella, Clinical Infectious Diseases, vol.6, issue.3, pp.345-356, 1984.
DOI : 10.1093/clinids/6.3.345

A. Balfour, R. Lewis, and S. Ahmed, Convalescent excretion of Salmonella enteritidis in infants, Journal of Infection, vol.38, issue.1, pp.24-25, 1999.
DOI : 10.1016/S0163-4453(99)90024-5

J. Greig, E. Todd, C. Bartleson, and B. Michaels, Outbreaks Where Food Workers Have Been Implicated in the Spread of Foodborne Disease. Part 1. Description of the Problem, Methods, and Agents Involved, Journal of Food Protection, vol.70, issue.7, pp.1752-1761, 2007.
DOI : 10.4315/0362-028X-70.7.1752

M. Bader, S. Sanowar, M. Daley, A. Schneider, and U. Cho, Recognition of Antimicrobial Peptides by a Bacterial Sensor Kinase, Cell, vol.122, issue.3, pp.461-472, 2005.
DOI : 10.1016/j.cell.2005.05.030

J. Gunn, K. Lim, J. Krueger, K. Kim, and L. Guo, PmrA-PmrB-regulated genes necessary for 4-aminoarabinose lipid A modification and polymyxin resistance, Molecular Microbiology, vol.4, issue.6, pp.1171-1182, 1998.
DOI : 10.1046/j.1365-2958.1998.00757.x

A. Brown and C. Hormaeche, The antibody response to salmonellae in mice and humans studied by immunoblots and ELISA, Microbial Pathogenesis, vol.6, issue.6, pp.445-454, 1989.
DOI : 10.1016/0882-4010(89)90086-7

H. Mittrucker, B. Raupach, A. Kohler, and S. Kaufmann, Cutting Edge: Role of B Lymphocytes in Protective Immunity Against Salmonella typhimurium Infection, The Journal of Immunology, vol.164, issue.4, pp.1648-1652, 2000.
DOI : 10.4049/jimmunol.164.4.1648

T. Uren, O. Wijburg, C. Simmons, F. Johansen, and P. Brandtzaeg, Vaccine-induced protection against gastrointestinal bacterial infections in the absence of secretory antibodies, European Journal of Immunology, vol.141, issue.1, pp.180-188, 2005.
DOI : 10.1002/eji.200425492

C. Maaser, M. Housley, M. Iimura, J. Smith, and B. Vallance, Clearance of Citrobacter rodentium Requires B Cells but Not Secretory Immunoglobulin A (IgA) or IgM Antibodies, Infection and Immunity, vol.72, issue.6, pp.3315-3324, 2004.
DOI : 10.1128/IAI.72.6.3315-3324.2004

B. Stecher, S. Chaffron, R. Kappeli, S. Hapfelmeier, and S. Freedrich, Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria, PLoS Pathogens, vol.77, issue.1, p.1000711, 2010.
DOI : 10.1371/journal.ppat.1000711.s014

B. Stecher, R. Robbiani, A. Walker, A. Westendorf, and M. Barthel, Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota, PLoS Biology, vol.73, issue.10, p.244, 2007.
DOI : 10.1371/journal.pbio.0050244.st002

S. Hapfelmeier, B. Stecher, M. Barthel, M. Kremer, and A. Müller, The Salmonella Pathogenicity Island (SPI)-2 and SPI-1 Type III Secretion Systems Allow Salmonella Serovar typhimurium to Trigger Colitis via MyD88-Dependent and MyD88-Independent Mechanisms, The Journal of Immunology, vol.174, issue.3, pp.1675-1685, 2005.
DOI : 10.4049/jimmunol.174.3.1675

B. Coombes, B. Coburn, A. Potter, S. Gomis, and K. Mirakhur, Analysis of the Contribution of Salmonella Pathogenicity Islands 1 and 2 to Enteric Disease Progression Using a Novel Bovine Ileal Loop Model and a Murine Model of Infectious Enterocolitis, Infection and Immunity, vol.73, issue.11, pp.7161-7169, 2005.
DOI : 10.1128/IAI.73.11.7161-7169.2005

S. Hapfelmeier and W. Hardt, A mouse model for S. typhimurium-induced enterocolitis, Trends in Microbiology, vol.13, issue.10, 2005.
DOI : 10.1016/j.tim.2005.08.008

