S. Amini, H. Goodarzi, and S. Tavazoie, Genetic Dissection of an Exogenously Induced Biofilm in Laboratory and Clinical Isolates of E. coli, PLoS Pathogens, vol.164, issue.1, p.1000432, 2009.
DOI : 10.1371/journal.ppat.1000432.s024

J. Anderl, M. Franklin, and P. Stewart, Role of Antibiotic Penetration Limitation in Klebsiella pneumoniae Biofilm Resistance to Ampicillin and Ciprofloxacin, Antimicrobial Agents and Chemotherapy, vol.44, issue.7, pp.1818-1824, 2000.
DOI : 10.1128/AAC.44.7.1818-1824.2000

T. Baba, A. T. Hasegawa, M. Takai, Y. Okumura, Y. Baba et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1038/msb4100050

H. Bandara, O. Lam, R. Watt, L. Jin, and L. Samaranayake, Bacterial lipopolysaccharides variably modulate in vitro biofilm formation of Candida species, Journal of Medical Microbiology, vol.59, issue.10, pp.1225-1234, 2010.
DOI : 10.1099/jmm.0.021832-0

C. Beloin, K. Michaelis, K. Lindner, P. Landini, J. Hacker et al., The Transcriptional Antiterminator RfaH Represses Biofilm Formation in Escherichia coli, Journal of Bacteriology, vol.188, issue.4, pp.1316-1331, 2006.
DOI : 10.1128/JB.188.4.1316-1331.2006
URL : https://hal.archives-ouvertes.fr/pasteur-01372312

R. Bennett-lovsey, A. Herbert, M. Sternberg, and L. Kelley, Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre, Proteins: Structure, Function, and Bioinformatics, vol.12, issue.Suppl 1, pp.611-625, 2008.
DOI : 10.1002/prot.21688

H. Berger, J. Hacker, A. Juarez, C. Hughes, and W. Goebel, Cloning of the chromosomal determinants encoding hemolysin production and mannose-resistant hemagglutination in Escherichia coli, Journal of Bacteriology, vol.152, pp.1241-1247, 1982.

C. Bernier, P. Gounon, L. Bouguenec, and C. , 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

S. Bernier, D. Lebeaux, A. Defrancesco, A. Valomon, G. Soubigou et al., Starvation, Together with the SOS Response, Mediates High Biofilm-Specific Tolerance to the Fluoroquinolone Ofloxacin, PLoS Genetics, vol.73, issue.1, p.1003144, 2013.
DOI : 10.1371/journal.pgen.1003144.s008
URL : https://hal.archives-ouvertes.fr/pasteur-01385427

B. Boles and P. Singh, Endogenous oxidative stress produces diversity and adaptability in biofilm communities, Proceedings of the National Academy of Sciences, vol.105, issue.34, pp.12503-12508, 2008.
DOI : 10.1073/pnas.0801499105

J. Boudeau, A. Glasser, E. Masseret, B. Joly, and A. Darfeuille-michaud, Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease, Infect Immun, vol.67, pp.4499-4509, 1999.

V. Bucci, C. Nadell, and J. Xavier, The Evolution of Bacteriocin Production in Bacterial Biofilms, The American Naturalist, vol.178, issue.6, pp.162-173, 2011.
DOI : 10.1086/662668

M. Carrolo, M. Frias, F. Pinto, J. Melo-cristino, and M. Ramirez, Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae, PLoS ONE, vol.4, issue.12, p.15678, 2010.
DOI : 10.1371/journal.pone.0015678.g004

L. Chao and B. Levin, Structured habitats and the evolution of anticompetitor toxins in bacteria., Proceedings of the National Academy of Sciences, vol.78, issue.10, pp.6324-6328, 1981.
DOI : 10.1073/pnas.78.10.6324

K. Chater, Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.7, issue.5, pp.761-768, 2006.
DOI : 10.1101/gad.7.5.895

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, p.97, 2000.
DOI : 10.1093/nar/28.22.e97

C. Ciornei, A. Novikov, C. Beloin, C. Fitting, M. Caroff et al., Biofilm-forming Pseudomonas aeruginosa bacteria undergo lipopolysaccharide structural modifications and induce enhanced inflammatory cytokine response in human monocytes, Innate Immunity, vol.151, issue.5, pp.288-301, 2010.
DOI : 10.1177/1753425909341807
URL : https://hal.archives-ouvertes.fr/hal-00414282

