C. Kuo, N. A. Moran, and H. Ochman, The consequences of genetic drift for bacterial genome complexity, Genome Research, vol.19, issue.8, pp.1450-1454, 2009.
DOI : 10.1101/gr.091785.109

T. Michael, T. D. Madigan, and . Brock, Brock biology of microorganisms, 2012.

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes: The unseen majority, Proceedings of the National Academy of Sciences, vol.26, issue.1-2, pp.6578-6583, 1998.
DOI : 10.1007/BF02111285
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC33863/pdf

C. Dye, After 2015: infectious diseases in a new era of health and development, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.15, issue.11, p.20130426, 1645.
DOI : 10.5588/ijtld.11.0503

S. E. Rollins, M. , S. M. Rollins, E. T. Phd, and M. Ryan, Yersinia pestis and the Plague, Pathology Patterns Reviews, vol.119, issue.0, pp.78-85, 2003.
DOI : 10.1309/DQM93R8QNQWBFYU8

P. William, J. J. Robins, and . Mekalanos, Genomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen, Curr. Top. Microbiol. Immunol, vol.379, pp.211-229, 2014.

A. K. Siddique and R. Cash, Cholera Outbreaks in the Classical Biotype Era, Curr. Top. Microbiol. Immunol, vol.379, pp.1-16, 2014.
DOI : 10.1007/82_2013_361

K. Surendra, A. Sharma, and . Mohan, Tuberculosis: From an incurable scourge to a curable disease -journey over a millennium, Indian J. Med. Res, vol.137, issue.3, pp.455-493, 2013.
DOI : 10.5005/jp/books/10992

J. Peter, M. Turnbaugh, T. Hamady, B. L. Yatsunenko, A. Cantarel et al., A core gut microbiome in obese and lean twins, Nature, issue.7228, pp.457480-484, 2009.

P. Benjamin, A. Willing, M. Vacharaksa, T. Croxen, B. B. Thanachayanont et al., Altering Host Resistance to Infections through Microbial Transplantation, PLoS ONE, vol.6, issue.10, p.26988, 2011.

R. Diaz-heijtz, S. Wang, F. Anuar, Y. Qian, B. Björkholm et al., Normal gut microbiota modulates brain development and behavior, Proceedings of the National Academy of Sciences, vol.17, issue.10, pp.3047-3052, 2011.
DOI : 10.1016/j.euroneuro.2007.02.014

T. Largus, K. Angenent, . Karim, H. Muthanna, B. A. Al-dahhan et al., Production of bioenergy and biochemicals from industrial and agricultural wastewater, Trends in Biotechnology, vol.22, issue.9, pp.477-485, 2004.

Y. J. , L. , and K. J. Jeong, Challenges to production of antibodies in bacteria and yeast, J. Biosci. Bioeng, 2015.

W. Mu, T. Zhang, and B. Jiang, An overview of biological production of L-theanine, Biotechnology Advances, vol.33, issue.3-4, 2015.
DOI : 10.1016/j.biotechadv.2015.04.004

A. Sukan, I. Roy, and T. Keshavarz, Dual production of biopolymers from bacteria, Carbohydrate Polymers, vol.126, pp.47-51, 2015.
DOI : 10.1016/j.carbpol.2015.03.001

R. Bernard and . Glick, The enhancement of plant growth by free-living bacteria, Can. J. Microbiol, vol.41, issue.2, pp.109-117, 1995.

J. Joris-am-missotten, J. Michiels, S. Degroote, and . Smet, Fermented liquid feed for pigs: an ancient technique for the future, Journal of Animal Science and Biotechnology, vol.6, issue.1, p.4, 2015.
DOI : 10.1016/0301-6226(86)90006-0

O. Diego, R. Serra, and . Hengge, Stress responses go three dimensional ? the spatial order of physiological differentiation in bacterial macrocolony biofilms, Environ Microbiol, vol.16, issue.6, pp.1455-1471, 2014.

L. Hall-stoodley, J. William-costerton, and P. Stoodley, 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

F. Westall, J. Maarten, J. De-wit, S. Dann, . Van-der-gaast et al., Early Archean fossil bacteria and biofilms in hydrothermally-influenced sediments from the Barberton greenstone belt, South Africa, Precambrian Research, vol.106, issue.1-2, pp.93-116, 2001.
DOI : 10.1016/S0301-9268(00)00127-3

B. Rasmussen, Filamentous microfossils in a 3,235-million-year- old volcanogenic massive sulphide deposit, Nature, vol.405, issue.6787, pp.676-679, 2000.
DOI : 10.1038/35015063

C. E. Zobell, The Effect of Solid Surfaces upon Bacterial Activity, J Bacteriol, vol.46, issue.1, pp.39-56, 1943.

T. J. Battin, A. Wille, B. Sattler, and R. Psenner, Phylogenetic and Functional Heterogeneity of Sediment Biofilms along Environmental Gradients in a Glacial Stream, Applied and Environmental Microbiology, vol.67, issue.2, pp.799-807, 2001.
DOI : 10.1128/AEM.67.2.799-807.2001

M. E. Davey and G. A. O-'toole, Microbial Biofilms: from Ecology to Molecular Genetics, Microbiology and Molecular Biology Reviews, vol.64, issue.4, pp.847-867, 2000.
DOI : 10.1128/MMBR.64.4.847-867.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99016

S. W. Wessel, Y. Chen, A. Maitra, E. R. Van-den-heuvel, A. M. Slomp et al., Adhesion Forces and Composition of Planktonic and Adhering Oral Microbiomes, Journal of Dental Research, vol.93, issue.1, pp.84-88, 2014.
DOI : 10.1177/0022034513511822

O. Ciofu, T. Tolker-nielsen, P. Ø. Jensen, H. Wang, and N. Høiby, Antimicrobial resistance, respiratory tract infections and role of biofilms in lung infections in cystic fibrosis patients, Advanced Drug Delivery Reviews, vol.85, 2014.
DOI : 10.1016/j.addr.2014.11.017

A. H. Nobbs, R. J. Lamont, and H. F. Jenkinson, Streptococcus Adherence and Colonization, Microbiology and Molecular Biology Reviews, vol.73, issue.3, pp.407-450, 2009.
DOI : 10.1128/MMBR.00014-09
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738137

I. Francolini and G. Donelli, Prevention and control of biofilm-based medical-device-related infections, FEMS Immunology & Medical Microbiology, vol.59, issue.3, pp.227-238, 2010.
DOI : 10.1111/j.1574-695X.2010.00665.x

P. Michael, G. W. Schultz, and . Swain, The influence of biofilms on skin friction drag, Biofouling, vol.15, issue.1-3, pp.129-139, 2000.