R. Curtiss, S. Kelly, and J. Hassan, Live oral avirulent Salmonella vaccines, Veterinary Microbiology, vol.37, issue.3-4, pp.397-405, 1993.
DOI : 10.1016/0378-1135(93)90038-9

J. Simonsen, K. Molbak, G. Falkenhorst, K. Krogfelt, and A. Linneberg, Estimation of incidences of infectious diseases based on antibody measurements, Statistics in Medicine, vol.135, issue.14, pp.1882-1895, 2009.
DOI : 10.1017/S0950268806006686

H. Angelakopoulos and E. Hohmann, Pilot Study of phoP/phoQ-Deleted Salmonella enterica Serovar Typhimurium Expressing Helicobacter pylori Urease in Adult Volunteers, Infection and Immunity, vol.68, issue.4, pp.2135-2141, 2000.
DOI : 10.1128/IAI.68.4.2135-2141.2000

H. Kang, J. Srinivasan, and R. Curtiss, Immune Responses to Recombinant Pneumococcal PspA Antigen Delivered by Live Attenuated Salmonella enterica Serovar Typhimurium Vaccine, Infection and Immunity, vol.70, issue.4, pp.3-1739, 2002.
DOI : 10.1128/IAI.70.4.1739-1749.2002

M. Bergman, L. Cummings, S. Barrett, K. Smith, and J. Lara, CD4+ T Cells and Toll-Like Receptors Recognize Salmonella Antigens Expressed in Bacterial Surface Organelles, Infection and Immunity, vol.73, issue.3, pp.1350-1356, 2005.
DOI : 10.1128/IAI.73.3.1350-1356.2005

E. Slack, S. Hapfelmeier, B. Stecher, Y. Velykoredko, and M. Stoel, Innate and Adaptive Immunity Cooperate Flexibly to Maintain Host-Microbiota Mutualism, Science, vol.325, issue.5940, pp.617-620, 2009.
DOI : 10.1126/science.1172747
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730530

C. Martinoli, A. Chiavelli, and M. Rescigno, Entry Route of Salmonella typhimurium Directs the Type of Induced Immune Response, Immunity, vol.27, issue.6, pp.975-984, 2007.
DOI : 10.1016/j.immuni.2007.10.011

O. Wijburg, T. Uren, K. Simpfendorfer, F. Johansen, and P. Brandtzaeg, infection, The Journal of Experimental Medicine, vol.96, issue.1, pp.21-26, 2006.
DOI : 10.1136/gut.38.3.348

A. Macpherson, D. Gatto, E. Sainsbury, G. Harriman, and H. Hengartner, A Primitive T Cell-Independent Mechanism of Intestinal Mucosal IgA Responses to Commensal Bacteria, Science, vol.288, issue.5474, pp.2222-2226, 2000.
DOI : 10.1126/science.288.5474.2222

P. Brandtzaeg, Mucosal Immunity: Induction, Dissemination, and Effector Functions, Scandinavian Journal of Immunology, vol.2, issue.Suppl. 2, pp.505-515, 2009.
DOI : 10.1111/j.1365-3083.2009.02319.x

M. Suar, B. Periaswamy, P. Songhet, B. Misselwitz, and A. Muller, Accelerated Type III Secretion System 2-Dependent Enteropathogenesis by a Salmonella enterica Serovar Enteritidis PT4/6 Strain, Infection and Immunity, vol.77, issue.9, pp.3569-3577, 2009.
DOI : 10.1128/IAI.00511-09

K. Ilg, K. Endt, B. Misselwitz, B. Stecher, and M. Aebi, O-Antigen-Negative Salmonella enterica Serovar Typhimurium Is Attenuated in Intestinal Colonization but Elicits Colitis in Streptomycin-Treated Mice, Infection and Immunity, vol.77, issue.6, pp.2568-2575, 2009.
DOI : 10.1128/IAI.01537-08

P. Turnbaugh, M. Hamady, T. Yatsunenko, B. Cantarel, and A. Duncan, A core gut microbiome in obese and lean twins, Nature, vol.8, issue.7228, 2008.
DOI : 10.1038/nature07540

B. Duerkop, S. Vaishnava, and L. Hooper, Immune Responses to the Microbiota at the Intestinal Mucosal Surface, Immunity, vol.31, issue.3, pp.368-376, 2009.
DOI : 10.1016/j.immuni.2009.08.009

