Interactions Among Microorganisms of the Indigenous Intestinal Flora and Their Influence on the Host, Clinical Infectious Diseases, vol.6, issue.Supplement 1, pp.73-79, 1984. ,
DOI : 10.1093/clinids/6.Supplement_1.S73
Spatial Organization and Composition of the Mucosal Flora in Patients with Inflammatory Bowel Disease, Journal of Clinical Microbiology, vol.43, issue.7, pp.3380-3389, 2005. ,
DOI : 10.1128/JCM.43.7.3380-3389.2005
The gut flora as a forgotten organ, EMBO reports, vol.13, issue.7, pp.688-693, 2006. ,
DOI : 10.1097/00001574-200411000-00011
Microbial Ecology of the Gastrointestinal Tract, Annual Review of Microbiology, vol.31, issue.1, pp.107-133, 1977. ,
DOI : 10.1146/annurev.mi.31.100177.000543
Host-Bacterial Mutualism in the Human Intestine, Science, vol.307, issue.5717, pp.1915-1920, 2005. ,
DOI : 10.1126/science.1104816
Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host, PLoS Biology, vol.356, issue.12, p.413, 2006. ,
DOI : 10.1371/journal.pbio.0040413.st015
The Human Microbiome Project, Nature, vol.112, issue.7164, pp.804-810, 2007. ,
DOI : 10.1038/nature06244
Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host, Environmental Microbiology, vol.57, issue.Suppl. 2, pp.2194-2206, 2009. ,
DOI : 10.1111/j.1462-2920.2009.01941.x
Pathogenic Escherichia coli, Nature Reviews Microbiology, vol.63, issue.2, pp.123-140, 2004. ,
DOI : 10.1128/IAI.69.1.315-324.2001
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
Colonization resistance., Antimicrobial Agents and Chemotherapy, vol.38, issue.3, pp.409-414, 1994. ,
DOI : 10.1128/AAC.38.3.409
Can bacterial interference prevent infection?, Trends in Microbiology, vol.9, issue.9, pp.424-428, 2001. ,
DOI : 10.1016/S0966-842X(01)02132-1
The Front Line of Enteric Host Defense against Unwelcome Intrusion of Harmful Microorganisms: Mucins, Antimicrobial Peptides, and Microbiota, Clinical Microbiology Reviews, vol.19, issue.2, pp.315-337, 2006. ,
DOI : 10.1128/CMR.19.2.315-337.2006
URL : https://hal.archives-ouvertes.fr/inserm-00180612
Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10, Nature Biotechnology, vol.21, issue.7, pp.785-789, 2003. ,
DOI : 10.1038/nbt840
Cellular and Physiological Effects of Probiotics and Prebiotics, Mini-Reviews in Medicinal Chemistry, vol.4, issue.8, pp.889-896, 2004. ,
DOI : 10.2174/1389557043403369
The intestine and its microflora are partners for the protection of the host: report on the Danone Symposium ''The Intelligent Intestine, Am J Clin Nutr, vol.78, pp.675-683, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00416301
Antagonistic interactions amongst bacteriocin-producing enteric bacteria in dual species biofilms, Journal of Applied Microbiology, vol.48, issue.2, pp.345-352, 2002. ,
DOI : 10.1016/S0966-842X(99)01459-6
Self-generated diversity produces "insurance effects" in biofilm communities, Proceedings of the National Academy of Sciences, vol.101, issue.47, pp.16630-16635, 2004. ,
DOI : 10.1073/pnas.0407460101
Quorum sensing and motility mediate interactions between Pseudomonas aeruginosa and Agrobacterium tumefaciens in biofilm cocultures, Proceedings of the National Academy of Sciences, vol.103, issue.10, pp.3828-3833, 2006. ,
DOI : 10.1073/pnas.0511323103
Broad-spectrum biofilm inhibition by a secreted bacterial polysaccharide, Proceedings of the National Academy of Sciences, vol.103, issue.33, pp.12558-12563, 2006. ,
DOI : 10.1073/pnas.0605399103
Evolution of species interactions in a biofilm community, Nature, vol.146, issue.7127, pp.533-536, 2007. ,
DOI : 10.1038/nature05514
The Amino Acid Valine Is Secreted in Continuous-Flow Bacterial Biofilms, Journal of Bacteriology, vol.190, issue.1, pp.264-274, 2008. ,
DOI : 10.1128/JB.01405-07
URL : https://hal.archives-ouvertes.fr/hal-00195548