M. Morikawa, Beneficial biofilm formation by industrial bacteria Bacillus subtilis and related species, Journal of Bioscience and Bioengineering, vol.101, issue.1, pp.1-8, 2006.
DOI : 10.1263/jbb.101.1

T. Shaw, M. Winston, C. J. Rupp, I. Klapper, and P. Stoodley, Commonality of Elastic Relaxation Times in Biofilms, Physical Review Letters, vol.93, issue.9, p.98102, 2004.
DOI : 10.1103/PhysRevLett.93.098102

H. Flemming and J. Wingender, The biofilm matrix, Nature Reviews Microbiology, vol.79, issue.9, pp.623-633, 2010.
DOI : 10.1038/nrmicro2415

J. W. Costerton, Z. Lewandowski, D. E. Caldwell, D. R. Korber, and H. M. Lappin-scott, Microbial Biofilms, Annual Review of Microbiology, vol.49, issue.1, pp.711-745, 1995.
DOI : 10.1146/annurev.mi.49.100195.003431

T. F. Mah and G. A. O-'toole, Mechanisms of biofilm resistance to antimicrobial agents, 35] P. Gilbert, J. Das, and I. Foley. Biofilm susceptibility to antimicrobials, pp.34-39, 2001.
DOI : 10.1016/S0966-842X(00)01913-2

J. Algirdas, M. J. Jesaitis, D. Franklin, M. Berglund, C. I. Sasaki et al., Compromised host defense on Pseudomonas aeruginosa biofilms: characterization of neutrophil and biofilm interactions, J. Immunol, issue.8, pp.1714329-4339, 2003.

T. D. Scherr, C. E. Heim, J. M. Morrison, and T. Kielian, Hiding in Plain Sight: Interplay between Staphylococcal Biofilms and Host Immunity, Frontiers in Immunology, vol.5, p.37, 2014.
DOI : 10.3389/fimmu.2014.00037
URL : http://doi.org/10.3389/fimmu.2014.00037

M. O. Elasri and R. V. Miller, Study of the response of a biofilm bacterial community to UV radiation, Appl. Environ. Microbiol, vol.65, issue.5, pp.2025-2031, 1999.

E. M. Espeland and R. G. Wetzel, Complexation, Stabilization, and UV Photolysis of Extracellular and Surface-Bound Glucosidase and Alkaline Phosphatase: Implications for Biofilm Microbiota, Microbial Ecology, vol.42, issue.4, pp.572-585, 2001.
DOI : 10.1007/s00248-001-1023-7

W. Chang, M. Van-de-mortel, L. Nielsen, G. Nino-de-guzman, X. Li et al., Alginate Production by Pseudomonas putida Creates a Hydrated Microenvironment and Contributes to Biofilm Architecture and Stress Tolerance under Water-Limiting Conditions, Journal of Bacteriology, vol.189, issue.22, pp.8290-8299, 2007.
DOI : 10.1128/JB.00727-07
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168710

J. J. Harrison, H. Ceri, and R. J. Turner, Multimetal resistance and tolerance in microbial biofilms, Nature Reviews Microbiology, vol.5, issue.12, pp.928-938, 2007.
DOI : 10.1038/nrmicro1774

S. Koechler, J. Farasin, J. Cleiss-arnold, and F. Arsène-ploetze, Toxic metal resistance in biofilms: diversity of microbial responses and their evolution, Research in Microbiology, vol.166, issue.10, 2015.
DOI : 10.1016/j.resmic.2015.03.008

C. Matz, D. Mcdougald, A. M. Moreno, P. Y. Yung, F. H. Yildiz et al., Biofilm formation and phenotypic variation enhance predation-driven persistence of Vibrio cholerae, Proceedings of the National Academy of Sciences, vol.102, issue.17, pp.16819-16824, 2005.
DOI : 10.1073/pnas.0502069102
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1283802

P. Stoodley, I. Dodds, J. D. Boyle, and H. M. Lappin-scott, Influence of hydrodynamics and nutrients on biofilm structure, Journal of Applied Microbiology, vol.28, issue.S1, pp.19-28, 1998.
DOI : 10.1111/j.1365-2672.1998.tb05279.x

M. Klausen, A. Heydorn, P. Ragas, L. Lambertsen, A. Aaes-jørgensen et al., Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants, Molecular Microbiology, vol.413, issue.6, pp.1511-1524, 2003.
DOI : 10.1046/j.1365-2958.2003.03525.x

E. Banin, M. L. Vasil, E. Peter, and . Greenberg, From The Cover: Iron and Pseudomonas aeruginosa biofilm formation, Proceedings of the National Academy of Sciences, vol.50, issue.1, pp.11076-11081, 2005.
DOI : 10.1046/j.1365-2958.2003.03677.x
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182440

C. P. Kempes, C. Okegbe, Z. Mears-clarke, M. J. Follows, and L. E. Dietrich, Morphological optimization for access to dual oxidants in biofilms, Proceedings of the National Academy of Sciences, vol.61, issue.5, pp.208-213, 2014.
DOI : 10.1111/j.1365-2958.2006.05306.x

I. Dogsa, M. Brloznik, D. Stopar, and I. Mandic-mulec, Exopolymer Diversity and the Role of Levan in Bacillus subtilis Biofilms, PLoS ONE, vol.177, issue.4, p.2013
DOI : 10.1371/journal.pone.0062044.s004

R. Glud and R. , PHOTOSYNTHESIS AND PHOTOSYNTHESIS-COUPLED RESPIRATION IN NATURAL BIOFILMS QUANTIFIED WITH OXYGEN MICROSENSORS1, Journal of Phycology, vol.28, issue.1, pp.51-60, 1992.
DOI : 10.1111/j.0022-3646.1992.00051.x

A. Schramm, L. Larsen, N. Revsbech, N. Ramsing, K. Amann et al., Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes

B. Suriani-abdul-rani, H. Pitts, R. A. Beyenal, Z. Veluchamy, W. M. Lewandowski et al., Spatial Patterns of DNA Replication, Protein Synthesis, and Oxygen Concentration within Bacterial Biofilms Reveal Diverse Physiological States, Journal of Bacteriology, vol.189, issue.11, pp.4223-4233, 2007.
DOI : 10.1128/JB.00107-07

M. Jurrien, K. J. Vroom, H. C. De-grauw, D. J. Gerritsen, P. D. Bradshaw et al., Depth Penetration and Detection of pH Gradients in Biofilms by Two-Photon Excitation Microscopy, Appl. Environ. Microbiol, issue.8, pp.653502-3511, 1999.

S. Philip, R. Stewart, D. Kolter, A. Siegele, and . Tormo, Diffusion in Biofilms The Stationary-Phase of the Bacterial Life-Cycle, J. Bacteriol. Annu. Rev. Microbiol, vol.185, issue.47, pp.1485-1491855, 1993.

