A. Prazmowski, Untersuchung über die Entwickelungsgeschichte und Fermentwirking einiger Bakterien-Arten

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

C. Wells and T. Wilkins, Clostridia: spore forming anaerobic bacilli Baron's medical microbiology, 1996.

C. Rodriguez, B. Taminiau, J. Van-broeck, M. Delmée, and G. Daube, Clostridium difficile infection and intestinal microbiota interactions, Microbial Pathogenesis, vol.89, pp.201-210, 2015.
DOI : 10.1016/j.micpath.2015.10.018

R. Rosselló-móra, DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation Molecular identification, systematics, and population structure of prokaryotes, pp.23-50, 2006.

L. Wayne, D. Brenner, P. Colwell, P. Grimont, O. Kandler et al., Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics, International Journal of Systematic and Evolutionary Microbiology, vol.37, issue.4, pp.463-467, 1987.
DOI : 10.1099/00207713-37-4-463

A. Viale, A. Arakaki, F. Soncini, and R. Ferreyra, Evolutionary Relationships among Eubacterial Groups as Inferred from GroEL (Chaperonin) Sequence Comparisons, International Journal of Systematic Bacteriology, vol.44, issue.3, pp.527-560, 1944.
DOI : 10.1099/00207713-44-3-527

E. Seck, J. Rathored, S. Khelaifia, O. Croce, C. Robert et al., Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut, New Microbes and New Infections, vol.8, pp.116-142, 2015.
DOI : 10.1016/j.nmni.2015.09.014

T. Alou, M. Nguyen, T. Armstrong, N. Rathored, J. Khelaifia et al., Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut, pp.76-85, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01476280

C. Lo, R. Padhmanabhan, O. Mediannikov, A. Caputo, C. Michelle et al., High-quality genome sequence and description of Bacillus ndiopicus strain FF3T sp. nov., New Microbes and New Infections, vol.8, pp.154-63, 2015.
DOI : 10.1016/j.nmni.2015.10.009

C. Lo, S. Sankar, C. Ehounoud, O. Mediannikov, N. Labas et al., High-quality genome sequencing and description of Dermabacter indicis sp. nov., New Microbes and New Infections, vol.11, pp.59-67, 2016.
DOI : 10.1016/j.nmni.2016.02.007

J. Lagier, F. Armougom, A. Mishra, T. Nguyen, D. Raoult et al., Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov., Standards in Genomic Sciences, vol.35, issue.3, pp.315-339, 2012.
DOI : 10.1093/nar/gkm160

T. Reddy, A. Thomas, D. Stamatis, J. Bertsch, M. Isbandi et al., The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification, Nucleic Acids Research, vol.27, issue.D1, pp.1099-106, 2015.
DOI : 10.1038/nbt.1552

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

B. Fall, C. Lo, B. Samb-ba, N. Perrot, S. Diawara et al., The Ongoing Revolution of MALDI-TOF Mass Spectrometry for Microbiology Reaches Tropical Africa, The American Journal of Tropical Medicine and Hygiene, vol.92, issue.3, pp.641-648, 2015.
DOI : 10.4269/ajtmh.14-0406

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

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

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

C. Lo, B. Fall, B. Sambe-ba, S. Diawara, M. Gueye et al., MALDI-TOF mass spectrometry: a powerful tool for clinical microbiology at Hôpital Principal de Dakar

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.

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

M. Sasser, C. Kunitsky, G. Jackoway, J. Ezzell, J. Teska et al., Identification of Bacillus anthracis from culture using gas chromatographic analysis of fatty acid methyl esters, J AOAC Int, vol.88, pp.178-81, 2005.

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

M. Cresci, I. Lo, C. Khelaifia, S. Mouelhi, D. Delerce et al., Corynebacterium phoceense sp. nov., strain MC1 T a new bacterial species isolated from human urine, pp.73-82, 2016.

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

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. Rodland, 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

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

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

M. Lechner, S. Findeib, 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

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.117-154, 2010.
DOI : 10.1101/gr.229202. Article published online before March 2002

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

B. Himelbloom and E. Canale-parola, Clostridium methylpentosum sp. nov.: a ring-shaped intestinal bacterium that ferments only methylpentoses and pentoses, Archives of Microbiology, vol.25, issue.4, pp.287-93, 1989.
DOI : 10.1016/B978-0-12-341280-5.50012-4

D. Freier, C. Mothershed, and J. Wiegel, Characterization of Clostridium thermocellum JW20, Appl Environ Microbiol, vol.54, pp.204-215, 1988.

C. Lo, A. Mishra, R. Padhmanabhan, B. Samb-ba, A. Gassama-sow et al., Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov., Standards in Genomic Sciences, vol.12, issue.1, pp.14-27, 2013.
DOI : 10.1186/1471-2105-12-124

S. Keis, R. Shaheen, and T. David, Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.51, issue.6, pp.2095-103, 2001.
DOI : 10.1099/00207713-51-6-2095