Unravelling the pathogenesis of inflammatory bowel disease, Nature, vol.124, issue.7152, pp.427-461, 2007. ,
DOI : 10.1038/nature06005
Association analyses identify 38 susceptibility loci for 422 ,
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
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. ,
Intestinal dysbiosis in inflammatory bowel disease, Gut Microbes, vol.2, issue.4, pp.211-217, 2011. ,
DOI : 10.4161/gmic.2.4.17863
Complete genome sequence of crohn's disease- 434 associated adherent-invasive e. Coli strain lf82, PLoS One, vol.5, issue.8, 2010. ,
Ceacam6 acts as a receptor for adherent-invasive e, p.438 ,
supporting ileal mucosa colonization in crohn disease, J Clin Invest, vol.117, issue.439, pp.1566-74, 2007. ,
Crohn's disease adherent-invasive escherichia coli 440 ,
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
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
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
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
Travelers can import colistin-resistant 456 enterobacteriaceae, including those possessing the plasmid-mediated mcr-1 gene, p.457 ,
Mobile genetic elements of the human gastrointestinal tract, Gut Microbes, vol.63, issue.4, pp.271-80, 2013. ,
DOI : 10.1371/journal.pcbi.1002358
Phage treatment of human infections, Bacteriophage, vol.7, issue.2, p.463 ,
DOI : 10.1016/S0041-1345(03)00525-6
Antibacterial Bioagents Based on Principles of Bacteriophage Biology: An Overview, Clinical Infectious Diseases, vol.58, issue.4, p.465 ,
DOI : 10.1093/cid/cit771
Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.11, issue.7304, pp.334-342, 2010. ,
DOI : 10.1038/nature09199
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
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
Oral phage therapy of acute bacterial diarrhea with, p.474 ,
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. ,
Novel mouse model for carcinoembryonic antigen-based therapy, Molecular Therapy, vol.9, issue.6 ,
DOI : 10.1016/j.ymthe.2004.03.009
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
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
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
Standard reference strains of escherichia coli from natural 488 populations, J Bacteriol, vol.157, issue.489, pp.690-693, 1984. ,
Virulent bacteriophages can target 490 o104:H4 enteroaggregative escherichia coli in the mouse intestine, Antimicrob Agents, p.491 ,
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
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
The treatment-naive microbiome in new-onset 498 ,
Oral phage therapy of acute bacterial diarrhea with 500 ,
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 ,
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 bistable switch and anatomical site control 509 ,
DOI : 10.1371/journal.ppat.1001102
URL : http://doi.org/10.1371/journal.ppat.1001102
The outer mucus layer hosts a distinct intestinal microbial niche, Nature Communications, vol.41, issue.512, pp.8292-8333, 2015. ,
DOI : 10.1038/ncomms9292
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
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
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
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. ,
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
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
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
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