E. Werner, F. Roe, A. Bugnicourt, M. J. Franklin, A. Heydorn et al., Stratified Growth in Pseudomonas aeruginosa Biofilms, Applied and Environmental Microbiology, vol.70, issue.10, pp.6188-6196, 2004.
DOI : 10.1128/AEM.70.10.6188-6196.2004
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC522130

K. S. Williamson, L. A. Richards, A. C. Perez-osorio, B. Pitts, K. Mcinnerney et al., Heterogeneity in Pseudomonas aeruginosa Biofilms Includes Expression of Ribosome Hibernation Factors in the Antibiotic-Tolerant Subpopulation and Hypoxia-Induced Stress Response in the Metabolically Active Population, Journal of Bacteriology, vol.194, issue.8, pp.1942062-2073, 2012.
DOI : 10.1128/JB.00022-12

D. O. Serra, A. M. Richter, G. Klauck, F. Mika, and R. Hengge, Microanatomy at Cellular Resolution and Spatial Order of Physiological Differentiation in a Bacterial Biofilm, mBio, vol.4, issue.2, pp.103-116, 2013.
DOI : 10.1128/mBio.00103-13

H. Vlamakis, C. Aguilar, R. Losick, and R. Kolter, Control of cell fate by the formation of an architecturally complex bacterial community, Genes & Development, vol.22, issue.7, pp.945-953, 2008.
DOI : 10.1101/gad.1645008

J. Adler and B. Templeton, The Effect of Environmental Conditions on the Motility of Escherichia coli, Journal of General Microbiology, vol.46, issue.2, pp.175-184, 1967.
DOI : 10.1099/00221287-46-2-175

C. D. Amsler, M. Cho, and P. Matsumura, Multiple factors underlying the maximum motility of Escherichia coli as cultures enter post-exponential growth., Journal of Bacteriology, vol.175, issue.19, pp.6238-6244, 1993.
DOI : 10.1128/jb.175.19.6238-6244.1993

M. Liu, T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin et al., Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli, Journal of Biological Chemistry, vol.280, issue.16, pp.15921-15927, 2005.
DOI : 10.1074/jbc.M414050200

R. Lange and R. Hengge-aronis, Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S., Journal of Bacteriology, vol.173, issue.14, pp.4474-4481, 1991.
DOI : 10.1128/jb.173.14.4474-4481.1991

D. O. Serra, A. M. Richter, and R. Hengge, Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms, Journal of Bacteriology, vol.195, issue.24, pp.5540-5554, 2013.
DOI : 10.1128/JB.00946-13
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889604

C. Pesavento, G. Becker, N. Sommerfeldt, A. Possling, N. Tschowri et al., Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli, Genes & Development, vol.22, issue.17, pp.2434-2446, 2008.
DOI : 10.1101/gad.475808

M. Kirisits, L. Prost, M. Starkey, and M. R. Parsek, Characterization of Colony Morphology Variants Isolated from Pseudomonas aeruginosa Biofilms, Applied and Environmental Microbiology, vol.71, issue.8, pp.4809-4821, 2005.
DOI : 10.1128/AEM.71.8.4809-4821.2005

R. Blaise, M. Boles, P. K. Thoendel, and . Singh, Selfgenerated diversity produces " insurance effects " in biofilm communities, pp.16630-16635, 2004.

S. Philip, M. J. Stewart, and . Franklin, Physiological heterogeneity in biofilms, Nat Rev Micro, vol.6, issue.3, pp.199-210, 2008.

P. Lebaron, P. Bauda, M. C. Lett, Y. Duval-iflah, P. Simonet et al., strains in seven sterile microcosms, Canadian Journal of Microbiology, vol.43, issue.6, pp.534-540, 1997.
DOI : 10.1139/m97-076

B. B. Christensen, C. Sternberg, J. B. Andersen, L. Eberl, S. Moller et al., Establishment of new genetic traits in a microbial biofilm community, Appl. Environ. Microbiol, vol.64, issue.6, pp.2247-2255, 1998.

A. P. Roberts, J. Pratten, M. Wilson, and P. Mullany, in a model oral biofilm, FEMS Microbiology Letters, vol.177, issue.1, pp.63-66, 1999.
DOI : 10.1111/j.1574-6968.1999.tb13714.x

C. W. Michiels-rob-van-houdt, Role of bacterial cell surface structures in Escherichia coli biofilm formation, Research in microbiology, vol.156, pp.5-6626, 2005.

D. Monroe, Looking for Chinks in the Armor of Bacterial Biofilms, PLoS Biology, vol.5, issue.11, p.307, 2007.
DOI : 10.1371/journal.pbio.0050307.g002

D. Russell, G. A. Monds, and . Toole, The developmental model of microbial biofilms: ten years of a paradigm up for review, Trends in Microbiology, vol.17, issue.2, pp.73-87, 2009.

T. Matthew, C. Cabeen, and . Jacobs-wagner, Bacterial cell shape, Nat Rev Micro, vol.3, issue.8, pp.601-610, 2005.

L. G. Burman, J. Raichler, and J. T. Park, Evidence for diffuse growth of the cylindrical portion of the Escherichia coli murein sacculus, J. Bacteriol, vol.155, issue.3, pp.983-988, 1983.

A. Miguel, H. De-pedro, A. L. Schwarz, and . Koch, Patchiness of murein insertion into the sidewall of Escherichia coli, Microbiology, vol.149, issue.7, pp.1753-1761, 2003.

A. Miguel, C. G. De-pedro, H. Grünfelder, and . Schwarz, Restricted Mobility of Cell Surface Proteins in the Polar Regions of Escherichia coli, J Bacteriol, vol.186, issue.9, pp.2594-2602, 2004.

A. Richard, J. Daniel, and . Errington, Control of Cell Morphogenesis in Bacteria: Two Distinct Ways to Make a Rod-Shaped Cell, Cell, vol.113, issue.6, pp.767-776, 2003.

M. Letek, M. Fiuza, E. Ordóñez, A. F. Villadangos, A. Ramos et al., Cell growth and cell division in the rod-shaped actinomycete Corynebacterium glutamicum, Antonie van Leeuwenhoek, vol.153, issue.1
DOI : 10.1007/s10482-008-9224-4

J. B. Pamela, M. A. Brown, D. T. De-pedro, C. Kysela, J. Van-der-henst et al., Polar growth in the Alphaproteobacterial order Rhizobiales, Proc. Natl. Acad. Sci. U.S.A, vol.109, issue.5, pp.1697-1701, 2012.

E. David, K. D. Nelson, and . Young, Contributions of PBP 5 anddd- Carboxypeptidase Penicillin Binding Proteins to Maintenance of Cell Shape in Escherichia coli, J. Bacteriol, vol.183, issue.10, pp.3055-3064, 2001.

J. F. Laura, R. Jones, J. Carballido-lópez, and . Errington, Control of Cell Shape in Bacteria: Helical, Actin-like Filaments in Bacillus subtilis, Cell, vol.104, issue.6, pp.913-922, 2001.

