M. Wainwright and J. Lederberg, History of microbiology. Encyclopedia of microbiology, vol.2, pp.419-456, 1992.

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, Clin Microbiol Rev, vol.28, issue.1, pp.237-64, 2015.

L. M. Prescott, J. M. Willey, L. M. Sherwood, C. J. Woolverton, and . Microbiologie, , 2018.

J. Pommerville, Fundamentals of microbiology, 2013.

B. Weeks, Alcamo's Microbes and Society, vol.3, 2012.

R. Gillen-allan and . Gibbs, Serratia Marcescens: The Miracle Bacillus. Answers in Genesis, 2011.

P. R. Murray, K. S. Rosenthal, and M. Pfaller, Medical microbiology. 8, 2015.

T. Sandle, History and development of microbiological culture media. The Journal (Institute of Science and Technology), pp.10-14, 2011.

, La génération spontanée, le grand débat, Institut Pasteur

. Disponible,

S. Kumar, Textbook of microbiology, JP Medical Ltd, 2012.

D. A. Power and J. A. Johnson, Difco? & BBL? manual. 2 nd edition. Sparks: Becton, Dickinson and Company, 2009.

R. M. Atlas, Handbook of microbiological media, 2010.

J. P. Latge, Croissance et sporulation de 6 espèces d'Entomophthorales II. Influence de diverses sources d'azote, Mycopathologia, vol.57, issue.1, pp.53-60, 1975.

V. V. Yurkov and J. Beatty, Aerobic anoxygenic phototrophic bacteria, Microbiol Mol. Biol Rev, vol.62, issue.3, pp.695-724, 1998.

R. K. Thauer, K. Jungermann, and K. Decker, Energy conservation in chemotrophic anaerobic bacteria, Bacteriol Rev, vol.41, issue.1, p.100, 1977.

H. M. Van-der, J. Key, and K. J. Hellingwerf, Photosensing in chemotrophic, nonphototrophic bacteria: let there be light sensing too, Trends Microbiol, vol.15, issue.12, pp.554-62, 2007.

C. H. Werkman and P. W. Wilson, Bacterial physiology

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, Nat Microbiol, vol.7, issue.1, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

M. J. Claesson, S. Cusack, O. O'sullivan, R. Greene-diniz, H. De-weerd et al., Composition, variability, and temporal stability of the intestinal microbiota of the elderly, Proc Natl Acad Sci, vol.15, pp.4586-91, 2011.

D. Ramasamy, J. C. Lagier, T. T. Nguyen, D. Raoult, and P. E. Fournier, Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the family Erysipelotrichaceae, Stand Genomic Sci, vol.8, pp.336-51, 2013.

N. O. Kaakoush, Insights into the role of Erysipelotrichaceae in the human host, Front Cell Infect Microbiol, vol.5, p.84, 2015.

P. E. Fournier and M. Drancourt, New microbes new infections promotes modern prokaryotic taxonomy: a new section 'Taxonogenomics: new genomes of microorganisms in humans, New Microb New Infect, vol.7, pp.48-57, 2015.

P. Seng, C. Abat, J. M. Rolain, P. Colson, J. C. 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, J Clin Microbiol, vol.51, pp.2182-94, 2013.

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, Clin Infect Dis, vol.49, pp.543-51, 2009.

M. Drancourt, C. Bollet, A. Carlioz, R. Martelin, J. P. 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.

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, Clin Microbiol Rev, vol.28, pp.237-64, 2015.

E. Matuschek, D. Brown, and G. Kahlmeter, Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories, Clin Microbiol Infect, vol.20, pp.255-66, 2014.

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

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

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-830, 2008.

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, J Comput Biol, vol.19, pp.455-77, 2012.

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenov02: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.1, p.18, 2012.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.1, issue.30, pp.2114-2134, 2014.

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 Bioinform, vol.11, p.119, 2010.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-64, 1997.

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

L. Käll, A. Krogh, and E. Sonnhammer, A combined transmembrane topology and signal peptide prediction method, J Mol Biol, vol.338, pp.1027-1063, 2004.

A. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-403, 2004.

P. Gouret, J. D. Thompson, and P. Pontarotti, PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees, BMC Bioinform, vol.10, p.298, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00663932

M. Lechner, S. Findeib, L. Steiner, M. Marz, P. F. Stadler et al., Proteinortho: detection of (co-)orthologs in large-scale analysis, BMC Bioinform, vol.12, p.124, 2011.

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, V. Vitiello, N. Balandraud, A. Gilles, P. Pontarotti et al., Figenix: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinform, vol.6, 0198.

A. F. Auch, M. Von-jan, H. P. Klenk, and M. Göker, Digital DNA-DNA hybridization for microbial species delineation by means of genome-togenome sequence comparison, Stand Genomic Sci, vol.28, issue.2, pp.117-151, 2010.

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 Bioinform, vol.21, issue.14, p.60, 2013.

D. Ramasamy, A. K. Mishra, J. C. Lagier, R. Padhmanabhan, M. Rossi et al., A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species, Int J Syst Evol Microbiol, vol.64, pp.84-91, 2014.

A. Oren and G. M. Garrity, List of new names and new combinations previously effectively, but not validly, published, Int J Syst Evol Microbiol, vol.66, pp.4299-305, 2016.

E. Stackebrandt and B. M. Goebel, Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology, Int J Syst Evol Microbiol, vol.44, pp.846-855, 1994.

W. Moore, J. L. Johnson, and L. V. Holdeman, Emendation of Bacteroidaceae and Butyrivibrio and descriptions of Desulfomonas gen. nov. and ten new species in the genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus, Int J Syst Evol Micrbiol, vol.26, pp.238-52, 1976.

C. De-maesschalck, F. Van-immerseel, V. Eeckhaut, D. Baere, S. Cnockaert et al., Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus, Eubacterium biforme and Eubacterium cylindroides as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae, Int J Syst Evol Microbiol, vol.64, pp.3877-84, 2014.

H. L. Greetham, G. R. Gibson, C. Giffard, H. Hippe, B. Merkhoffer et al., Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces, Anaerobe, vol.10, pp.301-308, 2004.

A. K. Mishra, J. C. Lagier, A. Pfleiderer, T. T. Nguyen, A. Caputo et al., Non-contiguous finished genome sequence and description of Holdemania massiliensis sp, Stand Genomic Sci, vol.9, pp.395-409, 2013.

A. Kageyama and Y. Benno, Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: description of Solobacterium moorei gen. nov., sp. nov, Microbiol Immunol, vol.44, pp.223-230, 2000.

J. Downes, B. Olsvik, S. J. Hiom, D. A. Spratt, S. L. Cheeseman et al., Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity, Int J Syst Evol Microbiol, vol.50, pp.979-83, 2000.

J. Lagier, S. Khelaifia, M. T. Alou, S. Ndongo, N. Dione et al., Culture of previously uncultured members of the human gut microbiota by culturomics, Nat Microbiol, vol.1, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

J. Lagier, F. Armougom, M. Million, P. Hugon, I. Pagnier et al., Microbial culturomics: paradigm shift in the human gut microbiome study, Clin Microbiol Infect, vol.18, pp.1185-93, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01478655

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, Clin Microbiol Rev, vol.28, pp.237-64, 2015.

P. Seng, C. Abat, J. M. Rolain, P. Colson, J. C. 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, J Clin Microbiol, vol.51, pp.2182-94, 2013.

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

M. Drancourt, C. Bollet, A. Carlioz, R. Martelin, J. P. 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.

A. 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, Eur J Clin Microbiol Infect Dis, vol.34, pp.561-70, 2015.

A. Diop, S. Khelaifia, N. Armstrong, N. Labas, P. Fournier et al., Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp, Microb Ecol Health Dis, vol.27, 2016.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-830, 2008.

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, J Comput Biol, vol.19, pp.455-77, 2012.

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, p.18, 2012.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2134, 2014.

I. Lee, O. Kim, Y. Park, S. Chun, and J. , OrthoANI: an improved algorithm and software for calculating average nucleotide identity, Int J Syst Evol Microbiol, vol.66, pp.1100-1103, 2016.

