P. Stoodley, K. Sauer, D. G. Davies, and J. W. Costerton, Biofilms as complex differentiated communities, Annu Rev Microbiol, vol.56, pp.187-209, 2002.
DOI : 10.1146/annurev.micro.56.012302.160705

H. Flemming and J. Wingender, The biofilm matrix, Nat Rev Microbiol, vol.8, pp.623-656, 2010.

D. P. Delmer and Y. Amor, Cellulose biosynthesis, Plant Cell, vol.7, pp.987-1000, 1995.

U. Römling, Molecular biology of cellulose production in bacteria, Res Microbiol, vol.153, pp.205-217, 2002.

U. Römling and M. Y. Galperin, HHS Public Access, vol.23, pp.545-57, 2016.

F. Hilali, R. Ruimy, P. Saulnier, C. Barnabé, C. Lebouguénec et al., Prevalence of virulence genes and clonality in Escherichia coli strains that cause bacteremia in cancer patients, Infect Immun, vol.68, pp.3983-3992, 2000.

O. Clermont, S. Bonacorsi, and E. Bingen, Rapid and simple determination of the Escherichia coli phylogenetic group, Appl Environ Microbiol, vol.66, pp.4555-4563, 2000.

S. Da-re and J. Ghigo, A CsgD-independent pathway for cellulose production and biofilm formation in Escherichia coli, J Bacteriol, vol.188, pp.3073-87, 2006.

L. Quéré, B. Ghigo, and J. , BcsQ is an essential component of the Escherichia coli cellulose biosynthesis apparatus that localizes at the bacterial cell pole

, Mol Microbiol, vol.72, pp.724-764, 2009.

P. V. Krasteva, J. Bernal-bayard, L. Travier, F. A. Martin, P. Kaminski et al., Insights into the structure and assembly of a bacterial cellulose secretion system, Nat Commun, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01688314

E. Skippington and M. A. Ragan, Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities, Open Biol, vol.2, p.120112, 2012.

D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut et al., The minimum information about a genome sequence (MIGS) specification, Nat Biotechnol, vol.26, pp.541-548, 2008.
DOI : 10.1038/nbt1360

URL : https://www.nature.com/articles/nbt1360.pdf

C. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake et al., finished microbial genome assemblies from long-read SMRT sequencing data, Nat Methods, vol.10, pp.563-572, 2013.
DOI : 10.1038/nmeth.2474

H. Li and R. Durbin, Fast and accurate short read alignment with burrowswheeler transform, Bioinformatics, vol.25, pp.1754-60, 2009.
DOI : 10.1093/bioinformatics/btp324

URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-843, 2010.
DOI : 10.1093/bioinformatics/btq033

URL : https://academic.oup.com/bioinformatics/article-pdf/26/6/841/16897802/btq033.pdf

S. Nurk, A. Bankevich, D. Antipov, A. A. Gurevich, A. Korobeynikov et al., Assembling single-cell genomes and mini-metagenomes from chimeric MDA products, J Comput Biol, vol.20, pp.714-751, 2013.
DOI : 10.1089/cmb.2013.0084

URL : http://europepmc.org/articles/pmc3791033?pdf=render

D. Antipov, N. Hartwick, M. Shen, M. Raiko, and P. A. Pevzner, plasmidSPAdes : assembling plasmids from whole. BioRxiv, pp.2014-2019, 2016.
DOI : 10.1093/bioinformatics/btw493

URL : https://academic.oup.com/bioinformatics/article-pdf/32/22/3380/16920848/btw493.pdf

, Picard Tools by Broad Institute GitHub Pages, 2016.

T. A. Tatusova and T. L. Madden, BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences, FEMS Microbiol Lett, vol.174, pp.247-50, 1999.
DOI : 10.1111/j.1574-6968.1999.tb13575.x

URL : https://academic.oup.com/femsle/article-pdf/174/2/247/19102501/174-2-247.pdf

T. J. Carver, K. M. Rutherford, M. Berriman, M. A. Rajandream, B. G. Barrell et al., ACT: the Artemis comparison tool, Bioinformatics, vol.21, pp.3422-3425, 2005.
DOI : 10.1093/bioinformatics/bti553

URL : https://academic.oup.com/bioinformatics/article-pdf/21/16/3422/573752/bti553.pdf

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST server: rapid annotations using subsystems technology, BMC Genomics, vol.9, p.75, 2008.
DOI : 10.1186/1471-2164-9-75

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-75

. Blastclust,

, Accessed 6, 2015.

