D. Dowson, On the systematic position and generic names of the Gram negative bacterial plant pathogens, Zbl Bakteriol Parasitenkd Infekt Hyg Abt, vol.2, pp.177-93, 1939.

D. W. Dye and R. A. Lelliott, Bergey's manual of determinative bacteriology, pp.243-252, 1939.

L. Vauterin, B. Hoste, K. Kersters, and J. Swings, Reclassification of Xanthomonas, Int J Syst Bacteriol, vol.45, pp.472-89, 1995.

P. Yang, L. Vauterin, M. Vancanneyt, J. Swings, and K. Kersters, Application of fatty acid methyl esters for the taxonomic analysis of the genus Xanthomonas, Syst Appl Microbiol, vol.16, pp.47-71, 1993.

A. Darrasse, S. Carrère, V. Barbe, T. Boureau, M. L. Arrieta-ortiz et al., Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads, BMC Genomics, vol.14, p.761, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01134880

J. C. Lagier, S. Khelaifia, M. T. Alou, S. Ndongo, N. Dione et al., Culture of previously uncultured members of the human gut microbiota by culturomics, Nat Microbiol, vol.1, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

P. Seng, M. Drancourt, F. Gouriet, L. Scola, B. Fournier et al., Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry, Clin Infect Dis, vol.49, pp.543-51, 2009.

A. S. Morel, G. Dubourg, E. Prudent, S. Edouard, F. Gouriet et al., Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases, Eur J Clin Microbiol Infect Dis, vol.34, pp.561-70, 2015.

E. Stackebrandt and J. Ebers, Taxonomic parameters revisited: tarnished gold standards, pp.152-157, 2006.

M. Kim, H. S. Oh, S. C. Park, and J. Chun, Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, Int J Syst Evol Microbiol, vol.64, pp.346-51, 2014.

M. Sasser, Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME), 2006.

N. Dione, S. A. Sankar, J. C. Lagier, S. Khelaifia, M. C. Armstrong et al., Genome sequence and description of Anaerosalibacter massiliensis sp. nov, New Microbes New Infect, vol.10, pp.66-76, 2016.

J. C. Lagier, D. Ramasamy, R. Rivet, D. Raoult, and P. E. Fournier, Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov, Stand Genomic Sci, vol.7, pp.258-70, 2012.

J. C. Lagier, F. Bibi, D. Ramasamy, E. I. Azhar, C. Robert et al., Non contiguous-finished genome sequence and description of Clostridium jeddahense sp, Stand Genomic Sci, vol.9, pp.1003-1022, 2014.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-830, 2008.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, pp.455-77, 2012.

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.1, p.18, 201227.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2134, 2014.

D. Hyatt, G. L. Chen, P. F. Locascio, M. L. Land, F. W. Larimer et al., Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinform, vol.11, p.119, 2010.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-64, 1997.

K. Lagesen, P. Hallin, E. A. Rødland, H. H. Staerfeldt, T. Rognes et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res, vol.35, pp.3100-3108, 2007.

L. Käll, A. Krogh, and E. L. Sonnhammer, A combined transmembrane topology and signal peptide prediction method, J Mol Biol, vol.338, pp.1027-1063, 2004.

P. Gouret, J. D. Thompson, and P. Pontarotti, PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees, BMC Bioinform, vol.10, p.298, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00663932

M. Lechner, S. Findeiß, L. Steiner, M. Marz, P. F. Stadler et al., Proteinortho: detection of (co-)orthologs in large-scale analysis, BMC Bioinform, vol.12, p.124, 2011.

J. P. Meier-kolthoff, A. F. Auch, H. P. Klenk, and M. Göker, Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinform, vol.14, p.60, 2013.

A. G. Andrewes, C. L. Jenkins, M. P. Starr, J. Shepherd, and H. Hope, Structure of xanthomonadin I, a novel dibrominated arylpolyene pigment produced by the bacterium Xanthomonas juglandis, Tetrahedron Lett, vol.45, pp.4023-4027, 1976.