R. M. Figge, A. V. Divakaruni, and J. W. Gober, MreB, the cell shape-determining bacterial actin homologue, co-ordinates cell wall morphogenesis in Caulobacter crescentus, Molecular Microbiology, vol.171, issue.5, pp.1321-1332, 2004.
DOI : 10.1111/j.1365-2958.2003.03936.x

T. Nilsen, A. W. Yan, G. Gale, and M. B. Goldberg, Presence of Multiple Sites Containing Polar Material in Spherical Escherichia coli Cells That Lack MreB, Journal of Bacteriology, vol.187, issue.17, pp.6187-6196, 2005.
DOI : 10.1128/JB.187.17.6187-6196.2005

S. Wang, H. Arellano-santoyo, P. A. Combs, and J. W. Shaevitz, Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria, Proceedings of the National Academy of Sciences, vol.55, issue.1, pp.9182-9185, 2010.
DOI : 10.1111/j.1365-2958.2004.04367.x
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889055

K. D. Young, The Selective Value of Bacterial Shape, Microbiology and Molecular Biology Reviews, vol.70, issue.3, pp.660-703, 2006.
DOI : 10.1128/MMBR.00001-06

X. Yao, M. Jericho, D. Pink, and T. Beveridge, Thickness and Elasticity of Gram-Negative Murein Sacculi Measured by Atomic Force Microscopy, J. Bacteriol, vol.181, issue.22, pp.6865-6875, 1999.

K. Bush, Antimicrobial agents targeting bacterial cell walls and cell membranes, Revue Scientifique et Technique de l'OIE, vol.31, issue.1, pp.43-56, 2012.
DOI : 10.20506/rst.31.1.2096

H. Labischinski, E. W. Goodell, A. Goodell, and M. L. Hochberg, Direct proof of a "more-than-single-layered" peptidoglycan architecture of Escherichia coli W7: a neutron small-angle scattering study., Journal of Bacteriology, vol.173, issue.2, pp.751-756, 1991.
DOI : 10.1128/jb.173.2.751-756.1991

L. Gan, S. Chen, and G. J. Jensen, Molecular organization of Gram-negative peptidoglycan, Proceedings of the National Academy of Sciences, vol.161, issue.3, pp.18953-18957, 2008.
DOI : 10.1016/j.jsb.2007.08.002

J. V. Höltje, Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli, Microbiol. Mol. Biol. Rev, vol.62, issue.1, pp.181-203, 1998.

D. Scheffers and M. G. Pinho, Bacterial Cell Wall Synthesis: New Insights from Localization Studies, Microbiology and Molecular Biology Reviews, vol.69, issue.4, pp.585-607, 2005.
DOI : 10.1128/MMBR.69.4.585-607.2005
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1306805

A. Typas, M. Banzhaf, C. A. Gross, and W. Vollmer, From the regulation of peptidoglycan synthesis to bacterial growth and morphology, Nature Reviews Microbiology, vol.185, issue.2, pp.123-136, 2012.
DOI : 10.1038/nrmicro2677

T. Matthew, S. Swulius, H. J. Chen, Z. Ding, A. Li et al., Long helical filaments are not seen encircling cells in electron cryotomograms of rodshaped bacteria, Biochem. Biophys. Res. Commun, vol.407, issue.4, pp.650-655, 2011.

T. Matthew, G. J. Swulius, and . Jensen, The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag, J. Bacteriol, vol.194, issue.23, pp.6382-6386, 2012.

C. L. William-margolin, A. White, J. W. Kitich, and . Gober, The price of tags in protein localization studies Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD, J. Bacteriol. Mol. Microbiol, vol.194103, issue.763, pp.6369-6371616, 2010.

T. Mohammadi, A. Karczmarek, M. Crouvoisier, A. Bouhss, D. Mengin-lecreulx et al., The essential peptidoglycan glycosyltransferase MurG forms a complex with proteins involved in lateral envelope growth as well as with proteins involved in cell division in Escherichia coli, Molecular Microbiology, vol.171, issue.4, pp.1106-1121, 2007.
DOI : 10.1016/S0003-2697(02)00622-X

J. Domínguez-escobar, A. Chastanet, A. H. Crevenna, and V. Fromion, Roland Wedlich-Söldner, and Rut Carballido-López. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria, Science, issue.6039, pp.333225-228, 2011.

E. C. Garner, R. Bernard, W. Wang, X. Zhuang, D. Z. Rudner et al., Coupled, Circumferential Motions of the Cell Wall Synthesis Machinery and MreB Filaments in B. subtilis, Science, vol.190, issue.11, pp.333222-225, 2011.
DOI : 10.1128/JB.00207-08

L. Courtney, J. W. White, and . Gober, MreB: pilot or passenger of cell wall synthesis?, Trends in Microbiology, vol.20, issue.2, pp.74-79, 2012.

J. Löwe and L. A. Amos, Crystal structure of the bacterial cell-division protein FtsZ, Nature, issue.6663, pp.391203-206, 1998.

P. Harold, D. W. Erickson, K. A. Taylor, D. Taylor, and . Bramhill, Bacterial Cell Division Protein FtsZ Assembles into Protofilament Sheets and Minirings, Structural Homologs of Tubulin Polymers, Proceedings of the National Academy of Sciences of the United States of America, vol.93, issue.1, p.519, 1996.

D. E. Anderson, F. J. Gueiros-filho, and H. P. Erickson, Assembly Dynamics of FtsZ Rings in Bacillus subtilis and Escherichia coli and Effects of FtsZ-Regulating Proteins, Journal of Bacteriology, vol.186, issue.17, pp.5775-5781, 2004.
DOI : 10.1128/JB.186.17.5775-5781.2004

S. Pichoff and J. Lutkenhaus, Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA, Molecular Microbiology, vol.187, issue.6, pp.1722-1734, 2005.
DOI : 10.1111/j.1365-2958.2005.04522.x

P. Harold and . Erickson, The FtsZ protofilament and attachment of ZipA? structural constraints on the FtsZ power stroke, Current Opinion in Cell Biology, vol.13, issue.1, pp.55-60, 2001.

D. M. Raskin and P. A. De-boer, Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli, Proceedings of the National Academy of Sciences, vol.12, issue.21, pp.4971-4976, 1999.
DOI : 10.1101/gad.12.21.3419

J. Halatek and E. Frey, Highly Canalized MinD Transfer and MinE Sequestration Explain the Origin of Robust MinCDE-Protein Dynamics, Cell Reports, vol.1, issue.6, pp.741-752, 2012.
DOI : 10.1016/j.celrep.2012.04.005

Z. Li, M. J. Trimble, Y. V. Brun, and G. J. Jensen, The structure of FtsZ filaments in vivo suggests a force-generating role in cell division, The EMBO Journal, vol.188, issue.22, pp.4694-4708, 2007.
DOI : 10.1038/sj.emboj.7601895

C. Lu, M. Reedy, and H. P. Erickson, Straight and Curved Conformations of FtsZ Are Regulated by GTP Hydrolysis, Journal of Bacteriology, vol.182, issue.1, pp.164-170, 2000.
DOI : 10.1128/JB.182.1.164-170.2000

M. Osawa, D. E. Anderson, and H. P. Erickson, Reconstitution of Contractile FtsZ Rings in Liposomes, Science, vol.29, issue.7, pp.792-794, 2008.
DOI : 10.1002/bies.20601

W. David, J. Adams, and . Errington, Bacterial cell division: assembly , maintenance and disassembly of the Z ring, Nat. Rev. Microbiol, vol.7, issue.9, pp.642-653, 2009.

