R. Xavier and D. Podolsky, Unravelling the pathogenesis of inflammatory bowel disease, Nature, vol.124, issue.7152, pp.427-461, 2007.
DOI : 10.1038/nature06005

J. Liu, S. Van-sommeren, and H. Huang, Association analyses identify 38 susceptibility loci for 422

E. Legaki and M. Gazouli, Influence of environmental factors in the development of inflammatory bowel diseases, World Journal of Gastrointestinal Pharmacology and Therapeutics, vol.7, issue.1, pp.112-137, 2016.
DOI : 10.4292/wjgpt.v7.i1.112

F. Carbonnel, P. Jantchou, E. Monnet, J. Cosnes, A. St-amand et al., Environmental risk factors in crohn's disease 427 and ulcerative colitis: An update Molecular-phylogenetic characterization of 429 microbial community imbalances in human inflammatory bowel diseases, Gastroenterol Clin Biol Proc Natl Acad Sci, vol.33, p.430, 2009.

N. Kaur, C. Chen, J. Luther, and J. Kao, Intestinal dysbiosis in inflammatory bowel disease, Gut Microbes, vol.2, issue.4, pp.211-217, 2011.
DOI : 10.4161/gmic.2.4.17863

S. Miquel, E. Peyretaillade, and L. Claret, Complete genome sequence of crohn's disease- 434 associated adherent-invasive e. Coli strain lf82, PLoS One, vol.5, issue.8, 2010.

N. Barnich, F. Carvalho, and A. Glasser, Ceacam6 acts as a receptor for adherent-invasive e, p.438

. Coli, supporting ileal mucosa colonization in crohn disease, J Clin Invest, vol.117, issue.439, pp.1566-74, 2007.

F. Carvalho, N. Barnich, and A. Sivignon, Crohn's disease adherent-invasive escherichia coli 440

J. Hansen and R. Sartor, Therapeutic Manipulation of the Microbiome in IBD: Current Results and Future Approaches, Current Treatment Options in Gastroenterology, vol.289, issue.5483, pp.105-125, 2015.
DOI : 10.1007/s11938-014-0042-7

M. Nicolas-chanoine, X. Bertrand, and J. Madec, Escherichia coli st131, an intriguing clonal 448 group, Clin Microbiol Rev, vol.1327, issue.449, pp.543-74, 2014.
DOI : 10.1128/cmr.00125-13

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135899

Y. Liu, Y. Wang, and T. Walsh, Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study, The Lancet Infectious Diseases, vol.16, issue.2, pp.161-169, 2016.
DOI : 10.1016/S1473-3099(15)00424-7

C. Lubbert, L. Straube, and C. Stein, Colonization with extended-spectrum beta-lactamase-producing and carbapenemase-producing Enterobacteriaceae in international travelers returning to Germany, International Journal of Medical Microbiology, vol.305, issue.1, pp.148-56, 2015.
DOI : 10.1016/j.ijmm.2014.12.001

O. Bernasconi, E. Kuenzli, and J. Pires, Travelers can import colistin-resistant 456 enterobacteriaceae, including those possessing the plasmid-mediated mcr-1 gene, p.457

E. Broaders, C. Gahan, and J. Marchesi, Mobile genetic elements of the human gastrointestinal tract, Gut Microbes, vol.63, issue.4, pp.271-80, 2013.
DOI : 10.1371/journal.pcbi.1002358

S. Abedon, S. Kuhl, B. Blasdel, and E. Kutter, Phage treatment of human infections, Bacteriophage, vol.7, issue.2, p.463
DOI : 10.1016/S0041-1345(03)00525-6

B. Knoll and E. Mylonakis, Antibacterial Bioagents Based on Principles of Bacteriophage Biology: An Overview, Clinical Infectious Diseases, vol.58, issue.4, p.465
DOI : 10.1093/cid/cit771

A. Reyes, M. Haynes, and N. Hanson, Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.11, issue.7304, pp.334-342, 2010.
DOI : 10.1038/nature09199

L. Hoyles, A. Mccartney, and H. Neve, Characterization of virus-like particles associated with the human faecal and caecal microbiota, Research in Microbiology, vol.165, issue.10, pp.803-815, 2014.
DOI : 10.1016/j.resmic.2014.10.006

S. Mccallin, A. Sarker, S. Barretto, and C. , Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects, Virology, vol.443, issue.2, pp.187-472, 2013.
DOI : 10.1016/j.virol.2013.05.022

S. Sarker, S. Sultana, and G. Reuteler, Oral phage therapy of acute bacterial diarrhea with, p.474

M. Galtier, D. Sordi, L. Maura, and D. , Bacteriophages to reduce gut carriage of antibiotic 477 resistant uropathogens with low impact on microbiota composition, Environ Microbiol, vol.47818, issue.479, pp.2237-2282, 2016.