Polymicrobial interactions stimulate resistance to host innate immunity through metabolite perception, Proceedings of the National Academy of Sciences, vol.106, issue.5, pp.1578-1583, 2009. ,
DOI : 10.1073/pnas.0809533106
Bacterial competition: surviving and thriving in the microbial jungle, Nature Reviews Microbiology, vol.44, issue.1, pp.15-25, 2010. ,
DOI : 10.1038/nrmicro2259
Multi-species biofilms: how to avoid unfriendly neighbors, FEMS Microbiology Reviews, vol.36, issue.5, pp.972-989, 2012. ,
DOI : 10.1111/j.1574-6976.2012.00328.x
Screening of Escherichia coli Species Biodiversity Reveals New Biofilm-Associated Antiadhesion Polysaccharides, mBio, vol.2, issue.3, pp.43-54, 2011. ,
DOI : 10.1128/mBio.00043-11
Bacterial biofilms: from the Natural environment to infectious diseases, Nature Reviews Microbiology, vol.146, issue.2, pp.95-108, 2004. ,
DOI : 10.1016/S0167-7012(99)00097-4
Microbial biofilms in the human gastrointestinal tract, Journal of Applied Microbiology, vol.62, issue.5, pp.1187-1196, 2007. ,
DOI : 10.1128/AEM.68.7.3401-3407.2002
The Life of Commensal Escherichia coli in the Mammalian Intestine, EcoSal Plus, vol.1, issue.1, 2004. ,
DOI : 10.1128/ecosalplus.8.3.1.2
Escherichia coli Biofilms, Curr Top Microbiol Immunol, vol.322, pp.249-289, 2008. ,
DOI : 10.1007/978-3-540-75418-3_12
URL : https://hal.archives-ouvertes.fr/pasteur-00473297
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009. ,
DOI : 10.1371/journal.pgen.1000344.s016
URL : https://hal.archives-ouvertes.fr/hal-00390293
A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Research, vol.28, issue.22, p.97, 2000. ,
DOI : 10.1093/nar/28.22.e97
Tight Modulation of Escherichia coli Bacterial Biofilm Formation through Controlled Expression of Adhesion Factors, Applied and Environmental Microbiology, vol.73, issue.10, pp.3391-3403, 2007. ,
DOI : 10.1128/AEM.02625-06
URL : https://hal.archives-ouvertes.fr/pasteur-00331439
Identification of an Aggregative Adhesion Fimbria (AAF) Type III-Encoding Operon in Enteroaggregative Escherichia coli as a Sensitive Probe for Detecting the AAF-Encoding Operon Family, Infection and Immunity, vol.70, issue.8, pp.4302-4311, 2002. ,
DOI : 10.1128/IAI.70.8.4302-4311.2002
Mechanisms of Cyclic-di-GMP Signaling in Bacteria, Annual Review of Genetics, vol.40, issue.1, pp.385-407, 2006. ,
DOI : 10.1146/annurev.genet.40.110405.090423
Escherichia coli tol and rcs genes participate in the complex network affecting curli synthesis, Microbiology, vol.151, issue.7, pp.2487-2497, 2005. ,
DOI : 10.1099/mic.0.27913-0
RcsA, an unstable positive regulator of capsular polysaccharide synthesis., Journal of Bacteriology, vol.173, issue.5, pp.1738-1747, 1991. ,
DOI : 10.1128/jb.173.5.1738-1747.1991
Proteomic screening and identification of differentially distributed membrane proteins in Escherichia coli, Molecular Microbiology, vol.141, issue.1, pp.1029-1044, 2004. ,
DOI : 10.1111/j.1365-2958.2004.04040.x
Functional Analysis of Antigen 43 in Uropathogenic Escherichia coli Reveals a Role in Long-Term Persistence in the Urinary Tract, Infection and Immunity, vol.75, issue.7, pp.3233-3244, 2007. ,
DOI : 10.1128/IAI.01952-06
URL : https://hal.archives-ouvertes.fr/pasteur-00331433
Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors, Clinical microbiology reviews, vol.11, pp.589-603, 1998. ,
The characterization of functions involved in the establishment and maturation of Klebsiella pneumoniae in vitro biofilm reveals dual roles for surface exopolysaccharides, Environmental Microbiology, vol.62, issue.3, pp.685-701, 2008. ,
DOI : 10.1073/pnas.96.7.4028
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling, Applied and Environmental Microbiology, vol.72, issue.4, pp.2449-2459, 2006. ,
DOI : 10.1128/AEM.72.4.2449-2459.2006
