E. K. Costello, C. L. Lauber, M. Hamady, N. Fierer, and J. I. Gordon, Bacterial community variation in human body habitats across space and time, Science, vol.326, pp.1694-1697, 2009.

N. Fierer, C. L. Lauber, N. Zhou, D. Mcdonald, and E. K. Costello, From the cover: Forensic identification using skin bacterial communities, Proceedings of the National Academy of Sciences, vol.107, pp.6477-6481, 2010.

P. J. Turnbaugh, C. Quince, J. J. Faith, A. C. Mchardy, and T. Yatsunenko, Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins, Proceedings of the National Academy of Sciences, vol.107, pp.7503-7508, 2010.

P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-liggett, and R. Knight, The human microbiome project, Nature, vol.449, pp.804-810, 2007.

P. J. Turnbaugh, B. Henrissat, and J. I. Gordon, Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes, Acta Crystallographica Section F, vol.66, pp.1261-1264, 2010.

P. J. Turnbaugh and J. I. Gordon, The core gut microbiome, energy balance and obesity, The Journal of Physiology, vol.587, pp.4153-4158, 2009.

A. Giongo, K. A. Gano, D. B. Crabb, N. Mukherjee, and L. L. Novelo, Toward defining the autoimmune microbiome for type 1 diabetes, ISME J, vol.5, pp.82-91, 2011.

D. A. Peterson, N. P. Mcnulty, J. L. Guruge, and J. I. Gordon, IgA Response to Symbiotic Bacteria as a Mediator of Gut Homeostasis, Cell Host & Microbe, vol.2, pp.328-339, 2007.

D. Bouskra, C. Brézillon, M. Bérard, C. Werts, and R. Varona, Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis, Nature, vol.456, pp.507-510, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-01402759

A. J. Macpherson, M. B. Geuking, and K. D. Mccoy, A: a bridge between innate and adaptive immunity, Current Opinion in Gastroenterology, vol.27, pp.529-533, 2011.

S. Boutin, L. Bernatchez, C. Audet, and N. Derôme, Antagonistic effect of indigenous skin bacteria of brook charr (Salvelinus fontinalis) against Flavobacterium columnare and F.psychrophilum, Veterinary Microbiology, vol.155, pp.355-361, 2012.

J. Balcázar, I. De-blas, I. Ruiz-zarzuela, D. Vendrell, and J. Muzquiz, Probiotics: a tool for the future of fish and shellfish health management, Journal of Aquaculture in the Tropics, vol.19, pp.239-242, 2004.

F. Backhed, Host-bacterial mutualism in the human intestine, Science, vol.307, pp.1915-1920, 2005.

L. V. Hooper and J. I. Gordon, Commensal host-bacterial relationships in the gut, Science, vol.292, pp.1115-1118, 2001.

A. M. O'hara and F. Shanahan, The gut flora as a forgotten organ, EMBO Reports, vol.7, pp.688-693, 2006.

B. Stecher and W. Hardt, The role of microbiota in infectious disease, Trends in Microbiology, vol.16, pp.107-114, 2008.

C. Loiseau, M. Richard, S. Garnier, O. Chastel, and R. Julliard, Diversifying selection on MHC class I in the house sparrow (Passer domesticus), Molecular Ecology, vol.18, pp.1331-1340, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00377400

M. Krawczyk and W. Reith, Regulation of MHC class II expression, a unique regulatory system identified by the study of a primary immunodeficiency disease, Tissue Antigens, vol.67, pp.183-197, 2006.

M. Dionne, K. M. Miller, J. J. Dodson, and L. Bernatchez, MHC standing genetic variation and pathogen resistance in wild Atlantic salmon, Philosophical Transactions of the Royal Society B-Biological Sciences, vol.364, pp.1555-1565, 2009.

C. Alexander and E. T. Rietschel, Invited review: Bacterial lipopolysaccharides and innate immunity, Journal of Endotoxin Research, vol.7, pp.167-202, 2001.

S. Boutin, C. Audet, and N. Derôme, Probiotic treatment by indigenous bacteria decreases mortality without disturbing the natural microbiota of Salvelinus fontinalis, Canadian Journal of Microbiology In press, 2013.

S. Boutin, L. Bernatchez, C. Audet, and N. Derôme, Network Analysis Highlights Complex Interactions between Pathogen, Host and Commensal Microbiota, PLoS ONE, vol.8, p.84772, 2013.

C. Sauvage, M. Vagner, N. Derôme, C. Audet, and L. Bernatchez, Coding gene single nucleotide polymorphism mapping and quantitative trait loci detection for physiological reproductive traits in brook charr, vol.2, pp.379-392, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02107010

L. Livia, A. P. Hovirag, L. Mauro, N. Panara, and F. , A nondestructive, rapid, reliable and inexpensive method to sample, store and extract high-quality DNA from fish body mucus and buccal cells, Molecular Ecology Notes, vol.6, pp.257-260, 2006.

S. Turner, K. M. Pryer, V. Miao, and J. D. Palmer, Investigating deep phylogenetic relationships among Cyanobacteria and plastids by small subunit rRNA sequence analysis, Journal of Eukaryotic Microbiology, vol.46, pp.327-338, 1999.