D. Cornforth and K. Foster, Competition sensing: the social side of bacterial stress responses, Nature Reviews Microbiology, vol.49, issue.4, pp.285-293, 2013.
DOI : 10.1038/nrmicro2977

F. Corpet, Multiple sequence alignment with hierarchical clustering, Nucleic Acids Research, vol.16, issue.22, pp.10881-10890, 1988.
DOI : 10.1093/nar/16.22.10881
URL : http://doi.org/10.1093/nar/16.22.10881

J. Courcelle, A. Khodursky, B. Peter, P. Brown, and P. Hanawalt, Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli, Genetics, vol.158, pp.41-64, 2001.

T. Czaran, R. Hoekstra, and L. Pagie, Chemical warfare between microbes promotes biodiversity, Proceedings of the National Academy of Sciences, vol.99, issue.2, pp.786-790, 2002.
DOI : 10.1073/pnas.012399899
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117383

S. Da-re, L. Quere, B. Ghigo, J. Beloin, and C. , 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

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.97, issue.12, pp.6640-6645, 2000.
DOI : 10.1073/pnas.120163297

S. Duquesne, V. Petit, J. Peduzzi, and S. Rebuffat, Structural and Functional Diversity of Microcins, Gene-Encoded Antibacterial Peptides from Enterobacteria, Journal of Molecular Microbiology and Biotechnology, vol.13, issue.4, pp.200-209, 2007.
DOI : 10.1159/000104748
URL : https://hal.archives-ouvertes.fr/hal-00146785

R. Durrett and S. Levin, Allelopathy in Spatially Distributed Populations, Journal of Theoretical Biology, vol.185, issue.2, pp.165-171, 1997.
DOI : 10.1006/jtbi.1996.0292

J. Eraso, M. Chidambaram, and G. Weinstock, Increased production of colicin E1 in stationary phase., Journal of Bacteriology, vol.178, issue.7, pp.1928-1935, 1996.
DOI : 10.1128/jb.178.7.1928-1935.1996

A. Fernandez-de-henestrosa, T. Ogi, S. Aoyagi, D. Chafin, J. Hayes et al., Identification of additional genes belonging to the LexA regulon in Escherichia coli, Molecular Microbiology, vol.180, issue.6, pp.1560-1572, 2000.
DOI : 10.1046/j.1365-2958.2000.01826.x

A. Gardner, S. West, and A. Buckling, Bacteriocins, spite and virulence, Proceedings of the Royal Society B: Biological Sciences, vol.271, issue.1547, pp.1529-1535, 2004.
DOI : 10.1098/rspb.2004.2756
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691756

J. Ghigo, Are there biofilm-specific physiological pathways beyond a reasonable doubt?, Research in Microbiology, vol.154, issue.1, pp.1-8, 2003.
DOI : 10.1016/S0923-2508(02)00012-8

O. Gillor, B. Kirkup, and M. Riley, Colicins and Microcins: The Next Generation Antimicrobials, Adv Appl Microbiol, vol.54, pp.129-146, 2004.
DOI : 10.1016/S0065-2164(04)54005-4

O. Gillor, J. Vriezen, and M. Riley, The role of SOS boxes in enteric bacteriocin regulation, Microbiology, vol.154, issue.6, pp.1783-1792, 2008.
DOI : 10.1099/mic.0.2007/016139-0

B. Giwercman, A. Fomsgaard, B. Mansa, and N. Hoiby, Polyacrylamide gel electrophoresis analysis of lipopolysaccharide from Pseudomonas aeruginosa growing planktonically and as biofilm, FEMS Microbiol Immunol, vol.4, pp.225-229, 1992.

W. Hamilton, The genetical evolution of social behaviour. II, Journal of Theoretical Biology, vol.7, issue.1, pp.1-52, 1964.
DOI : 10.1016/0022-5193(64)90039-6

M. Hibbing, C. Fuqua, M. Parsek, and S. Peterson, Bacterial competition: surviving and thriving in the microbial jungle, Nature Reviews Microbiology, vol.44, issue.1, pp.15-25, 2010.
DOI : 10.1038/nrmicro2259

N. Hoiby, T. Bjarnsholt, M. Givskov, S. Molin, and O. Ciofu, Antibiotic resistance of bacterial biofilms, International Journal of Antimicrobial Agents, vol.35, issue.4, pp.322-332, 2010.
DOI : 10.1016/j.ijantimicag.2009.12.011
URL : https://hal.archives-ouvertes.fr/hal-00567285

