A. Nemec, Classification and nomenclature of the genus Acinetobacter, 2016.

H. Seifert and L. Dijkshoorn, ???Overview of the Microbial Characteristics, Taxonomy, and Epidemiology of Acinetobacter???, Acinetobacter Biology and Pathogenesis, pp.14-45, 2009.
DOI : 10.1007/978-0-387-77944-7_2

J. Jung, E. Madsen, C. Jeon, and W. Park, Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation, Applied and Environmental Microbiology, vol.77, issue.20, pp.7418-7442, 2011.
DOI : 10.1128/AEM.05231-11

Y. Zhan, Y. Yan, W. Zhang, M. Chen, W. Lu et al., Comparative analysis of the complete genome of an Acinetobacter calcoaceticus strain adapted to a phenol-polluted environment, Research in Microbiology, vol.163, issue.1, pp.36-43, 2012.
DOI : 10.1016/j.resmic.2011.10.006

T. Pédron, C. Mulet, C. Dauga, L. Frangeul, C. Chervaux et al., A Crypt-Specific Core Microbiota Resides in the Mouse Colon, mBio, vol.3, issue.3, pp.116-118, 2012.
DOI : 10.1128/mBio.00116-12

B. Marteyn, N. West, D. Browning, J. Cole, J. Shaw et al., Modulation of Shigella virulence in response to available oxygen in vivo, Nature, vol.168, issue.7296, pp.355-363, 2010.
DOI : 10.1007/s004240050455
URL : https://hal.archives-ouvertes.fr/pasteur-00493767

P. Baumann, Isolation of Acinetobacter from soil and water, JBacteriol, vol.96, pp.39-42, 1968.

O. Toole, G. Pratt, L. Watnick, P. Newman, D. Weaver et al., [6] Genetic approaches to study of biofilms, Methods Enzymol, vol.310, pp.91-109, 1999.
DOI : 10.1016/S0076-6879(99)10008-9

A. Tomaras, C. Dorsey, R. Edelmann, and L. Actis, Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system, Microbiology, vol.149, issue.12, pp.3473-84, 2003.
DOI : 10.1099/mic.0.26541-0

A. Saffarian, C. Mulet, T. Naito, C. Bouchier, M. Tichit et al., Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue, Genome Announc, vol.3, issue.5, pp.1089-1501089, 2015.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle et al., Real-Time DNA Sequencing from Single Polymerase Molecules, Science, vol.26, issue.14, pp.133-141, 2009.
DOI : 10.1038/sj.emboj.7601780

C. Chin, D. Alexander, P. Marks, A. Klammer, J. Drake et al., Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nature Methods, vol.472, issue.6, pp.563-572, 2013.
DOI : 10.1016/S0076-6879(10)72001-2

A. Darling, B. Mau, F. Blattner, and N. Perna, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-403, 2004.
DOI : 10.1101/gr.2289704

R. Aziz, D. Bartels, A. Best, M. Dejongh, T. Disz et al., The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, issue.1, pp.75-85, 2008.
DOI : 10.1186/1471-2164-9-75

R. Overbeek, R. Olson, G. Pusch, G. Olsen, J. Davis et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Research, vol.42, issue.D1, pp.206-220, 2014.
DOI : 10.1093/nar/gkt1226

D. Vallenet, E. Belda, A. Calteau, S. Cruveiller, S. Engelen et al., MicroScope???an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data, Nucleic Acids Research, vol.41, issue.D1, pp.636-683, 2013.
DOI : 10.1093/nar/gks1194

M. Touchon, J. Cury, E. Yoon, L. Krizova, G. Cerqueira et al., The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences, Genome Biology and Evolution, vol.6, issue.10, pp.2866-82, 2014.
DOI : 10.1093/gbe/evu225
URL : https://hal.archives-ouvertes.fr/pasteur-01132634

M. Touchon, C. Hoede, O. Tenaillon, V. Barbe, S. Baeriswyl et al., Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, 2009.
DOI : 10.1371/journal.pgen.1000344.s016
URL : https://hal.archives-ouvertes.fr/hal-00390293