M. Aaron, G. Charbon, H. Lam, H. Schwarz, W. Vollmer et al., The tubulin homologue FtsZ contributes to cell elongation by guiding cell wall precursor synthesis in Caulobacter crescentus, Molecular Microbiology, vol.133, issue.4, pp.938-952, 2007.
DOI : 10.1128/MMBR.00001-06

H. Hasman, M. A. Schembri, and P. Klemm, Antigen 43 and Type 1 Fimbriae Determine Colony Morphology of Escherichia coli K-12, Journal of Bacteriology, vol.182, issue.4, pp.1089-1095, 2000.
DOI : 10.1128/JB.182.4.1089-1095.2000
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC94386/pdf

L. Pratt and R. Kolter, biofilm formation: roles of flagella, motility, chemotaxis and type I pili, Molecular Microbiology, vol.86, issue.2, pp.285-293, 1998.
DOI : 10.1046/j.1365-2958.1998.01061.x

I. Vallet, J. W. Olson, S. Lory, A. Lazdunski, and A. Filloux, The chaperone/usher pathways of Pseudomonas aeruginosa: Identification of fimbrial gene clusters (cup) and their involvement in biofilm formation, Proceedings of the National Academy of Sciences, vol.58, issue.1, pp.986911-6916, 2001.
DOI : 10.1128/JB.182.14.4012-4021.2000

C. Beloin, A. Houry, M. Froment, J. Ghigo, and N. Henry, A Short???Time Scale Colloidal System Reveals Early Bacterial Adhesion Dynamics, PLoS Biology, vol.21, issue.7, p.167, 2008.
DOI : 10.1371/journal.pbio.0060167.st001
URL : https://hal.archives-ouvertes.fr/pasteur-00342856

F. , P. Corona-izquierdo, and J. Membrillo-hernández, Biofilm formation in Escherichia coli is affected by 3-(N-morpholino)propane sulfonate (MOPS), Research in Microbiology, vol.153, issue.3, pp.181-185, 2002.
DOI : 10.1016/s0923-2508(02)01304-9

O. Vidal, R. Longin, C. Prigent-combaret, C. Dorel, M. Hooreman et al., Isolation of an Escherichia coli K-12 mutant strain BIBLIOGRAPHY able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression, J. Bacteriol, vol.180, issue.9, pp.2442-2449, 1998.

D. Cunliffe, C. A. Smart, C. Alexander, and E. N. Vulfson, Bacterial adhesion at synthetic surfaces, Applied and environmental microbiology, vol.65, issue.11, pp.4995-5002, 1999.

P. Rutter and R. Leech, The Deposition of Streptococcus sanguis NCTC 7868 from a Flowing Suspension, Microbiology, vol.120, issue.2, pp.301-307, 1980.
DOI : 10.1099/00221287-120-2-301

M. C. Van-loosdrecht, J. Lyklema, W. Norde, G. Schraa, and A. J. Zehnder, The role of bacterial cell wall hydrophobicity in adhesion

A. Razatos, Y. L. Ong, M. M. Sharma, and G. Georgiou, Molecular determinants of bacterial adhesion monitored by atomic force microscopy, Proceedings of the National Academy of Sciences, vol.67, issue.2, pp.9511059-11064, 1998.
DOI : 10.1146/annurev.micro.50.1.285

K. Agladze, X. Wang, and T. Romeo, Spatial Periodicity of Escherichia coli K-12 Biofilm Microstructure Initiates during a Reversible, Polar Attachment Phase of Development and Requires the Polysaccharide Adhesin PGA, Journal of Bacteriology, vol.187, issue.24, pp.8237-8246, 2005.
DOI : 10.1128/JB.187.24.8237-8246.2005

L. M. Nilsson, W. E. Thomas, E. Trintchina, V. Vogel, and E. V. Sokurenko, Catch Bond-mediated Adhesion without a Shear Threshold: TRIMANNOSE VERSUS MONOMANNOSE INTERACTIONS WITH THE FimH ADHESIN OF ESCHERICHIA COLI, Journal of Biological Chemistry, vol.281, issue.24, pp.28116656-16663, 2006.
DOI : 10.1074/jbc.M511496200

S. Lecuyer, R. Rusconi, Y. Shen, A. Forsyth, H. Vlamakis et al., Shear Stress Increases the Residence Time of Adhesion of Pseudomonas aeruginosa, Biophysical Journal, vol.100, issue.2, pp.341-350, 2011.
DOI : 10.1016/j.bpj.2010.11.078

W. E. Thomas, L. M. Nilsson, M. Forero, E. V. Sokurenko, and V. Vogel, Shear-dependent ???stick-and-roll??? adhesion of type 1 fimbriated Escherichia coli, Molecular Microbiology, vol.29, issue.5, pp.1545-1557, 2004.
DOI : 10.1111/j.1365-2958.2004.04226.x

L. De-la-fuente, E. Montanes, Y. Meng, Y. Li, T. J. Burr et al., Assessing Adhesion Forces of Type I and Type IV Pili of Xylella fastidiosa Bacteria by Use of a Microfluidic Flow Chamber, Applied and Environmental Microbiology, vol.73, issue.8, pp.732690-2696, 2007.
DOI : 10.1128/AEM.02649-06

A. Persat, C. D. Nadell, M. K. Kim, F. Ingremeau, A. Siryaporn et al., The Mechanical World of Bacteria, Cell, vol.161, issue.5, pp.988-997, 2015.
DOI : 10.1016/j.cell.2015.05.005

H. Ina, A. H. Pratt-terpstra, H. J. Weerkamp, and . Busscher, Adhesion of oral streptococci from a flowing suspension to uncoated and albumin-coated surfaces, Journal of general microbiology, vol.133, issue.11, pp.3199-3206, 1987.

A. Sénéchal, S. D. Carrigan, and M. Tabrizian, to Medical-Grade Polymers Using Atomic Force Microscopy, Langmuir, vol.20, issue.10, pp.4172-4177, 2004.
DOI : 10.1021/la035847y

W. Zhang, A. G. Stack, and Y. Chen, Interaction force measurement between E. coli cells and nanoparticles immobilized surfaces by using AFM, Colloids and Surfaces B: Biointerfaces, vol.82, issue.2, pp.316-324, 2011.
DOI : 10.1016/j.colsurfb.2010.09.003

H. Xu, A. E. Murdaugh, W. Chen, K. E. Aidala, M. A. Ferguson et al., Characterizing pilus-mediated adhesion of biofilm-forming E. coli to chemically diverse surfaces using atomic force microscopy, Langmuir, issue.9, pp.293000-3011, 2013.
DOI : 10.1021/la304745s
URL : http://doi.org/10.1021/la304745s

T. Zhang, Y. Chao, K. Shih, X. Li, and H. H. Fang, Quantification of the lateral detachment force for bacterial cells using atomic force microscope and centrifugation, Ultramicroscopy, vol.111, issue.2, pp.131-139, 2011.
DOI : 10.1016/j.ultramic.2010.10.005

M. Susan, M. H. Deupree, and . Schoenfisch, Quantitative method for determining the lateral strength of bacterial adhesion and application for characterizing adhesion kinetics, Langmuir, vol.24, issue.9, pp.4700-4707, 2008.