J. R. Marchesi, T. Sato, A. J. Weightman, T. A. Martin, and J. C. Fry, Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA, Applied and Environmental Microbiology, vol.64, pp.795-799, 1998.

P. Schloss, S. Westcott, T. Ryabin, J. Hall, and M. Hartmann, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Applied and Environmental Microbiology, vol.75, pp.7537-7541, 2009.

J. Siddharth, N. Holway, and S. J. Parkinson, A Western Diet Ecological Module Identified from the 'Humanized' Mouse Microbiota Predicts Diet in Adults and Formula Feeding in Children, PLoS ONE, vol.8, p.83689, 2013.

T. Takeshita, N. Suzuki, Y. Nakano, M. Yasui, and M. Yoneda, Discrimination of the oral microbiota associated with high hydrogen sulfide and methyl mercaptan production, 2012.

M. C. Horner-devine, M. Lage, J. B. Hughes, and B. Bohannan, A taxa-area relationship for bacteria, Nature, vol.432, pp.750-753, 2004.

J. R. White, N. Nagarajan, and M. Pop, Statistical methods for detecting differentially abundant features in clinical metagenomic samples, PLoS Computational Biology, vol.5, p.1000352, 2009.

A. M. Mcknite, M. E. Perez-munoz, L. Lu, E. G. Williams, and S. Brewer, Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits, PLoS ONE, vol.7, p.39191, 2012.

C. E. Starliper, Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum, Journal of Advanced Research, vol.2, pp.97-108, 2011.

T. Wiklund, L. Madsen, M. S. Bruun, and I. Dalsgaard, Detection of Flavobacterium psychrophilum from fish tissue and water samples by PCR amplification, Journal of Applied Microbiology, vol.88, pp.299-307, 2000.

J. Madetoja, P. Nyman, and T. Wiklund, Flavobacterium psychrophilum, invasion into and shedding by rainbow trout Oncorhynchus mykiss, Diseases of Aquatic Organisms, vol.43, pp.27-38, 2000.

K. Faust and J. Raes, Microbial interactions: from networks to models, Nat Rev Micro, vol.10, pp.538-550, 2012.

T. Defoirdt, D. Halet, H. Vervaeren, N. Boon, and T. Van-de-wiele, The bacterial storage compound poly-b-hydroxybutyrate protects Artemia franciscana from pathogenic Vibrio campbellii, Environmental Microbiology, vol.9, pp.445-452, 2007.

D. Halet, T. Defoirdt, P. Van-damme, H. Vervaeren, and I. Forrez, Polyb-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii, FEMS Microbiology Ecology, vol.60, pp.363-369, 2007.

Y. Desai, Production of poly-3-hydroxybutyrate from lactose and whey by Methylobacterium sp. ZP24, Letters in Applied Microbiology, vol.26, pp.391-394, 1998.

G. Mothes, J. Ackermann, and W. Babel, Regulation of poly(b-hydroxybutyrate) synthesis in Methylobacterium rhodesianum MB 126 growing on methanol or fructose, Archives of Microbiology, vol.169, pp.360-363, 1998.

E. J. Bormann and M. Roth, The production of polyhydroxybutyrate by Methylobacterium rhodesianum and Ralstonia eutropha in media containing glycerol and casein hydrolysates, Biotechnology Letters, vol.21, pp.1059-1063, 1999.

E. J. Bormann, M. Roth, W. Linb, and M. Leibner, Selection of capsule deficient strains of Methylobacterium rhodesianum producing polyhydroxybutyrate, Biotechnology Techniques, vol.13, pp.539-544, 1999.

C. Balachandran, V. Duraipandiyan, and S. Ignacimuthu, Cytotoxic (A549) and antimicrobial effects of Methylobacterium sp. isolate (ERI-135) from Nilgiris forest soil, India. Asian Pacific Journal of Tropical Biomedicine, vol.2, pp.712-716, 2012.

N. Korotkova, L. Chistoserdova, and M. E. Lidstrom, Poly-b-Hydroxybutyrate Biosynthesis in the Facultative Methylotroph Methylobacterium extorquens AM1: Identification and Mutation of gap11, gap20, and phaR, Journal of Bacteriology, vol.184, pp.6174-6181, 2002.

W. Chen, C. Lin, and S. Sheu, Investigating antimicrobial activity in Rheinheimera sp. due to hydrogen peroxide generated by l-lysine oxidase activity, Enzyme and Microbial Technology, vol.46, pp.487-493, 2010.

W. Chen, C. Lin, C. Young, and S. Sheu, Rheinheimera aquatica sp. nov., antimicrobial activity-producing bacterium isolated from freshwater culture pond, vol.7, 2010.

H. Reichenbach, M. ;-dworkin, S. Falkow, E. Rosenberg, K. Schleifer et al., The genus Lysobacter, The Prokaryotes, pp.939-957, 2006.

R. Dillon and K. Charnley, Mutualism between the desert locust Schistocerca gregaria and its gut microbiota, Research in Microbiology, vol.153, pp.503-509, 2002.

C. Langevin, M. Blanco, S. Martin, L. Jouneau, and J. Bernardet, Transcriptional responses of resistant and susceptible fish clones to the bacterial pathogen Flavobacterium psychrophilum, PLoS ONE, vol.7, p.39126, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01000286