B. B. Afolabi, O. E. Moses, and O. O. Oduyebo, Bacterial vaginosis and pregnancy outcome in, Open Forum Infectious Diseases, vol.3, 2016.

M. T. Alou, J. Rathored, C. Michelle, G. Dubourg, C. Andrieu et al., Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant, Antonie van Leeuwenhoek, vol.110, pp.737-750, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01573737

A. F. 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.2, pp.117-134, 2010.

G. Avgu?tin, R. J. Wallace, and H. J. Flint, Phenotypic diversity among ruminal isolates of Prevotella ruminicola: Proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola, International Journal of Systematic and Evolutionary Microbiology, vol.47, pp.284-288, 1997.

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, Journal of Computational Biology, vol.19, pp.455-477, 2012.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

C. S. Bradshaw, S. N. Tabrizi, C. K. Fairley, A. N. Morton, E. Rudland et al., The association of Atopobium vaginae and Gardnerella vaginalis with bacterial vaginosis and recurrence after oral metronidazole therapy, Journal of Infectious Diseases, vol.194, pp.828-836, 2006.

J. Chun, A. Oren, A. Ventosa, H. Christensen, D. R. Arahal et al., Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes, International Journal of Systematic and Evolutionary Microbiology, vol.68, pp.461-466, 2018.

D. M. Citron, M. I. Ostovari, A. Karlsson, and E. J. Goldstein, Evaluation of the E test for susceptibility testing of anaerobic bacteria, Journal of Clinical Microbiology, vol.29, pp.2197-2203, 1991.

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

G. A. Durand, T. Pham, S. Ndongo, S. I. Traore, G. Dubourg et al., Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia, Anaerobe, vol.43, pp.47-55, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01521359

T. Ezaki, Y. Kawamura, N. Li, Z. Li, L. Zhao et al., Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus, International Journal of Systematic and Evolutionary Microbiology, vol.51, pp.1521-1528, 2001.

P. E. Fournier, J. C. 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.73-78, 2015.

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, pp.71-87, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00827323

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

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, p.1, 2005.

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 Bioinformatics, vol.11, p.1, 2010.

C. N. Johnson, T. R. Whitehead, M. A. Cotta, R. E. Rhoades, and P. A. Lawson, Peptoniphilus stercorisuis sp. nov., isolated from a swine manure storage tank and description of Peptoniphilaceae fam. nov, International Journal of Systematic and Evolutionary Microbiology, vol.64, pp.3538-3545, 2014.

L. Käll, A. Krogh, and E. L. Sonnhammer, A combined transmembrane topology and signal peptide prediction method, Journal of Molecular Biology, vol.338, pp.1027-1036, 2004.

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.64, pp.346-351, 2014.

J. A. Klappenbach, J. Goris, P. Vandamme, T. Coenye, K. T. Konstantinidis et al., DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, International Journal of Systematic and Evolutionary Microbiology, vol.57, pp.81-91, 2007.

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

J. C. Lagier, P. Hugon, S. Khelaifia, P. E. 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, pp.237-264, 2015.

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, Nature Microbiology, vol.12, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

J. G. Lawrence and H. Ochman, Amelioration of bacterial genomes: Rates of change and exchange, Journal of Molecular Evolution, vol.44, pp.383-397, 1997.

J. P. Lepargneur and V. Rousseau, Protective role of the Doderleïn flora, Obstetrique et Biologie de la Reproduction, vol.31, pp.485-494, 2002.

N. Li, Y. Hashimoto, S. Adnan, H. Miura, H. Yamamoto et al., Three new species of the genus Peptostreptococcus isolated from humans: Peptostreptococcus vaginalis sp. nov., Peptostreptococcus lacrimalis sp. nov., and Peptostreptococcus lactolyticus sp. nov, International Journal of Systematic and Evolutionary Microbiology, vol.42, pp.602-605, 1992.

J. Li, J. Mccormick, A. Bocking, and G. Reid, Importance of vaginal microbes in reproductive health, Reproductive Sciences, vol.19, pp.235-242, 2012.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Research, vol.25, pp.955-964, 1997.

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, 2012.

D. H. Martin and J. M. Marrazzo, The vaginal microbiome: Current understanding and future directions, Journal of Infectious Diseases, vol.214, pp.36-41, 2016.

E. Matuschek, D. F. Brown, and G. Kahlmeter, Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories, Clinical Microbiology & Infection, vol.20, pp.255-266, 2014.