M. Bohnhoff, B. Drake, and C. Miller, Effect of Streptomycin on Susceptibility of Intestinal Tract to Experimental Salmonella Infection., Experimental Biology and Medicine, vol.86, issue.1, pp.132-137, 1954.
DOI : 10.3181/00379727-86-21030

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

S. Huse, L. Dethlefsen, J. Huber, D. Welch, and D. Relman, Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing, PLoS Genetics, vol.16, issue.11, p.1000255, 2008.
DOI : 10.1371/journal.pgen.1000255.t003

R. Sarma-rupavtarm, Z. Ge, D. Schauer, J. Fox, and M. Polz, Spatial Distribution and Stability of the Eight Microbial Species of the Altered Schaedler Flora in the Mouse Gastrointestinal Tract, Applied and Environmental Microbiology, vol.70, issue.5, pp.2791-2800, 2004.
DOI : 10.1128/AEM.70.5.2791-2800.2004

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

R. Nardi, M. Silva, E. Vieira, E. Bambirra, and J. Nicoli, Intragastric infection of germfree and conventional mice with Salmonella typhimurium, 1989.

J. Rawls, Enteric Infection and Inflammation Alter Gut Microbial Ecology, Cell Host & Microbe, vol.2, issue.2, pp.73-74, 2007.
DOI : 10.1016/j.chom.2007.07.006
URL : http://doi.org/10.1016/j.chom.2007.07.006

V. Gaboriau-routhiau, S. Rakotobe, E. Lecuyer, I. Mulder, and A. Lan, The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses, Immunity, vol.31, issue.4, pp.677-689, 2009.
DOI : 10.1016/j.immuni.2009.08.020

H. Mittrucker and S. Kaufmann, Immune response to infection with Salmonella typhimurium in mice, J Leukoc Biol, vol.67, pp.457-463, 2000.

J. Chen, M. Trounstine, F. Alt, F. Young, and C. Kurahara, locus, International Immunology, vol.5, issue.6, pp.647-656, 1993.
DOI : 10.1093/intimm/5.6.647
URL : https://hal.archives-ouvertes.fr/hal-00181924

G. Harriman, M. Bogue, P. Rogers, M. Finegold, and S. Pacheco, Targeted deletion of the IgA constant region in mice leads to IgA deficiency with alterations in expression of other Ig isotypes, J Immunol, vol.162, pp.2521-2529, 1999.

T. Uren, F. Johansen, O. Wijburg, F. Koentgen, and P. Brandtzaeg, Role of the Polymeric Ig Receptor in Mucosal B Cell Homeostasis, The Journal of Immunology, vol.170, issue.5, pp.2531-2539, 2003.
DOI : 10.4049/jimmunol.170.5.2531

P. Mombaerts, E. Mizoguchi, H. Ljunggren, J. Iacomini, and H. Ishikawa, Peripheral lymphoid development and function in TCR mutant mice, International Immunology, vol.6, issue.7, pp.1061-1070, 1994.
DOI : 10.1093/intimm/6.7.1061

B. Stecher, M. Barthel, M. Schlumberger, L. Haberli, and W. Rabsch, Motility allows S.??Typhimurium to benefit from the mucosal defence, Cellular Microbiology, vol.172, issue.5, pp.1166-1180, 2008.
DOI : 10.1073/pnas.1734063100
URL : http://mediatum.ub.tum.de/doc/675856/document.pdf

S. Hapfelmeier, A. Muller, B. Stecher, P. Kaiser, and M. Barthel, . Typhimurium colitis, The Journal of Experimental Medicine, vol.58, issue.2, pp.437-450, 2008.
DOI : 10.1038/312548a0

B. Stecher, S. Hapfelmeier, C. Muller, M. Kremer, and T. Stallmach, Flagella and Chemotaxis Are Required for Efficient Induction of Salmonella enterica Serovar Typhimurium Colitis in Streptomycin-Pretreated Mice, Infection and Immunity, vol.72, issue.7, pp.4138-4150, 2004.
DOI : 10.1128/IAI.72.7.4138-4150.2004

C. Mueller, Tumour necrosis factor in mouse models of chronic intestinal inflammation, Immunology, vol.105, issue.1, pp.1-8, 2002.
DOI : 10.1126/science.274.5285.262

S. Eilebrecht, F. Pellay, P. Odenwalder, G. Brysbaert, and B. Benecke, EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection, BMC Research Notes, vol.1, issue.1, p.100, 2008.
DOI : 10.1186/1756-0500-1-100
URL : http://doi.org/10.1186/1756-0500-1-100

