D. Gevers, F. Cohan, J. Lawrence, B. Spratt, T. Coenye et al., Re-evaluating prokaryotic species, Nature Reviews Microbiology, vol.71, issue.9, pp.733-742, 2005.
DOI : 10.1128/AEM.71.2.930-939.2005

E. Moore, S. Mihaylova, P. Vandamme, M. Krichevsky, and L. Dijkshoorn, Microbial systematics and taxonomy: relevance for a microbial commons, Research in Microbiology, vol.161, issue.6, pp.430-438, 2010.
DOI : 10.1016/j.resmic.2010.05.007

D. Minnikin, L. Alshamaony, and M. Goodfellow, Differentiation of Mycobacterium, Nocardia, and Related Taxa by Thin-layer Chromatographic Analysis of Whole-organism Methanolysates, Journal of General Microbiology, vol.88, issue.1, pp.200-204, 1975.
DOI : 10.1099/00221287-88-1-200

D. Brenner, G. Fanning, K. Johnson, R. Citarella, and S. Falkow, Polynucleotide sequence relationships among members of Enterobacteriaceae, J Bacteriol, vol.98, pp.637-50, 1969.
DOI : 10.1016/s0065-2660(08)60355-7

T. Coenye and P. Vandamme, Use of the Genomic Signature in Bacterial Classification and Identification, Systematic and Applied Microbiology, vol.27, issue.2, pp.175-85, 2004.
DOI : 10.1078/072320204322881790

K. Konstantinidis and J. Tiedje, Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead, Current Opinion in Microbiology, vol.10, issue.5, pp.504-513, 2007.
DOI : 10.1016/j.mib.2007.08.006

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.35, issue.D1, pp.590-596, 2013.
DOI : 10.1093/nar/gkl856

URL : https://academic.oup.com/nar/article-pdf/41/D1/D590/3690367/gks1219.pdf

P. Vandamme, B. Pot, M. Gillis, D. Vos, P. Kersters et al., Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol Rev, vol.60, pp.407-445, 1996.

B. Tindall, R. Rossello-mora, H. Busse, W. Ludwig, and P. Kämpfer, Notes on the characterization of prokaryote strains for taxonomic purposes, International Journal of Systematic and Evolutionary Microbiology, vol.190, issue.1, pp.249-66, 2010.
DOI : 10.1128/JB.01919-07

URL : http://ijs.microbiologyresearch.org/deliver/fulltext/ijsem/60/1/249.pdf?itemId=/content/journal/ijsem/10.1099/ijs.0.016949-0&mimeType=pdf&isFastTrackArticle=

E. Stackebrandt and B. Goebel, Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology, International Journal of Systematic and Evolutionary Microbiology, vol.44, issue.4, pp.846-855, 1994.
DOI : 10.1099/00207713-44-4-846

E. Stackebrandt and J. Ebers, Taxonomic parameters revisited: tarnished gold standards, Microbiol Today, vol.33, pp.152-157, 2006.

M. Kim, H. Oh, S. Park, and J. Chun, Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.328, issue.2, pp.346-51, 2014.
DOI : 10.1111/j.1574-6968.2011.02485.x

URL : http://ijs.microbiologyresearch.org/deliver/fulltext/ijsem/64/5/1825_ijs064931.pdf?itemId=/content/journal/ijsem/10.1099/ijs.0.064931-0&mimeType=pdf&isFastTrackArticle=

M. Rossi-tamisier, S. Benamar, D. Raoult, and P. Fournier, Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species, International Journal of Systematic and Evolutionary Microbiology, vol.179, issue.6, pp.1929-1963, 2015.
DOI : 10.1128/jb.179.10.3270-3276.1997

P. Woo, H. Tsoi, K. Leung, P. Lum, A. Leung et al., Identification of Mycobacterium neoaurum isolated from a neutropenic patient with catheter-related bacteremia by 16S rRNA sequencing, J Clin Microbiol, vol.38, pp.3515-3522, 2000.

E. Tortoli, Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s, Clinical Microbiology Reviews, vol.16, issue.2, pp.319-54, 2003.
DOI : 10.1128/CMR.16.2.319-354.2003

R. Edgar, K. Tamura, D. Peterson, N. Peterson, G. Stecher et al., MUSCLE: a multiple sequence alignment method with reduced time and space complexity MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, BMC Bioinform Mol Biol Evol, vol.51828, pp.1132731-1132740, 2004.

P. Bosshard, R. Zbinden, S. Abels, B. Boddinghaus, M. Altwegg et al., 16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory, Journal of Clinical Microbiology, vol.44, issue.4, pp.1359-66, 2006.
DOI : 10.1128/JCM.44.4.1359-1366.2006

S. Mignard and J. Flandrois, 16S rRNA sequencing in routine bacterial identification: A 30-month experiment, Journal of Microbiological Methods, vol.67, issue.3, pp.574-81, 2006.
DOI : 10.1016/j.mimet.2006.05.009

URL : https://hal.archives-ouvertes.fr/hal-00427881

A. Pei, W. Oberdorf, C. Nossa, A. Agarwal, P. Chokshi et al., Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes, Applied and Environmental Microbiology, vol.76, issue.12, pp.3886-97, 2010.
DOI : 10.1128/AEM.02953-09

URL : http://aem.asm.org/content/76/12/3886.full.pdf

S. Acinas, L. Marcelino, V. Klepac-ceraj, and M. Polz, Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons, Journal of Bacteriology, vol.186, issue.9, pp.2629-2664, 2004.
DOI : 10.1128/JB.186.9.2629-2635.2004

URL : http://jb.asm.org/content/186/9/2629.full.pdf

N. Beye, 16S rRNA for Mycobacterium taxonomy