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 Bioinformatics, vol.14, p.1, 2013.

J. P. Menard, F. Fenollar, M. Henry, F. Bretelle, and D. Raoult, Molecular quantification of Gardnerella vaginalis and Atopobium vaginae loads to predict bacterial vaginosis, Clinical Infectious Diseases, vol.47, pp.33-43, 2008.

A. K. Mishra, J. C. Lagier, T. T. Nguyen, D. Raoult, and P. Fournier, Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov, Standards in Genomic Sciences, vol.7, pp.370-381, 2013.

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, European Journal of Clinical Microbiology and Infectious Diseases, vol.34, pp.561-570, 2015.

D. A. Murdoch, Gram-positive anaerobic cocci, Clinical Microbiology Reviews, vol.11, pp.81-120, 1998.

D. A. Murdoch, I. J. Mitchelmore, and S. Tabaqchali, The clinical importance of gram-positive anaerobic cocci isolated at St Bartholomew's Hospital, London, in 1987, Journal of Medical Microbiology, vol.41, pp.36-44, 1994.

P. R. Murray, E. J. Baron, J. H. Jorgensen, M. L. Landry, and M. A. Pfaller, Manual of clinical microbiology, 2007.

A. B. Onderdonk, M. L. Delaney, and R. N. Fichorova, The human microbiome during bacterial vaginosis, Clinical Microbiology Reviews, vol.29, pp.223-238, 2016.

S. Pandya, K. Ravi, V. Srinivas, S. Jadhav, A. Khan et al., Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora, Journal of Medical Microbiology, vol.66, pp.149-153, 2017.

N. B. Patel, R. Y. Tito, A. J. Obregón-tito, L. O'neal, O. Trujillo-villaroel et al., Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru, Anaerobe, vol.32, pp.43-48, 2015.

M. Richter and R. Rosselló-móra, Shifting the genomic gold standard for the prokaryotic species definition, Proceedings of the National Academy of Sciences, vol.106, pp.19126-19131, 2009.

L. M. Rodriguez-r and K. T. Konstantinidis, Bypassing cultivation to identify bacterial species, Microbe, vol.9, pp.111-118, 2014.
DOI : 10.1128/microbe.9.111.1

URL : http://www.asmscience.org/deliver/fulltext/microbe/9/3/znw00314000111.pdf?itemId=/content/journal/microbe/10.1128/microbe.9.111.1&mimeType=pdf

A. P. Rooney, J. L. Swezey, R. Pukall, P. Schumann, and S. Spring, Peptoniphilus methioninivorax sp. nov., a Gram-positive anaerobic coccus isolated from retail ground beef, International Journal of Systematic and Evolutionary Microbiology, vol.61, pp.1962-1967, 2011.

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

P. Seng, M. Drancourt, F. Gouriet, B. La-scola, P. E. 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, pp.543-551, 2009.

E. Shipitsyna, A. Roos, R. Datcu, A. Hallén, H. Fredlund et al., Composition of the vaginal microbiota in women of reproductive age-sensitive and specific molecular diagnosis of bacterial vaginosis is possible?, PLoS ONE, vol.8, issue.4, 2013.

S. Srinivasan and D. N. Fredricks, The human vaginal bacterial biota and bacterial vaginosis, Interdisciplinary Perspectives on Infectious Diseases, pp.1-22, 2008.

S. Srinivasan, M. M. Munch, M. V. Sizova, T. L. Fiedler, C. M. Kohler et al., More easily cultivated than identified: Classical isolation with molecular identification of vaginal bacteria, Journal of Infectious Diseases, vol.214, pp.21-28, 2016.

E. Stackebrandt and J. Ebers, Taxonomic parameters revisited: Tarnished gold standards, Microbiology Today, p.152, 2006.

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, vol.30, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, pp.4673-4680, 1994.

N. Ulger-toprak, P. A. Lawson, P. Summanen, L. O'neal, and S. M. Finegold, Peptoniphilus duerdenii sp. nov. and Peptoniphilus koenoeneniae sp. nov., isolated from human clinical specimens, International Journal of Systematic and Evolutionary Microbiology, vol.62, pp.2336-2341, 2012.

P. Yarza, P. Yilmaz, E. Pruesse, F. O. Glöckner, W. Ludwig et al., Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences, Nature Reviews Microbiology, vol.12, pp.635-645, 2014.

D. R. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, pp.821-829, 2008.