M. Forero, O. Yakovenko, V. Evgeni, . Sokurenko, E. Wendy et al., Uncoiling Mechanics of Escherichia coli Type I Fimbriae Are Optimized for Catch Bonds, PLoS Biology, vol.177, issue.9, p.298, 2006.
DOI : 10.1371/journal.pbio.0040298.sv001

E. Fällman, S. Schedin, J. Jass, M. Andersson, O. Bernt-eric-uhlin et al., Optical tweezers based force measurement system for quantitating binding interactions: system design and application for the study of bacterial adhesion Nanoscale mapping and functional analysis of individual adhesins on living bacteria, Biosensors and Bioelectronics Nat. Methods, vol.19145, issue.27, pp.1429-1437515, 2004.

N. Michael, S. P. Liang, S. J. Smith, I. S. Metallo, M. Choi et al., Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces, Proceedings of the National Academy of Sciences, pp.9713092-13096, 2000.

K. H. Simpson, G. Bowden, M. Höök, and B. Anvari, Measurement of Adhesive Forces between Individual Staphylococcus aureus MSCRAMMs and Protein-Coated Surfaces by Use of Optical Tweezers, Journal of Bacteriology, vol.185, issue.6, pp.2031-2035, 2003.
DOI : 10.1128/JB.185.6.2031-2035.2003

N. P. Boks, W. Norde, H. C. Van-der-mei, and H. J. Busscher, Forces involved in bacterial adhesion to hydrophilic and hydrophobic surfaces, Microbiology, vol.154, issue.10, pp.1543122-3133, 2008.
DOI : 10.1099/mic.0.2008/018622-0

P. Isolde-le-trong, B. A. Aprikian, M. Kidd, V. Forero-shelton, P. Tchesnokova et al., Structural Basis for Mechanical Force Regulation of the Adhesin FimH via Finger Trap-like ?? Sheet Twisting, Cell, vol.141, issue.4, pp.645-655, 2010.
DOI : 10.1016/j.cell.2010.03.038

D. I. Kisiela, J. J. Kramer, V. Tchesnokova, P. Aprikian, V. Yarov-yarovoy et al., Allosteric Catch Bond Properties of the FimH Adhesin from Salmonella enterica Serovar Typhimurium, Journal of Biological Chemistry, vol.286, issue.44, pp.28638136-38147, 2011.
DOI : 10.1074/jbc.M111.237511

F. Song and D. Ren, Stiffness of Cross-Linked Poly(Dimethylsiloxane) Affects Bacterial Adhesion and Antibiotic Susceptibility of Attached Cells, Langmuir, vol.30, issue.34, pp.10354-10362, 2014.
DOI : 10.1021/la502029f

J. A. Lichter, M. T. Thompson, M. Delgadillo, T. Nishikawa, M. F. Rubner et al., Substrata Mechanical Stiffness Can Regulate Adhesion of Viable Bacteria, Biomacromolecules, vol.9, issue.6, pp.1571-1578, 2008.
DOI : 10.1021/bm701430y

C. Korea, J. Ghigo, and C. Beloin, The sweet connection: Solving the riddle of multiple sugar-binding fimbrial adhesins in Escherichia coli, BioEssays, vol.7, issue.4, pp.300-311, 2011.
DOI : 10.1002/bies.201000121
URL : https://hal.archives-ouvertes.fr/pasteur-01393506

P. Natale, T. Brüser, and A. J. Driessen, Secand Tat-mediated protein secretion across the bacterial cytoplasmic membrane?Distinct translocases and mechanisms, Biochimica et Biophysica ActaBiomembranes, issue.9, pp.17781735-1756, 2008.
DOI : 10.1016/j.bbamem.2007.07.015
URL : http://doi.org/10.1016/j.bbamem.2007.07.015

M. Vetsch, C. Puorger, T. Spirig, U. Grauschopf, U. Eilika et al., Pilus chaperones represent a new type of protein-folding catalyst, Nature, vol.16, issue.7006, pp.431329-333, 2004.
DOI : 10.1016/S0022-2836(03)00591-6

S. Geibel, E. Procko, S. J. Hultgren, D. Baker, and G. Waksman, Structural and energetic basis of folded-protein transport by the FimD usher, Nature, vol.22, issue.7444, pp.496243-246, 2013.
DOI : 10.1038/nature12007

G. Waksman and S. J. Hultgren, Structural biology of the chaperone???usher pathway of pilus biogenesis, Nature Reviews Microbiology, vol.3, issue.11, 2009.
DOI : 10.1038/nrmicro2220

A. Busch and G. Waksman, Chaperone-usher pathways: diversity and pilus assembly mechanism, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.103, issue.47, pp.1112-1122, 1592.
DOI : 10.1073/pnas.0606795103
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297437

S. Geibel and G. Waksman, The molecular dissection of the chaperone???usher pathway, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1843, issue.8, pp.1559-1567, 2014.
DOI : 10.1016/j.bbamcr.2013.09.023

R. D. Tiago, C. Costa, A. Felisberto-rodrigues, M. S. Meir, A. Prevost et al., Secretion systems in Gram-negative bacteria: structural and mechanistic insights, Nat. Rev. Microbiol, vol.13, issue.6, pp.343-359, 2015.

I. Barry and . Eisenstein, Phase Variation of Type 1 Fimbriae in Escherichia coli is under Transcriptional Control, Science, vol.214, issue.4518, p.337, 1981.

E. Hahn, P. Wild, U. Hermanns, P. Sebbel, R. Glockshuber et al., Exploring the 3D Molecular Architecture of Escherichia coli Type 1 Pili, Journal of Molecular Biology, vol.323, issue.5, pp.845-857, 2002.
DOI : 10.1016/S0022-2836(02)01005-7

A. Reisner, M. Maierl, M. Jörger, R. Krause, D. Berger et al., Type 1 Fimbriae Contribute to Catheter-Associated Urinary Tract Infections Caused by Escherichia coli, Journal of Bacteriology, vol.196, issue.5, pp.931-939, 2014.
DOI : 10.1128/JB.00985-13
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957706

K. Krogfelt, P. Bergmans, and . Klemm, Direct evidence that the FimH protein is the mannose-specific adhesin of Escherichia coli type 1 fimbriae, Infect Immun, vol.58, issue.6, pp.1995-1998, 1990.

