Arbique JC, Poyart C, Trieu-Cuot P, et al (2004) Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42:4686–4696. https://doi.org/10.1128/JCM.42.10.4686-4696.2004
Bakour S, Rathored J, Lo CI, et al (2016) Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov. New Microbes New Infect 11:93–102. https://doi.org/10.1016/j.nmni.2016.03.004
Balouiri M, Sadiki M, Ibnsouda SK (2016) Methods for in vitro evaluating antimicrobial activity: A review. Journal of Pharmaceutical Analysis 6:71–79. https://doi.org/10.1016/j.jpha.2015.11.005
Bankevich A, Nurk S, Antipov D, et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Belkacemi S, Bou Khalil J, Ominami Y, et al (2019) Passive Filtration, Rapid Scanning Electron Microscopy, and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Treponema Culture and Identification from the Oral Cavity. J Clin Microbiol 57:. https://doi.org/10.1128/JCM.00517-19
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Boxberger M, Anani H, La Scola B (2019) Genome sequence and description of Alterileibacterium massiliense gen. nov., sp. nov., a new bacterium isolated from human ileum of a patient with Crohn’s disease. New Microbes New Infect 30:. https://doi.org/10.1016/j.nmni.2019.100533
Citron DM, Ostovari MI, Karlsson A, Goldstein EJ (1991) Evaluation of the E test for susceptibility testing of anaerobic bacteria. J Clin Microbiol 29:2197–2203
Cole JN, Henningham A, Gillen CM, et al (2008) Human pathogenic streptococcal proteomics and vaccine development. Proteomics Clin Appl 2:387–410. https://doi.org/10.1002/prca.200780048
Colson P, Dhiver C, Tamalet C, et al (2020) Full-length title: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection. Sci Rep 10:. https://doi.org/10.1038/s41598-020-58969-6
Dione N, Sankar SA, Lagier J-C, et al (2016) Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 10:66–76. https://doi.org/10.1016/j.nmni.2016.01.002
Drancourt M, Bollet C, Carlioz A, et al (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38:3623–3630
Drancourt M, Roux V, Fournier P-E, Raoult D (2004) rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42:497–504. https://doi.org/10.1128/jcm.42.2.497-504.2004
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Facklam R (2002) What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613–630. https://doi.org/10.1128/cmr.15.4.613-630.2002
Fournier P-E, Lagier J-C, Dubourg G, Raoult D (2015) From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 36:73–78. https://doi.org/10.1016/j.anaerobe.2015.10.011
Hyatt D, Chen G-L, Locascio PF, et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. https://doi.org/10.1186/1471-2105-11-119
Kawamura Y, Hou XG, Sultana F, et al (1995) Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45:406–408. https://doi.org/10.1099/00207713-45-2-406
Kilian M, Poulsen K, Blomqvist T, et al (2008) Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3:e2683. https://doi.org/10.1371/journal.pone.0002683
Kilian M, Riley DR, Jensen A, et al (2014) Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles. mBio 5:e01490-01414. https://doi.org/10.1128/mBio.01490-14
Kim M, Oh H-S, Park S-C, Chun J (2014) 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 64:346–351. https://doi.org/10.1099/ijs.0.059774-0
Krzyściak W, Pluskwa KK, Jurczak A, Kościelniak D (2013) The pathogenicity of the Streptococcus genus. Eur J Clin Microbiol Infect Dis 32:1361–1376. https://doi.org/10.1007/s10096-013-1914-9
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Lagesen K, Hallin P, Rødland EA, et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160
Lagier J-C, Armougom F, Million M, et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193. https://doi.org/10.1111/1469-0691.12023
Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Llorens C, Futami R, Covelli L, et al (2011) The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39:D70–D74. https://doi.org/10.1093/nar/gkq1061
Lo CI, Fall B, Sambe-Ba B, et al (2015a) MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa). PLoS ONE 10:e0145889. https://doi.org/10.1371/journal.pone.0145889
Lo CI, Padhmanabhan R, Mediannikov O, et al (2015b) High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov. Stand Genomic Sci 10:41. https://doi.org/10.1186/s40793-015-0019-8
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Martínez-Lamas L, Limeres-Posse J, Diz-Dios P, Álvarez-Fernández M (2020) Streptococcus downii sp. nov., isolated from the oral cavity of a teenager with Down syndrome. Int J Syst Evol Microbiol 70:4098–4104. https://doi.org/10.1099/ijsem.0.004180
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications 10:1–10. https://doi.org/10.1038/s41467-019-10210-3
Ngom II, Hasni I, Lo CI, et al (2020) Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient. New Microbes New Infect 33:100624. https://doi.org/10.1016/j.nmni.2019.100624
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, et al (2020) List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.004332
Ramasamy D, Mishra AK, Lagier J-C, et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. https://doi.org/10.1099/ijs.0.057091-0
Ricaboni D, Mailhe M, Lagier J-C, et al (2016) Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach. New Microbes New Infect 15:77–88. https://doi.org/10.1016/j.nmni.2016.11.013
Sasser M Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters (GC-FAME). 6
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Shinozaki-Kuwahara N, Takada K, Hirasawa M (2011) Streptococcus ursoris sp. nov., isolated from the oral cavities of bears. Int J Syst Evol Microbiol 61:40–44. https://doi.org/10.1099/ijs.0.019638-0
Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36
(2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 43:D6–D17. https://doi.org/10.1093/nar/gku1130