N. Ngom, Mediterranea massiliensis genome References Microbial culturomics: paradigm shift in the human gut microbiome study, Clin Microbiol Infect, vol.18, issue.1, pp.1185-93, 2012.

J. Lagier, P. Hugon, S. Khelaifia, P. Fournier, L. Scola et al., The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota, Clinical Microbiology Reviews, vol.28, issue.1, pp.237-64, 2015.
DOI : 10.1128/CMR.00014-14

J. Lagier, S. Khelaifia, M. Alou, S. Ndongo, N. Dione et al., Culture of previously uncultured members of the human gut microbiota by culturomics, Nature Microbiology, vol.2, issue.12, p.16203, 2016.
DOI : 10.1006/jmbi.1990.9999
URL : https://hal.archives-ouvertes.fr/hal-01453324

P. Fournier, J. Lagier, G. Dubourg, and D. Raoult, From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology, Anaerobe, vol.36, pp.73-81, 2015.
DOI : 10.1016/j.anaerobe.2015.10.011

E. Sentausa and P. Fournier, Advantages and limitations of genomics in prokaryotic taxonomy, Clinical Microbiology and Infection, vol.19, issue.9, pp.790-795, 2013.
DOI : 10.1111/1469-0691.12181

I. Pagani, K. Liolios, J. Jansson, I. Chen, T. Smirnova et al., The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Research, vol.3, issue.3, pp.571-580, 2012.
DOI : 10.4056/aigs.1443528

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

E. Stackebrandt, Taxonomic parameters revisited: tarnished gold standards, Microbiol Today, vol.6, pp.152-157, 2006.

Y. Benno, J. Watabe, and T. Mitsuoka, Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Species from Abscesses and Feces of Pigs, Systematic and Applied Microbiology, vol.4, issue.3, pp.396-407, 1983.
DOI : 10.1016/S0723-2020(83)80024-1

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. Mailhe, D. Ricaboni, A. Benezech, K. Saber, P. Fournier et al., ??? Mediterranea massiliensis ??? gen. nov., sp. nov., a new human-associated bacterium isolated from the right and left colon lavage of a 58-year-old patient, New Microbes and New Infections, vol.13, pp.54-59, 2016.
DOI : 10.1016/j.nmni.2016.06.002

L. Scola, B. Khelaifia, S. Lagier, J. Raoult, and D. , Aerobic culture of anaerobic bacteria using antioxidants: a preliminary report, European Journal of Clinical Microbiology & Infectious Diseases, vol.21, issue.10, pp.1781-1784, 2014.
DOI : 10.1128/JCM.00492-13

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, Clinical Infectious Diseases, vol.49, issue.4, pp.543-51, 2009.
DOI : 10.1086/600885

P. Seng, J. Rolain, P. Fournier, L. Scola, B. Drancourt et al., MALDI-TOF-mass spectrometry applications in clinical microbiology, Future Microbiology, vol.391, issue.11, pp.1733-54, 2010.
DOI : 10.1007/s00216-008-2161-2

S. Sankar, J. Lagier, P. Pontarotti, D. Raoult, and P. Fournier, The human gut microbiome, a taxonomic conundrum, Systematic and Applied Microbiology, vol.38, issue.4, pp.276-86, 2015.
DOI : 10.1016/j.syapm.2015.03.004

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340
URL : https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003
URL : http://doi.org/10.1371/journal.pone.0009490

H. Shimodaira and M. Hasegawa, Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1120, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026201
URL : https://academic.oup.com/mbe/article-pdf/16/8/1114/9592375/mbe1114.pdf

N. Ngom, Mediterranea massiliensis genome
URL : https://hal.archives-ouvertes.fr/hal-01795914

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

N. Dione, S. Sankar, J. Lagier, S. Khelaifia, C. Michele et al., Genome sequence and description of Anaerosalibacter massiliensis sp. nov., New Microbes and New Infections, vol.10, pp.66-76, 2016.
DOI : 10.1016/j.nmni.2016.01.002
URL : https://doi.org/10.1016/j.nmni.2016.01.002