W. E. Thomas, E. Trintchina, M. Forero, V. Vogel, and E. V. Sokurenko, Bacterial Adhesion to Target Cells Enhanced by Shear Force, Cell, vol.109, issue.7, pp.913-923, 2002.
DOI : 10.1016/S0092-8674(02)00796-1
URL : http://doi.org/10.1016/s0092-8674(02)00796-1

W. Thomas, M. Forero, O. Yakovenko, L. Nilsson, P. Vicini et al., Catch-Bond Model Derived from Allostery Explains Force-Activated Bacterial Adhesion, Biophysical Journal, vol.90, issue.3, pp.753-764, 2006.
DOI : 10.1529/biophysj.105.066548
URL : http://doi.org/10.1529/biophysj.105.066548

S. Nuccio and A. J. Bäumler, Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek, Microbiology and Molecular Biology Reviews, vol.71, issue.4, pp.551-575, 2007.
DOI : 10.1128/MMBR.00014-07

C. Giraud, C. Bernard, S. Ruer, and S. D. Bentzmann, Biological ???glue??? and ???Velcro???: molecular tools for adhesion and biofilm formation in the hairy and gluey bug Pseudomonas aeruginosa, Environmental Microbiology Reports, vol.4, issue.3, pp.343-358, 2010.
DOI : 10.1111/j.1758-2229.2009.00070.x

R. Ian, F. Henderson, . Navarro-garcia, P. James, and . Nataro, The great escape: structure and function of the autotransporter proteins, Trends in Microbiology, vol.6, issue.9, pp.370-378, 1998.

C. David, G. Oliver, R. C. Huang, and . Fernandez, Identification of Secretion Determinants of the Bordetella pertussis BrkA Autotransporter, J. Bacteriol, vol.185, issue.2, pp.489-495, 2003.

M. Desvaux, N. J. Parham, and I. R. Henderson, The autotransporter secretion system, Research in Microbiology, vol.155, issue.2, pp.53-60, 2004.
DOI : 10.1016/j.resmic.2003.10.002

I. R. Henderson, M. Meehan, and P. Owen, Antigen 43, a phase-variable bipartite outer membrane protein, determines colony morphology and autoaggregation in Escherichia coli K-12, FEMS Microbiology Letters, vol.149, issue.1, pp.115-120, 1997.
DOI : 10.1111/j.1574-6968.1997.tb10317.x

G. C. Ulett, R. I. Webb, and M. A. Schembri, Antigen-43- mediated autoaggregation impairs motility in Escherichia coli, Microbiology (Reading, pp.1522101-2110, 2006.
DOI : 10.1099/mic.0.29296-0
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.335.9077

A. Chauhan, C. Sakamoto, J. Ghigo, and C. Beloin, Did I Pick the Right Colony? Pitfalls in the Study of Regulation of the Phase Variable Antigen 43 Adhesin, PLoS ONE, vol.188, issue.9, 2013.
DOI : 10.1371/journal.pone.0073568.s001
URL : https://hal.archives-ouvertes.fr/pasteur-01385431

A. Roux, C. Beloin, and J. Ghigo, Combined Inactivation and Expression Strategy To Study Gene Function under Physiological Conditions: Application to Identification of New Escherichia coli Adhesins, Journal of Bacteriology, vol.187, issue.3, pp.1001-1013, 2005.
DOI : 10.1128/JB.187.3.1001-1013.2005

Y. Gar-yun-chan, S. P. Riley, and J. Martinez, Adherence to and invasion of host cells by spotted fever group Rickettsia species, Rickettsia, vol.1, p.139, 2010.

L. Margery, M. R. Evans, and . Chapman, Curli biogenesis: Order out of disorder, Biochimica et Biophysica ActaMolecular Cell Research, issue.8, pp.18431551-1558, 2014.

D. B. Lewis, C. Evans, G. M. Hughes, and . Fraser, Building a flagellum outside the bacterial cell, Trends in Microbiology, vol.22, issue.10, pp.566-572, 2014.

L. Turner, W. S. Ryu, and H. C. Berg, Real-Time Imaging of Fluorescent Flagellar Filaments, Journal of Bacteriology, vol.182, issue.10, pp.2793-2801, 2000.
DOI : 10.1128/JB.182.10.2793-2801.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101988

A. A. Nenninger, L. S. Robinson, N. D. Hammer, E. A. Epstein, M. P. Badtke et al., CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation, Molecular Microbiology, vol.71, issue.2, pp.486-499, 2011.
DOI : 10.1111/j.1365-2958.2011.07706.x
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134098

N. D. Hammer, J. C. Schmidt, and M. R. Chapman, The curli nucleator protein, CsgB, contains an amyloidogenic domain that directs CsgA polymerization, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.12494-12499, 2007.
DOI : 10.1073/pnas.120163297
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941497

A. Olsén, A. Jonsson, and S. Normark, Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli Environmental regulation of curli production in Escherichia coli, Nature Infect Agents Dis, vol.338, issue.24, pp.652-655272, 1989.

U. Römling, Z. Bian, M. Hammar, W. D. Sierralta, and S. Normark, Curli fibers are highly conserved between Salmonella typhimurium and Escherichia coli with respect to operon structure and regulation, J. Bacteriol, vol.180, issue.3, pp.722-731, 1998.

C. Prigent-combaret, G. Prensier, T. T. Le-thi, O. Vidal, P. Lejeune et al., Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid, Environmental Microbiology, vol.181, issue.4, pp.450-464, 2000.
DOI : 10.1046/j.1365-2958.1999.01624.x

E. Brombacher, C. Dorel, A. J. Zehnder, and P. Landini, The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli, Microbiology, vol.149, issue.10, pp.1492847-2857, 2003.
DOI : 10.1099/mic.0.26306-0

A. Fadel, H. Samatey, K. Matsunami, S. Imada, T. R. Nagashima et al., Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism, Nature, issue.7012, pp.4311062-1068, 2004.

F. V. Fabienne, K. T. Chevance, and . Hughes, Coordinating assembly of a bacterial macromolecular machine, Nature Reviews Microbiology, vol.6, 2008.

R. Belas, Biofilms, flagella, and mechanosensing of surfaces by bacteria, Trends in Microbiology, vol.22, issue.9, pp.517-527, 2014.
DOI : 10.1016/j.tim.2014.05.002

L. Ping, The Asymmetric Flagellar Distribution and Motility of Escherichia coli, Journal of Molecular Biology, vol.397, issue.4, pp.906-916, 2010.
DOI : 10.1016/j.jmb.2010.02.008

B. Sarah, D. B. Guttenplan, and . Kearns, Regulation of flagellar motility during biofilm formation, FEMS Microbiology Reviews, vol.37, issue.6, pp.849-871, 2013.

P. Pushkar, . Lele, G. Basarab, H. C. Hosu, and . Berg, Dynamics of mechanosensing in the bacterial flagellar motor, pp.11839-11844, 2013.