T. Dandekar, B. Snel, M. Huynen, and P. Bork, Conservation of gene order: a fingerprint of proteins that physically interact, Trends in Biochemical Sciences, vol.23, issue.9, pp.324-332, 1998.
DOI : 10.1016/S0968-0004(98)01274-2

E. Rocha, M. Touchon, and E. Feil, Similar compositional biases are caused by very different mutational effects, Genome Research, vol.16, issue.12, pp.1537-1584, 2006.
DOI : 10.1101/gr.5525106

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, pp.10-1186, 2011.
DOI : 10.1186/1471-2105-8-396
URL : https://hal.archives-ouvertes.fr/hal-00698365

E. Nawrocki and S. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, vol.29, issue.22, pp.2933-2938, 2013.
DOI : 10.1093/bioinformatics/btt509

E. Nawrocki, S. Burge, A. Bateman, J. Daub, R. Eberhardt et al., Rfam 12.0: updates to the RNA families database, Nucleic Acids Research, vol.43, issue.D1, pp.130-137, 2015.
DOI : 10.1093/nar/gku1063

L. Nguyen, H. Schmidt, V. Haeseler, A. Minh, and B. , IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.32, issue.1, pp.268-74, 2015.
DOI : 10.1093/molbev/msu300

K. Katoh and D. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-80, 2013.
DOI : 10.1093/molbev/mst010

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, 2010.
DOI : 10.1186/1471-2148-10-210

A. Nemec, L. Radolfova-krizova, M. Maixnerova, E. Vrestiakova, P. Jezek et al., Taxonomy of haemolytic and/or proteolytic strains of the genus Acinetobacter with the proposal of Acinetobacter courvalinii sp. nov. (genomic species 14 sensu Bouvet & Jeanjean), Acinetobacter dispersus sp. nov. (genomic species 17), Acinetobacter modestus sp. nov., Acinetobacter proteolyticus sp. nov. and Acinetobacter vivianii sp. nov., International Journal of Systematic and Evolutionary Microbiology, vol.66, issue.4, pp.1673-85, 2016.
DOI : 10.1099/ijsem.0.000932

B. Krawczyk, K. Lewandowski, and J. Kur, Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences, Molecular and Cellular Probes, vol.16, issue.1, pp.1-11, 2002.
DOI : 10.1006/mcpr.2001.0388

M. Richter and R. Rosselló-móra, Shifting the genomic gold standard for the prokaryotic species definition, Proceedings of the National Academy of Sciences, vol.361, issue.12, pp.19126-19157, 2009.
DOI : 10.1098/rstb.2006.1914

E. Yoon, P. Courvalin, and C. Grillot-courvalin, RND-Type Efflux Pumps in Multidrug-Resistant Clinical Isolates of Acinetobacter baumannii: Major Role for AdeABC Overexpression and AdeRS Mutations, Antimicrobial Agents and Chemotherapy, vol.57, issue.7, pp.2989-95, 2013.
DOI : 10.1128/AAC.02556-12

S. Claus, H. Guillou, and S. Ellero-simatos, The gut microbiota: a major player in the toxicity of environmental pollutants? Npj biofilms and microbiomes

D. Eby, Z. Beharry, E. Coulter, D. Kurtz, and E. Neidl, Characterization and Evolution of Anthranilate 1,2-Dioxygenase from Acinetobacter sp. Strain ADP1, Journal of Bacteriology, vol.183, issue.1, 2001.
DOI : 10.1128/JB.183-1.109-118.2001

N. Elhosseiny, O. El-tayeb, A. Yassin, S. Lory, and A. Attia, The secretome of Acinetobacter baumannii ATCC 17978 type II secretion system reveals a novel plasmid encoded phospholipase that could be implicated in lung colonization, International Journal of Medical Microbiology, vol.306, issue.8, pp.633-674, 2016.
DOI : 10.1016/j.ijmm.2016.09.006

B. Weber, S. Hennon, M. Wright, N. Scott, V. De-berardinis et al., Genetic dissection of the type VI secretion system in Acinetobacter and identification of a novel peptidoglycan hydrolase, TagX, required for its biogenesis, MBio, vol.7, issue.5, pp.1253-1601253, 2016.