S. Noth, G. Brysbaert, and A. Benecke, Normalization Using Weighted Negative Second Order Exponential Error Functions (NeONORM) Provides Robustness Against Asymmetries in Comparative Transcriptome Profiles and Avoids False Calls, Genomics, Proteomics & Bioinformatics, vol.4, issue.2, pp.90-109, 2006.
DOI : 10.1016/S1672-0229(06)60021-1

V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz, Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environmental Microbiology, vol.64, issue.1, 2009.
DOI : 10.1111/j.1462-2920.2009.02051.x

T. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, and E. Brodie, Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Applied and Environmental Microbiology, vol.72, issue.7, pp.5069-5072, 2006.
DOI : 10.1128/AEM.03006-05

S. Eddy, A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure, BMC Bioinformatics, vol.3, issue.1, p.18, 2002.
DOI : 10.1186/1471-2105-3-18

J. Cole, Q. Wang, E. Cardenas, J. Fish, and B. Chai, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

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

M. Sogin, H. Morrison, J. Huber, D. Welch, and S. Huse, Microbial diversity in the deep sea and the underexplored "rare biosphere", Proceedings of the National Academy of Sciences, vol.103, issue.32, 2006.
DOI : 10.1073/pnas.0605127103

C. Quince, A. Lanzen, T. Curtis, R. Davenport, and N. Hall, Accurate determination of microbial diversity from 454 pyrosequencing data, Nature Methods, vol.25, issue.9, pp.639-641, 2009.
DOI : 10.1093/nar/gkh340

T. Kanagawa, Bias and artifacts in multitemplate polymerase chain reactions (PCR), Journal of Bioscience and Bioengineering, vol.96, issue.4, pp.317-323, 2003.
DOI : 10.1016/S1389-1723(03)90130-7

F. Johansen, M. Pekna, I. Norderhaug, B. Haneberg, and M. Hietala, Absence of Epithelial Immunoglobulin a Transport, with Increased Mucosal Leakiness, in Polymeric Immunoglobulin Receptor/Secretory Component???Deficient Mice, The Journal of Experimental Medicine, vol.16, issue.7, pp.915-922, 1999.
DOI : 10.1097/00004836-199709000-00005

L. Jensen, M. Kuhn, M. Stark, S. Chaffron, and C. Creevey, STRING 8--a global view on proteins and their functional interactions in 630 organisms, Nucleic Acids Research, vol.37, issue.Database, pp.412-416, 2009.
DOI : 10.1093/nar/gkn760

S. Hoiseth and B. Stocker, Aromatic-dependent Salmonella typhimurium are non-virulent and effective as live vaccines, Nature, vol.58, issue.5812, pp.238-239, 1981.
DOI : 10.1038/291238a0

S. Hapfelmeier, K. Ehrbar, B. Stecher, M. Barthel, and M. Kremer, Role of the Salmonella Pathogenicity Island 1 Effector Proteins SipA, SopB, SopE, and SopE2 in Salmonella enterica Subspecies 1 Serovar Typhimurium Colitis in Streptomycin-Pretreated Mice, Infection and Immunity, vol.72, issue.2, pp.795-809, 2004.
DOI : 10.1128/IAI.72.2.795-809.2004

M. Suar, J. Jantsch, S. Hapfelmeier, M. Kremer, and T. Stallmach, Virulence of Broad- and Narrow-Host-Range Salmonella enterica Serovars in the Streptomycin-Pretreated Mouse Model, Infection and Immunity, vol.74, issue.1, pp.632-644, 2006.
DOI : 10.1128/IAI.74.1.632-644.2006

S. Hapfelmeier, A. Muller, B. Stecher, P. Kaiser, and M. Barthel, . Typhimurium colitis, The Journal of Experimental Medicine, vol.58, issue.2, pp.437-450, 2008.
DOI : 10.1038/312548a0

R. Wang and S. Kushner, Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli, Gene, vol.100, pp.195-199, 1991.
DOI : 10.1016/0378-1119(91)90366-J

J. Hughes, J. Hellmann, T. Ricketts, and B. Bohannan, Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity, Applied and Environmental Microbiology, vol.67, issue.10, pp.4399-4406, 2001.
DOI : 10.1128/AEM.67.10.4399-4406.2001