N. Salazar, S. Arboleya, L. Valdés, C. Stanton, P. Ross et al., The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations, Frontiers in Genetics, vol.486, issue.1, p.406, 2014.
DOI : 10.1038/nature11053

URL : https://www.frontiersin.org/articles/10.3389/fgene.2014.00406/pdf

J. Lagier, M. Million, P. Hugon, F. Armougom, and D. Raoult, Human Gut Microbiota: Repertoire and Variations, Frontiers in Cellular and Infection Microbiology, vol.2, p.136, 2012.
DOI : 10.3389/fcimb.2012.00136

URL : http://journal.frontiersin.org/article/10.3389/fcimb.2012.00136/pdf

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

T. Alou, M. Lagier, J. Raoult, and D. , Diet influence on the gut microbiota and dysbiosis related to nutritional disorders, Human Microbiome Journal, vol.1, pp.3-11, 2016.
DOI : 10.1016/j.humic.2016.09.001

URL : https://hal.archives-ouvertes.fr/hal-01476119

M. Million, A. Diallo, and D. Raoult, Gut microbiota and malnutrition, Microbial Pathogenesis, vol.106, pp.127-165, 2017.
DOI : 10.1016/j.micpath.2016.02.003

URL : https://hal.archives-ouvertes.fr/hal-01573801

E. Angelakis and J. Lagier, Samples and techniques highlighting the links between obesity and microbiota, Microbial Pathogenesis, vol.106, pp.119-145, 2017.
DOI : 10.1016/j.micpath.2016.01.024

URL : https://hal.archives-ouvertes.fr/hal-01573800

M. Rajili-c-stojanovi-c and W. De-vos, The first 1000 cultured species of the human gastrointestinal microbiota, FEMS Microbiology Reviews, vol.64, issue.5, pp.996-1047, 2014.
DOI : 10.1038/ismej.2011.212

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, F. Armougom, M. Million, P. Hugon, I. Pagnier et al., Microbial culturomics: paradigm shift in the human gut microbiome study, Clinical Microbiology and Infection, vol.18, issue.12, pp.1185-93, 2012.
DOI : 10.1111/1469-0691.12023

URL : https://hal.archives-ouvertes.fr/hal-01478655

A. Parte, LPSN???list of prokaryotic names with standing in nomenclature, Nucleic Acids Research, vol.58, issue.D1, pp.613-619, 2014.
DOI : 10.1016/j.syapm.2008.07.001

URL : https://academic.oup.com/nar/article-pdf/42/D1/D613/3583564/gkt1111.pdf

P. Lawson, D. Citron, K. Tyrrell, and S. Finegold, Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O???Toole 1935) Pr??vot 1938, Anaerobe, vol.40, pp.95-104, 2016.
DOI : 10.1016/j.anaerobe.2016.06.008

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

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, C. Abat, J. Rolain, P. Colson, J. Lagier et al., Identification of Rare Pathogenic Bacteria in a Clinical Microbiology Laboratory: Impact of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, Journal of Clinical Microbiology, vol.51, issue.7, pp.2182-94, 2013.
DOI : 10.1128/JCM.00492-13

M. Drancourt, C. Bollet, A. Carlioz, R. Martelin, J. Gayral et al., 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates, J Clin Microbiol, vol.38, pp.3623-3653, 2000.

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=

J. Schindelin, C. Rueden, M. Hiner, and K. Eliceiri, The ImageJ ecosystem: An open platform for biomedical image analysis, Molecular Reproduction and Development, vol.15, issue.7-8, pp.518-547, 2015.
DOI : 10.1038/nmeth.2089

URL : http://onlinelibrary.wiley.com/doi/10.1002/mrd.22489/pdf

C. Schneider, W. Rasband, and K. Eliceiri, NIH Image to ImageJ: 25 years of image analysis, Nature Methods, vol.42, issue.7, pp.671-676, 2012.
DOI : 10.2144/000112257

URL : http://europepmc.org/articles/pmc5554542?pdf=render

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

E. Matuschek, D. Brown, and G. Kahlmeter, Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories, Clinical Microbiology and Infection, vol.20, issue.4, pp.255-66, 2014.
DOI : 10.1111/1469-0691.12373

URL : https://doi.org/10.1111/1469-0691.12373

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, I. Karsch-mizrachi, K. Clark, D. Lipman, J. Ostell et al., GenBank, Nucleic Acids Research, vol.36, issue.suppl_2, pp.48-53, 2012.
DOI : 10.1093/nar/gkn201

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

L. Käll, A. Krogh, and E. Sonnhammer, A Combined Transmembrane Topology and Signal Peptide Prediction Method, Journal of Molecular Biology, vol.338, issue.5, pp.1027-1063, 2004.
DOI : 10.1016/j.jmb.2004.03.016

Y. Zhou, Y. Liang, K. Lynch, J. Dennis, and D. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.113, issue.2, pp.347-52, 2011.
DOI : 10.1016/S0092-8674(03)00276-9

URL : https://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.pdf

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, p.75, 2008.
DOI : 10.1186/1471-2164-9-75

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

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

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

URL : http://genome.cshlp.org/content/14/7/1394.full.pdf

P. Gouret, J. Thompson, and P. Pontarotti, PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees, BMC Bioinformatics, vol.10, issue.1, p.298, 2009.
DOI : 10.1186/1471-2105-10-298

URL : https://hal.archives-ouvertes.fr/inserm-00663932

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

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, pp.117-151, 2010.
DOI : 10.1101/gr.229202. Article published online before March 2002

URL : http://standardsingenomics.org/content/2/1/117/pdf

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

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

W. Sturges and E. Drake, A complete description of Clostridium putrefaciens (McBryde), J Bacteriol, vol.14, pp.175-184, 1927.

N. Alou, Four new Clostridium species
URL : https://hal.archives-ouvertes.fr/hal-01795916