V. Koronakis, J. Eswaran, and C. Hughes, Structure and Function of TolC: The Bacterial Exit Duct for Proteins and Drugs, Annual Review of Biochemistry, vol.73, issue.1, pp.467-89, 2004.
DOI : 10.1146/annurev.biochem.73.011303.074104

B. Douzi, A. Filloux, and R. Voulhoux, On the path to uncover the bacterial type II secretion system, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.35, issue.6, pp.1059-72, 1592.
DOI : 10.1021/ar020082r
URL : https://hal.archives-ouvertes.fr/hal-01458255

B. Weber, S. Miyata, J. Iwashkiw, B. Mortensen, E. Skaar et al., Genomic and Functional Analysis of the Type VI Secretion System in Acinetobacter, PLoS ONE, vol.18, issue.1, 2013.
DOI : 10.1371/journal.pone.0055142.s006

G. Repizo, S. Gagné, M. Foucault-grunenwald, V. Borges, X. Charpentier et al., Differential Role of the T6SS in Acinetobacter baumannii Virulence, PLOS ONE, vol.73, issue.9, 2015.
DOI : 10.1371/journal.pone.0138265.s009

R. Vidal, M. Dominguez, H. Urrutia, H. Bello, G. Gonzalez et al., Biofilm formation by Acinetobacter Baumannii, Microbios, vol.86, issue.346, pp.49-58, 1996.

C. Harding, E. Tracy, M. Carruthers, P. Rather, L. Actis et al., Acinetobacter baumannii Strain M2 Produces Type IV Pili Which Play a Role in Natural Transformation and Twitching Motility but Not Surface-Associated Motility, mBio, vol.4, issue.4, pp.360-373, 2013.
DOI : 10.1128/mBio.00360-13

L. Antunes, F. Imperi, A. Carattoli, and P. Visca, Deciphering the Multifactorial Nature of Acinetobacter baumannii Pathogenicity, PLoS ONE, vol.108, issue.8, p.22674, 2011.
DOI : 10.1371/journal.pone.0022674.s004

A. Peleg, A. De-breij, M. Adams, G. Cerqueira, S. Mocali et al., The Success of Acinetobacter Species; Genetic, Metabolic and Virulence Attributes, PLoS ONE, vol.2009, issue.10, 2012.
DOI : 10.1371/journal.pone.0046984.s005

G. Wilharm, J. Piesker, M. Laue, and E. Skiebe, DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces, Journal of Bacteriology, vol.195, issue.18, pp.4146-53, 2013.
DOI : 10.1128/JB.00754-13

A. Symeonidis and M. Marangos, Iron and Microbial Growth, InTech, vol.2012, pp.289-330
DOI : 10.5772/34760

W. Penwell, N. Degrace, S. Tentarelli, L. Gauthier, C. Gilbert et al., Discovery and characterization of new Hydroxamate Siderophores, Baumannoferrin a and B, produced by Acinetobacter Baumannii, Chembiochem, 2015.

L. Antunes, F. Imperi, K. Towner, and P. Visca, Genome-assisted identification of putative iron-utilization genes in Acinetobacter baumannii and their distribution among a genotypically diverse collection of clinical isolates, Research in Microbiology, vol.162, issue.3, pp.279-84, 2011.
DOI : 10.1016/j.resmic.2010.10.010

R. Hughes and I. Rowland, Metabolic Activities of the Gut Microflora in Relation to Cancer, Microbial Ecology in Health & Disease, vol.12, issue.2, pp.179-185, 2000.
DOI : 10.3402/mehd.v12i2.8065

D. Janssen, I. Dinkla, G. Poelarends, and T. Terpstra, Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities, Environmental Microbiology, vol.40, issue.12, pp.1868-82, 2005.
DOI : 10.1128/jb.174.6.1932-1940.1992