D. Hyatt, G. Chen, P. Locascio, M. Land, F. Larimer et al., Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, issue.1, p.119, 2010.
DOI : 10.1186/1471-2105-11-119
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-119?site=bmcbioinformatics.biomedcentral.com

D. Benson, M. Cavanaugh, K. Clark, I. Karsch-mizrachi, D. Lipman et al., GenBank, Nucleic Acids Research, vol.14, issue.D1, pp.37-42, 2017.
DOI : 10.1093/nar/gkt282

T. Lowe and S. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.235, issue.4, pp.955-64, 1997.
DOI : 10.1006/jmbi.1994.1074

K. Lagesen, P. Hallin, E. Rødland, H. Staerfeldt, T. Rognes et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Research, vol.22, issue.1, pp.3100-3108, 2007.
DOI : 10.1145/974614.974647
URL : https://academic.oup.com/nar/article-pdf/35/9/3100/16760567/gkm160.pdf

D. Bendtsen, J. Nielsen, H. Von-heijne, G. Brunak, and S. , Improved Prediction of Signal Peptides: SignalP 3.0, Journal of Molecular Biology, vol.340, issue.4, pp.783-95, 2004.
DOI : 10.1016/j.jmb.2004.05.028

A. Krogh, B. Larsson, G. Von-heijne, and E. Sonnhammer, Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-80, 2001.
DOI : 10.1006/jmbi.2000.4315

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice et al., Artemis: sequence visualization and annotation, Bioinformatics, vol.16, issue.10, pp.944-949, 2000.
DOI : 10.1093/bioinformatics/16.10.944
URL : https://academic.oup.com/bioinformatics/article-pdf/16/10/944/598346/160944.pdf

T. Carver, N. Thomson, A. Bleasby, M. Berriman, and J. Parkhill, DNAPlotter: circular and linear interactive genome visualization, Bioinformatics, vol.21, issue.4, pp.119-139, 2009.
DOI : 10.1093/bioinformatics/bti054
URL : https://academic.oup.com/bioinformatics/article-pdf/25/1/119/859221/btn578.pdf

D. Ramasamy, A. Mishra, J. Lagier, R. Padhmanabhan, M. Rossi et al., A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.101, issue.1, pp.384-91, 2014.
DOI : 10.1007/s10482-011-9667-x

M. Lechner, S. Findeiß, L. Steiner, M. Marz, P. Stadler et al., Proteinortho: Detection of (Co-)orthologs in large-scale analysis, BMC Bioinformatics, vol.12, issue.1, p.124, 2011.
DOI : 10.1073/pnas.0708855104
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-124?site=bmcbioinformatics.biomedcentral.com

P. Gouret, J. Paganini, J. Dainat, D. Louati, E. Darbo et al., Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: the multi-agent software system DAGOBAH Evolutionary biology?concepts, biodiversity, macroevolution and genome evolution, pp.71-87, 2011.

P. Gouret, V. Vitiello, N. Balandraud, A. Gilles, P. Pontarotti et al., FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.6, issue.1, p.198, 2005.
DOI : 10.1186/1471-2105-6-198

J. Meier-kolthoff, A. Auch, H. Klenk, and M. Göker, Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, vol.14, issue.1, p.60, 2013.
DOI : 10.1128/JB.184.8.2072-2080.2002
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-60?site=bmcbioinformatics.biomedcentral.com

A. Auch, M. Von-jan, H. Klenk, and M. Göker, Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison, Standards in Genomic Sciences, vol.1, issue.1, p.117, 2010.
DOI : 10.1101/gr.229202. Article published online before March 2002
URL : http://standardsingenomics.org/content/2/1/117/pdf

H. Hayashi, K. Shibata, M. Bakir, M. Sakamoto, S. Tomita et al., Bacteroides coprophilus sp. nov., isolated from human faeces, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.57, issue.6, pp.1323-1329, 2007.
DOI : 10.1099/ijs.0.64979-0