C. Chan and C. Stanners, Novel mouse model for carcinoembryonic antigen-based therapy, Molecular Therapy, vol.9, issue.6
DOI : 10.1016/j.ymthe.2004.03.009

K. Datsenko and B. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proceedings of the National Academy of Sciences, vol.27, issue.2, pp.6640-6645, 2000.
DOI : 10.1093/nar/27.2.389

M. Chaveroche, J. Ghigo, and C. Enfert, A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Research, vol.28, issue.22, pp.97-485, 2000.
DOI : 10.1093/nar/28.22.e97

L. Debarbieux, D. Leduc, and D. Maura, Lung Infections, The Journal of Infectious Diseases, vol.201, issue.7, pp.1096-104, 2010.
DOI : 10.1086/651135

URL : https://hal.archives-ouvertes.fr/pasteur-01425464

H. Ochman and R. Selander, Standard reference strains of escherichia coli from natural 488 populations, J Bacteriol, vol.157, issue.489, pp.690-693, 1984.

D. Maura, M. Galtier, L. Bouguenec, C. Debarbieux, and L. , Virulent bacteriophages can target 490 o104:H4 enteroaggregative escherichia coli in the mouse intestine, Antimicrob Agents, p.491

J. Furet, O. Firmesse, and M. Gourmelon, Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR, FEMS Microbiology Ecology, vol.68, issue.3, pp.351-494, 2009.
DOI : 10.1111/j.1574-6941.2009.00671.x

G. Bouguen, A. Langlois, and M. Djouina, Intestinal steroidogenesis controls PPAR? expression in the colon and is impaired during ulcerative colitis, Gut, vol.63, issue.6, pp.901-911, 2015.
DOI : 10.1136/gutjnl-2014-307618

D. Gevers, S. Kugathasan, and L. Denson, The treatment-naive microbiome in new-onset 498

S. Sarker, S. Sultana, and G. Reuteler, Oral phage therapy of acute bacterial diarrhea with 500

N. Dufour, O. Clermont, L. Combe, and B. , Bacteriophage lm33_p1, a fast-acting weapon 502 against the pandemic st131-o25b:H4 escherichia coli clonal complex, J Antimicrob Chemother, vol.503, issue.504, pp.2016-2053

H. Jakobsson, A. Rodriguez-pineiro, and A. Schutte, The composition of the gut microbiota 505 shapes the colon mucus barrier The gastrointestinal mucus system in health and 507 disease, EMBO Rep Nat Rev Gastroenterol Hepatol, vol.1610, issue.508, pp.164-77352, 2013.

A. Nielsen, N. Dolganov, and T. Rasmussen, A bistable switch and anatomical site control 509
DOI : 10.1371/journal.ppat.1001102

URL : http://doi.org/10.1371/journal.ppat.1001102

H. Li, J. Limenitakis, and T. Fuhrer, The outer mucus layer hosts a distinct intestinal microbial niche, Nature Communications, vol.41, issue.512, pp.8292-8333, 2015.
DOI : 10.1038/ncomms9292

J. Barr, R. Auro, and M. Furlan, Bacteriophage adhering to mucus provide a non-host-derived immunity, Proceedings of the National Academy of Sciences, vol.66, issue.12, pp.10771-10777, 2013.
DOI : 10.1016/0022-2836(89)90464-6

J. Barr, R. Auro, and N. Sam-soon, Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters, Proceedings of the National Academy of Sciences, vol.7, issue.1, pp.13675-80, 2015.
DOI : 10.1016/j.jmb.2006.03.043

M. Weiss, E. Denou, and A. Bruttin, In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli, Virology, vol.393, issue.1, pp.16-23, 2009.
DOI : 10.1016/j.virol.2009.07.020

S. Chibani-chennoufi, J. Sidoti, and A. Bruttin, In vitro and in vivo bacteriolytic activities of 519 escherichia coli phages: Implications for phage therapy, Antimicrob Agents Chemother, vol.52048, pp.2558-69, 2004.

S. Sarker, S. Mccallin, and C. Barretto, Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh, Virology, vol.434, issue.2, pp.222-254, 2012.
DOI : 10.1016/j.virol.2012.09.002

URL : http://doi.org/10.1016/j.virol.2012.09.002

E. Lim, Y. Zhou, and G. Zhao, Early life dynamics of the human gut virome and bacterial microbiome in infants, Nature Medicine, vol.61, issue.10, pp.1228-1262, 2015.
DOI : 10.1073/pnas.1000080107

L. Debarbieux, Bacterial sensing of bacteriophages in communities: the search for the Rosetta stone, Current Opinion in Microbiology, vol.20, issue.527, pp.125-155, 2014.
DOI : 10.1016/j.mib.2014.05.015

M. De-paepe, M. Leclerc, C. Tinsley, and M. Petit, Bacteriophages: an underestimated role in human and animal health?, Frontiers in Cellular and Infection Microbiology, vol.181, issue.9, p.39, 2014.
DOI : 10.1086/315239

URL : https://hal.archives-ouvertes.fr/hal-01204359