J. S. Mattick, Type IV Pili and Twitching Motility, Annual Review of Microbiology, vol.56, issue.1, pp.289-314, 2002.
DOI : 10.1146/annurev.micro.56.012302.160938

N. Biais, B. Ladoux, D. Higashi, M. So, and M. Sheetz, Cooperative Retraction of Bundled Type IV Pili Enables Nanonewton Force Generation, PLoS Biology, vol.65, issue.4, p.87, 2008.
DOI : 10.1371/journal.pbio.0060087.sv004

N. Sauvonnet, P. Gounon, and A. P. Pugsley, PpdD Type IV Pilin of Escherichia coli K-12 Can Be Assembled into Pili in Pseudomonas aeruginosa, Journal of Bacteriology, vol.182, issue.3, pp.848-854, 2000.
DOI : 10.1128/JB.182.3.848-854.2000

A. James, C. Shapiro, and . Hsu, Escherichia coli K-12 cell-cell interactions seen by time-lapse video, Journal of bacteriology, vol.171, issue.11, p.5963, 1989.

M. Dienerowitz, L. V. Cowan, G. M. Gibson, R. Hay, M. J. Padgett et al., Optically Trapped Bacteria Pairs Reveal Discrete Motile Response to Control Aggregation upon Cell???Cell Approach, Current Microbiology, vol.21, issue.5, pp.669-674, 2014.
DOI : 10.1007/s00284-014-0641-5
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201752

H. Cho, H. Jönsson, K. Campbell, P. Melke, J. W. Williams et al., Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control, PLoS Biology, vol.48, issue.11, p.302, 2007.
DOI : 10.1371/journal.pbio.0050302.sv018
URL : http://doi.org/10.1371/journal.pbio.0050302

D. Volfson, S. Cookson, J. Hasty, and L. S. Tsimring, Biomechanical ordering of dense cell populations, Proceedings of the National Academy of Sciences, pp.15346-15351, 2008.
DOI : 10.1002/elps.200305584
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2563119

D. Boyer, W. Mather, O. Mondragón-palomino, S. Orozco-fuentes, T. Danino et al., Buckling instability in ordered bacterial colonies, Physical Biology, vol.8, issue.2, p.26008, 2011.
DOI : 10.1088/1478-3975/8/2/026008
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767764

A. A. Matthew, B. Grant, R. J. Wac?aw, P. Allen, and . Cicuta, The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies, J. R. Soc. Interface, issue.97, p.1120140400, 2014.

M. Asally, M. Kittisopikul, P. Rué, Y. Du, Z. Hu et al., Localized cell death focuses mechanical forces during 3D patterning in a biofilm, Proceedings of the National Academy of Sciences, vol.51, issue.12, pp.18891-18896, 2012.
DOI : 10.1167/iovs.10-5470

O. Galy, P. Latour-lambert, K. Zrelli, J. Ghigo, C. Beloin et al., Mapping of Bacterial Biofilm Local Mechanics by Magnetic Microparticle Actuation, Biophysical Journal, vol.103, issue.6, pp.1400-1408, 2012.
DOI : 10.1016/j.bpj.2012.07.001
URL : https://hal.archives-ouvertes.fr/hal-00950106

T. Julou, T. Mora, L. Guillon, V. Croquette, I. J. Schalk et al., Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies, Proceedings of the National Academy of Sciences, vol.41, issue.5, pp.11012577-12582, 2013.
DOI : 10.1038/nrmicro2056
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732961

N. Otsu, A Threshold Selection Method from Gray-Level Histograms, IEEE Transactions on Systems, Man, and Cybernetics, vol.9, issue.1, pp.62-66, 1979.
DOI : 10.1109/TSMC.1979.4310076

D. J. Kiviet, P. Nghe, N. Walker, S. Boulineau, V. Sunderlikova et al., Stochasticity of metabolism and growth at the single-cell level, Nature, vol.108, issue.7522, pp.514376-379, 2014.
DOI : 10.1038/nature13582

J. W. Young, J. C. Locke, A. Altinok, N. Rosenfeld, T. Bacarian et al., Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy, Nature Protocols, vol.460, issue.1, pp.80-88, 2012.
DOI : 10.1073/pnas.44.10.1072
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161363

J. Eric, R. Stewart, G. Madden, F. Paul, and . Taddei, Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division, PLoS Biol, vol.3, issue.2, 2005.

M. Dembo and Y. Wang, Stresses at the Cell-to-Substrate Interface during Locomotion of Fibroblasts, Biophysical Journal, vol.76, issue.4, pp.2307-2316, 1999.
DOI : 10.1016/S0006-3495(99)77386-8

S. Munevar, M. Wang, and . Dembo, Traction Force Microscopy of Migrating Normal and H-ras Transformed 3T3 Fibroblasts, Biophysical Journal, vol.80, issue.4, pp.1744-1757, 2001.
DOI : 10.1016/S0006-3495(01)76145-0

J. R. Tse and A. J. Engler, Preparation of Hydrogel Substrates with Tunable Mechanical Properties, Curr Protoc Cell Biol, Chapter, vol.19, 2010.
DOI : 10.1002/0471143030.cb1016s47

M. Ahearne, Y. Yang, A. J. El-haj, Y. Kong, K. Then et al., Characterizing the viscoelastic properties of thin hydrogel-based constructs for tissue engineering applications, Journal of The Royal Society Interface, vol.231, issue.5, pp.455-463, 2005.
DOI : 10.1098/rsif.2005.0065

M. Ahearne, E. Siamantouras, Y. Yang, and K. Liu, Mechanical characterization of biomimetic membranes by micro-shaft poking, Journal of The Royal Society Interface, vol.70, issue.5, pp.471-478, 2009.
DOI : 10.1016/j.medengphy.2007.06.011

J. P. Butler, I. M. Toli?-nørrelykke, B. Fabry, and J. J. Fredberg, Traction fields, moments, and strain energy that cells exert on their surroundings, AJP: Cell Physiology, vol.282, issue.3, pp.595-605, 2002.
DOI : 10.1152/ajpcell.00270.2001

I. Sonntag, H. Schwarz, Y. Hirota, and U. Henning, Cell envelope and shape of Escherichia coli: multiple mutants missing the outer membrane lipoprotein and other major outer membrane proteins, J. Bacteriol, vol.136, issue.1, pp.280-285, 1978.

P. Su, P. Yen, S. Wang, C. Lin, A. Chiou et al., Factors Affecting Daughter Cells' Arrangement during the Early Bacterial Divisions, PLoS ONE, vol.5, issue.2, 2010.
DOI : 10.1371/journal.pone.0009147.t006
URL : http://doi.org/10.1371/journal.pone.0009147

S. Hormoz, N. Desprat, and B. I. Shraiman, Inferring epigenetic dynamics from kin correlations, Proceedings of the National Academy of Sciences, 2015.
DOI : 10.1038/nrg2955
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426465

A. S. Curtis, THE MECHANISM OF ADHESION OF CELLS TO GLASS: A Study by Interference Reflection Microscopy, The Journal of Cell Biology, vol.20, issue.2, pp.199-215, 1964.
DOI : 10.1083/jcb.20.2.199