Bacterial Quorum Sensing: Signals, Circuits, and Implications for Biofilms and Disease, Annual Review of Biomedical Engineering, vol.10, issue.1, pp.145-167, 2008. ,
DOI : 10.1146/annurev.bioeng.10.061807.160536
Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization, Infection and immunity, vol.62, pp.5191-5194, 1994. ,
Consequences of reduction of Klebsiella pneumoniae capsule expression on interactions of this bacterium with epithelial cells, Infection and immunity, vol.67, pp.554-561, 1999. ,
Carbon nutrition of Escherichia coli in the mouse intestine, Proceedings of the National Academy of Sciences, vol.101, issue.19, pp.7427-7432, 2004. ,
DOI : 10.1073/pnas.0307888101
A Tripartite Efflux Pump Involved in Gastrointestinal Colonization by Klebsiella pneumoniae Confers a Tolerance Response to Inorganic Acid, Infection and Immunity, vol.76, issue.10, pp.4633-4641, 2008. ,
DOI : 10.1128/IAI.00356-08
Role of Deoxyribose Catabolism in Colonization of the Murine Intestine by Pathogenic Escherichia coli Strains, Infection and Immunity, vol.77, issue.4, pp.1442-1450, 2009. ,
DOI : 10.1128/IAI.01039-08
URL : https://hal.archives-ouvertes.fr/hal-00641985
Quorum sensing in Escherichia coli and Salmonella, International Journal of Medical Microbiology, vol.296, issue.2-3, pp.125-131, 2006. ,
DOI : 10.1016/j.ijmm.2006.01.041
Genetic Determinants of Self Identity and Social Recognition in Bacteria, Science, vol.321, issue.5886, pp.256-259, 2008. ,
DOI : 10.1126/science.1160033
Bacterial landlines: contact-dependent signaling in bacterial populations, Current Opinion in Microbiology, vol.12, issue.2, pp.177-181, 2009. ,
DOI : 10.1016/j.mib.2009.01.011
Conformation Change in a Self-recognizing Autotransporter Modulates Bacterial Cell-Cell Interaction, Journal of Biological Chemistry, vol.285, issue.14, pp.10616-10626, 2010. ,
DOI : 10.1074/jbc.M109.069070
Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB, Molecular Microbiology, vol.121, issue.2, pp.323-340, 2008. ,
DOI : 10.1111/j.1365-2958.2008.06404.x
Cryptic prophages, Escherichia coli and Salmonella Cellular and Molecular Biology, pp.2041-2046, 1996. ,
Prophages and bacterial genomics: what have we learned so far? Molecular microbiology 49, pp.277-300, 2003. ,
Phage therapy: Facts and fiction, International Journal of Medical Microbiology, vol.296, issue.1, pp.5-14, 2006. ,
DOI : 10.1016/j.ijmm.2005.09.002
Bacteriocins: nature, function and structure, Micron, vol.27, issue.6, pp.467-479, 1996. ,
DOI : 10.1016/S0968-4328(96)00028-5
Protein Translation and Cell Death: The Role of Rare tRNAs in Biofilm Formation and in Activating Dormant Phage Killer Genes, PLoS ONE, vol.30, issue.10, 2008. ,
DOI : 10.1371/journal.pone.0002394.s009
Prophages and bacterial genomics: what have we learned so far?, Molecular Microbiology, vol.141, issue.Suppl. 1, pp.277-300, 2003. ,
DOI : 10.1046/j.1365-2958.2003.03580.x
DNA Microarray-Mediated Transcriptional Profiling of the Escherichia coli Response to Hydrogen Peroxide, Journal of Bacteriology, vol.183, issue.15, pp.4562-4570, 2001. ,
DOI : 10.1128/JB.183.15.4562-4570.2001
Changes in Escherichia coli transcriptome during acclimatization at low temperature, Research in Microbiology, vol.154, issue.8, pp.573-580, 2003. ,
DOI : 10.1016/S0923-2508(03)00167-0
Regulon and promoter analysis of the E. coli heat-shock factor, ??32, reveals a multifaceted cellular response to heat stress, Genes & Development, vol.20, issue.13, pp.1776-1789, 2006. ,
DOI : 10.1101/gad.1428206
Low temperature (23 ??C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12, Microbiology, vol.154, issue.1, pp.148-166, 2008. ,
DOI : 10.1099/mic.0.2007/012021-0
Principles of c-di-GMP signalling in bacteria, Nature Reviews Microbiology, vol.178, issue.4, pp.263-273, 2009. ,
DOI : 10.1038/nrmicro2109