D. Ramasamy, A. K. Mishra, J. Lagier, R. Padhmanabhan, M. Rossi et al., A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species, Int J Syst Evol Microbiol, vol.64, pp.384-91, 2014.

, This is an open access article under the CC BY-NC-ND license, 2017.

, INSERM 1095, IHU -Méditerranée Infection, vol.63, pp.19-21

F. Marseille, E-mail address: matthieumillion@gmail.com (M. Million)

, Human Microbiome Journal, vol.4, pp.20-21, 2017.

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, Nat Microbiol, vol.1, p.16203, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

T. D. Mays, L. V. Holdeman, W. Moore, M. Rogosa, and J. L. Johnson, Taxonomy of the genus Veillonella Prévot, Int J Syst Evol Microbiol, vol.32, pp.28-36, 1982.

R. Cabrera-rubio, M. C. Collado, K. Laitinen, S. Salminen, E. Isolauri et al., The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery, Am J Clin Nutr, vol.96, pp.544-51, 2012.

M. Million, A. Diallo, and D. Raoult, Gut microbiota and malnutrition, Microb Pathog, issue.15, pp.30212-30218, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01573801

M. Million, T. Alou, M. Khelaifia, S. Bachar, D. Lagier et al., Increased gut redox and depletion of anaerobic and methanogenic prokaryotes in severe acute malnutrition, Sci Rep, vol.6, p.26051, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01439070

, Phylogenetic tree showing the position of ''Veillonella massiliensis" strain Marseille-P3594 T relative to the phylogenetically closest species. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only the bootstraps scores superior to 75 were retained

A. H. Togo, Human Microbiome Journal, vol.4, pp.20-21, 2017.

, Références bibliographiques

M. Wainwright and J. Lederberg, History of microbiology. Encyclopedia of microbiology, vol.2, pp.419-456, 1992.

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, Clin Microbiol Rev, vol.28, issue.1, pp.237-64, 2015.

T. Sandle, History and development of microbiological culture media. The Journal (Institute of Science and Technology), pp.10-14, 2011.

J. C. Lagier, S. Edouard, I. Pagnier, O. Mediannikov, M. Drancourt et al., Current and past strategies for bacterial culture in clinical microbiology, Clin Microbiol Infect, vol.28, issue.1, pp.208-244, 2015.

B. A. Helmink, M. W. Khan, A. Hermann, V. Gopalakrishnan, and J. Wargo, The microbiome, cancer, and cancer therapy, Nat Med, vol.1, 2019.

S. Vivarelli, R. Salemi, S. Candido, L. Falzone, M. Santagati et al., Gut microbiota and cancer: From pathogenesis to therapy, Cancers, vol.11, issue.1, p.38, 2019.

D. Rea, G. Coppola, G. Palma, A. Barbieri, A. Luciano et al., Microbiota effects on cancer: from risks to therapies, Oncotarget, vol.9, issue.25, p.17915, 2018.

R. Daillère, M. Vétizou, N. Waldschmitt, T. Yamazaki, C. Isnard et al., Enterococcus hirae and Barnesiella intestinihominis facilitate cyclophosphamideinduced therapeutic immunomodulatory effects, Immunity, vol.45, issue.4, pp.931-974, 2016.

N. Dione, S. Khelaifia, L. Scola, B. Lagier, J. C. Raoult et al., A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology, Clin Microbiol Infect, vol.22, issue.1, pp.53-61, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01459959

E. Thursby and N. Juge, Introduction to the human gut microbiota, Biochem J, vol.474, issue.11, pp.1823-1859, 2017.

A. M. Cassard and M. Thomas, Les microbiotes humains : des alliés pour notre santé, Encyclopédie de l'Environnement

M. S. Martin, R. Rossi, O. Bermudez-humaran, L. G. Chatel, J. M. Sokol et al., Faecalibacterium prausnitzii and human intestinal health, Curr Opin Microbiol, vol.16, issue.3, pp.255-261, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00842645