R. Inglis, A. Gardner, P. Cornelis, and A. Buckling, Spite and virulence in the bacterium Pseudomonas aeruginosa, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.5703-5707, 2009.
DOI : 10.1073/pnas.0810850106

G. James, L. Beaudette, and J. , Interspecies bacterial interactions in biofilms, Journal of Industrial Microbiology, vol.40, issue.4, pp.257-262, 1995.
DOI : 10.1007/BF01569978

B. Kirkup and M. Riley, Antibiotic-mediated antagonism leads to a bacterial game of rock???paper???scissors in vivo, Nature, vol.428, issue.6981, pp.412-414, 2004.
DOI : 10.1038/nature02429

I. Kolodkin-gal, D. Romero, S. Cao, J. Clardy, R. Kolter et al., D-Amino Acids Trigger Biofilm Disassembly, Science, vol.328, issue.5978, pp.627-629, 2010.
DOI : 10.1126/science.1188628
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921573

I. Kolodkin-gal, S. Cao, L. Chai, T. Bottcher, R. Kolter et al., RETRACTED: A Self-Produced Trigger for Biofilm Disassembly that Targets Exopolysaccharide, Cell, vol.149, issue.3, pp.684-692, 2012.
DOI : 10.1016/j.cell.2012.02.055
URL : http://doi.org/10.1016/j.cell.2012.02.055

J. Kreth, J. Merritt, C. Bordador, W. Shi, and F. Qi, Transcriptional analysis of mutacin I (mutA) gene expression in planktonic and biofilm cells of Streptococcus mutans using fluorescent protein and glucuronidase reporters, Oral Microbiology and Immunology, vol.148, issue.4, pp.252-256, 2004.
DOI : 10.1023/A:1013325627378

I. Kuhar and D. Zgur-bertok, Transcription regulation of the colicin K cka gene reveals induction of colicin synthesis by differential responses to environmental signals, Journal of Bacteriology, vol.181, pp.7373-7380, 1999.

C. Law, C. Penfold, D. Walker, G. Moore, R. James et al., cells from colicin E9 cytotoxicity, FEBS Letters, vol.6, issue.2-3, pp.127-132, 2003.
DOI : 10.1016/S0014-5793(03)00511-8

H. Lee and H. Kim, Lantibiotics, class I bacteriocins from the genus Bacillus, J Microbiol Biotechnol, vol.21, pp.229-235, 2011.

D. Liu and P. Reeves, Escherichia coli K12 regains its O antigen, Microbiology, vol.140, issue.1, pp.49-57, 1994.
DOI : 10.1099/13500872-140-1-49

J. Liu and J. Parkinson, Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control., Journal of Bacteriology, vol.171, issue.3, pp.1254-1261, 1989.
DOI : 10.1128/jb.171.3.1254-1261.1989

B. Lugtenberg, J. Meijers, R. Peters, P. Van-der-hoek, and L. Van-alphen, K12 into four bands, FEBS Letters, vol.248, issue.1-2, pp.254-258, 1975.
DOI : 10.1016/0014-5793(75)80272-9

H. Majeed, O. Gillor, B. Kerr, and M. Riley, Competitive interactions in Escherichia coli populations: the role of bacteriocins, The ISME Journal, vol.102, issue.1, pp.71-81, 2011.
DOI : 10.1098/rspb.2007.1461

J. Merritt and F. Qi, The mutacins of Streptococcus mutans: regulation and ecology, Molecular Oral Microbiology, vol.49, issue.Suppl, pp.57-69, 2012.
DOI : 10.1111/j.2041-1014.2011.00634.x

H. Mobley, D. Green, A. Trifillis, D. Johnson, G. Chippendale et al., Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: role of hemolysin in some strains, Infect Immun, vol.58, pp.1281-1289, 1990.