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats, Nucleic Acids Res, vol.36, p.145, 2008.
DOI : 10.1093/nar/gkn228

URL : https://hal.archives-ouvertes.fr/hal-00297231

B. Krogh-a,-larsson, G. Von-heijne, and E. L. Sonnhammer, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, vol.305, pp.567-80, 2001.

T. N. Petersen, S. Brunak, V. Heijne, G. Nielsen, and H. , SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, vol.8, pp.785-791, 2011.

R. D. Finn, P. Coggill, R. Y. Eberhardt, S. R. Eddy, J. Mistry et al., The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res, vol.44, pp.279-85, 2016.
DOI : 10.1093/nar/gkv1344

URL : https://hal.archives-ouvertes.fr/hal-01294685

T. J. Treangen, B. D. Ondov, S. Koren, and A. M. Phillippy, The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes, Genome Biol, vol.15, p.524, 2014.

Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, A greedy algorithm for aligning DNA sequences, J Comput Biol, vol.7, pp.203-217, 2000.
DOI : 10.1089/10665270050081478

D. O. Serra, A. M. Richter, and R. Hengge, Cellulose as an architectural element in spatially structured escherichia coli biofilms, J Bacteriol, vol.195, pp.5540-54, 2013.
DOI : 10.1128/jb.00946-13

URL : https://jb.asm.org/content/195/24/5540.full.pdf

J. A. Leigh, E. R. Signer, and G. C. Walker, Exopolysaccharide-deficient mutants of rhizobium meliloti that form ineffective nodules, Proc Natl Acad Sci, vol.82, pp.6231-6236, 1985.
DOI : 10.1073/pnas.82.18.6231

URL : http://www.pnas.org/content/82/18/6231.full.pdf

X. Fang, I. Ahmad, A. Blanka, M. Schottkowski, A. Cimdins et al., di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria, Mol Microbiol, vol.93, pp.439-52, 2014.

C. R. Woese, O. Kandlert, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains archaea, Bacteria, and Eucarya, Evolution (N Y), vol.87, pp.4576-4585, 1990.

G. M. Garrity and T. Lilburn, Bergey's man. Syst. Bacteriol, the Proteobacteria, part B: the Gammaproteobacteria, vol.2, 2005.

K. P. Williams and D. P. Kelly, Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria, Int J Syst Evol Microbiol, vol.63, pp.2901-2907, 2013.

R. E. Rahn, W. H. Ewing, J. J. Farmer, and D. Brenner, Proposal of Enterobacteriaceae fam. nov., norn. rev. to replace Enterobacteriaceae Rahn 1937, nom. fam. cons. (Opin. 15, Jud. Comm. 1958), which lost standing in nomenclature on 1, pp.674-679, 1980.

T. Escherich, Die Darmbakterien des Säuglings und ihre Beziehungen zur Physiologie der Verdauung; 1886, pp.63-74

, Editorial Board (for the Judicial Commission of the International Committee on Bacteriological Nomenclature). Bacterial Nomenclature and Taxonomy, Int J Syst Bacteriol, pp.35-41, 1959.

R. A. Welch, The genus Escherichia. Prokaryotes prokaryotic biol, pp.60-71, 2006.

F. Scheutz and N. A. Strockbine, Genus I. Escherichia Castellani and Chalmers 1919, 941T. Bergey's Man Syst Bacteriol, vol.2, pp.607-631, 2005.

M. J. Sullivan, N. K. Petty, and S. A. Beatson, Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, 2011.
DOI : 10.1093/bioinformatics/btr039

URL : https://academic.oup.com/bioinformatics/article-pdf/27/7/1009/624276/btr039.pdf