C. Nadell, J. Xavier, and K. Foster, The sociobiology of biofilms, FEMS Microbiology Reviews, vol.33, issue.1, pp.206-224, 2009.
DOI : 10.1111/j.1574-6976.2008.00150.x

H. Osada and T. Beppu, Lipopolysaccharide defective mutant of Escherichia coli with decreased sensitivity to colicin E2., Agricultural and Biological Chemistry, vol.49, issue.6, pp.1813-1819, 1985.
DOI : 10.1271/bbb1961.49.1813

C. Parker, A. Kloser, C. Schnaitman, M. Stein, S. Gottesman et al., Role of the rfaG and rfaP genes in determining the lipopolysaccharide core structure and cell surface properties of Escherichia coli K-12., Journal of Bacteriology, vol.174, issue.8, pp.2525-2538, 1992.
DOI : 10.1128/jb.174.8.2525-2538.1992

O. Rendueles, L. Travier, P. Latour-lambert, T. Fontaine, M. J. Denamur et al., 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

O. Rendueles and J. Ghigo, 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

O. Rendueles, J. Kaplan, and J. Ghigo, Antibiofilm polysaccharides, Environmental Microbiology, vol.39, issue.2, pp.334-346, 2013.
DOI : 10.1111/j.1462-2920.2012.02810.x
URL : https://hal.archives-ouvertes.fr/hal-01001499

M. Riley and D. Gordon, The ecological role of bacteriocins in bacterial competition, Trends in Microbiology, vol.7, issue.3, pp.129-133, 1999.
DOI : 10.1016/S0966-842X(99)01459-6

M. Riley, L. Cadavid, M. Collett, M. Neely, M. Adams et al., The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification, Microbiology, vol.146, issue.7, pp.1671-1677, 2000.
DOI : 10.1099/00221287-146-7-1671

M. Riley and J. Wertz, Bacteriocins: Evolution, Ecology, and Application, Annual Review of Microbiology, vol.56, issue.1, pp.117-137, 2002.
DOI : 10.1146/annurev.micro.56.012302.161024

D. Skurnik, R. Ruimy, A. Andremont, C. Amorin, P. Rouquet et al., Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli, Journal of Antimicrobial Chemotherapy, vol.57, issue.6, 2006.
DOI : 10.1093/jac/dkl122

D. Smajs, H. Pilsl, and V. Braun, Colicin U, a novel colicin produced by Shigella boydii., Journal of Bacteriology, vol.179, issue.15, pp.4919-4928, 1997.
DOI : 10.1128/jb.179.15.4919-4928.1997
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179342

D. Smajs, P. Matejkova, and G. Weinstock, Recognition of pore-forming colicin Y by its cognate immunity protein, FEMS Microbiol Lett, vol.258, pp.108-113, 2006.

A. Spiers and P. Rainey, The Pseudomonas fluorescens SBW25 wrinkly spreader biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity, Microbiology, vol.151, issue.9, pp.2829-2839, 2005.
DOI : 10.1099/mic.0.27984-0

P. Stewart and M. Franklin, Physiological heterogeneity in biofilms, Nature Reviews Microbiology, vol.167, issue.3, pp.199-210, 2008.
DOI : 10.1038/nrmicro1838

J. Strassmann, O. Gilbert, and D. Queller, Kin Discrimination and Cooperation in Microbes, Annual Review of Microbiology, vol.65, issue.1, pp.349-367, 2011.
DOI : 10.1146/annurev.micro.112408.134109

K. Tamura, N. Peterson, G. Stecher, M. Nei, and S. Kumar, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626

C. Tsai and C. Frasch, A sensitive silver stain for detecting lipopolysaccharides in polyacrylamide gels, Analytical Biochemistry, vol.119, issue.1, pp.115-119, 1982.
DOI : 10.1016/0003-2697(82)90673-X

J. Valle, S. Da-re, S. Schmid, D. Skurnik, D. 'ari et al., 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

H. Weltzien and M. Jesaitis, THE NATURE OF THE COLICIN K RECEPTOR OF ESCHERICHIA COLI CULLEN, Journal of Experimental Medicine, vol.133, issue.3, pp.534-553, 1971.
DOI : 10.1084/jem.133.3.534

S. Wenzel and R. Muller, Myxobacteria??????microbial factories??? for the production of bioactive secondary metabolites, Molecular BioSystems, vol.16, issue.19, pp.567-574, 2009.
DOI : 10.1039/b901287g

L. Yan, K. Boyd, D. Adams, and J. Burgess, Biofilm-Specific Cross-Species Induction of Antimicrobial Compounds in Bacilli, Applied and Environmental Microbiology, vol.69, issue.7, pp.3719-3727, 2003.
DOI : 10.1128/AEM.69.7.3719-3727.2003