1887

Abstract

Phylogenetic analyses based on 16S rRNA gene sequences of members of the family showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: was reduced in taxonomic rank as a later heterotypic synonym of ; subsp. as a later heterotypic synonym of subsp. ; the unification of subsp. and subsp. as ; the unification of subsp. and subsp. as ; the unification of subsp. and subsp. as ; subsp. as the novel species ; subsp. as the novel species ; subsp. as the novel species ; subsp. as the novel species ; subsp. as the novel species ; the reassignment of , , , and to the novel genus with as the type species; and the formal assignment of as a member of the family .

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2020-10-14
2020-11-25
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References

  1. Prévot AR. Manuel de classification et de determination des bacteries anaerobies 223, 1st ed. Paris: Masson; 1940
    [Google Scholar]
  2. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [CrossRef]
    [Google Scholar]
  3. Garrity GM, Holt JG. The road map to the manual. In Boone DR, Castenholz RW, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology 163 New York, NY: Springer; 2001
    [Google Scholar]
  4. Schleifer K-H, Bell JA et al. Family VIII. Staphylococcaceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology (The Firmicutes 3, 2nd ed. Springer; 2009 pp 392–433
    [Google Scholar]
  5. Alves M, Nogueira C, de Magalhães-Sant'ana A, Chung AP, Morais PV et al. Nosocomiicoccus ampullae gen. nov., sp. nov., isolated from the surface of bottles of saline solution used in wound cleansing. Int J Syst Evol Microbiol 2008; 58:2939–2944 [CrossRef][PubMed]
    [Google Scholar]
  6. Martin E, Klug K, Frischmann A, Busse HJ, Kämpfer P et al. Jeotgalicoccus coquinae sp. nov. and Jeotgalicoccus aerolatus sp. nov., isolated from poultry houses. Int J Syst Evol Microbiol 2011; 61:237–241 [CrossRef][PubMed]
    [Google Scholar]
  7. Mishra AK, Edouard S, Dangui NP, Lagier JC, Caputo A et al. Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci 2013; 9:205–219 [CrossRef][PubMed]
    [Google Scholar]
  8. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published (Validation List no. 168). Int J Syst Evol Microbiol 2016; 66:1603–1606 [CrossRef][PubMed]
    [Google Scholar]
  9. Amoozegar MA, Bagheri M, Makhdoumi-Kakhki A, Didari M, Schumann P et al. Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake. Int J Syst Evol Microbiol 2014; 64:1964–1969 [CrossRef][PubMed]
    [Google Scholar]
  10. Jiang Z, Yuan CG, Xiao M, Tian XP, Khan IU et al. Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean. Antonie van Leeuwenhoek 2016; 109:1153–1160 [CrossRef][PubMed]
    [Google Scholar]
  11. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published (Validation List no. 172). Int J Syst Evol Microbiol 2016; 66:4299–4305 [CrossRef][PubMed]
    [Google Scholar]
  12. Li Y, Wang SK, Xue H, Chang JP, Guo LM et al. Corticicoccus populi gen. nov., sp. nov., a member of the family Staphylococcaceae, isolated from symptomatic bark of Populus × euramericana canker. Int J Syst Evol Microbiol 2017; 67:789–794 [CrossRef][PubMed]
    [Google Scholar]
  13. Prakash O, Muduli S, Kumar R, Kumari C, Nimonkar Y et al. Description of Auricoccus indicus gen. nov., sp. nov., isolated from skin of human ear. Int J Syst Evol Microbiol 2017; 67:1212–1218 [CrossRef][PubMed]
    [Google Scholar]
  14. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 69: [CrossRef][PubMed]
    [Google Scholar]
  15. Lory S. The family Staphylococcaceae. In Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes: Firmicutes and Tenericutes 573, 4th ed. Springer Reference; 2014
    [Google Scholar]
  16. Jiang K, Xue Y, Ma Y. Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China. Stand Genomic Sci 2015; 10:116 [CrossRef][PubMed]
    [Google Scholar]
  17. Hyun D-W, Whon TW, Cho YJ, Chun J, Kim M-S et al. Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain CrmT (=DSM 23852T). Stand Genomic Sci 2013; 8:255–263 [CrossRef][PubMed]
    [Google Scholar]
  18. Mašlaňová I, Wertheimer Z, Sedláček I, Švec P, Indráková A et al. Description and comparative genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., novel macrococci from human clinical material with virulence potential and suspected uptake of foreign DNA by natural transformation. Front Microbiol 2018; 9:1178 [CrossRef][PubMed]
    [Google Scholar]
  19. Mazhar S, Hill C, McAuliffe O. The genus Macrococcus: an insight into its biology, evolution, and relationship with Staphylococcus. Adv Appl Microbiol 2018; 105:1–50 [CrossRef][PubMed]
    [Google Scholar]
  20. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  21. Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 2018; 9:67 [CrossRef][PubMed]
    [Google Scholar]
  22. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef]
    [Google Scholar]
  23. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [CrossRef][PubMed]
    [Google Scholar]
  24. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [CrossRef][PubMed]
    [Google Scholar]
  25. Staley JT, Krieg NR. Bacterial Classification I. Classification of prokaryotic organisms: an overview. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology Baltimore: Williams & Wilkins; 1984 pp 1–4
    [Google Scholar]
  26. Wayne L, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology: report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  27. Konstantinidis KT, Stackebrandt E. Defining taxonomic ranks. In Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes: Prokaryotic Biology and Symbiotic Associations 628, 4th ed. Springer Reference; 2013
    [Google Scholar]
  28. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [CrossRef][PubMed]
    [Google Scholar]
  29. Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470–4495 [CrossRef][PubMed]
    [Google Scholar]
  30. Zheng J, Wittouck S, Salvetti E, Franz C, Harris HMB et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782–2858 [CrossRef][PubMed]
    [Google Scholar]
  31. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [CrossRef][PubMed]
    [Google Scholar]
  32. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [CrossRef]
    [Google Scholar]
  33. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  34. Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR et al. Genome data provides high support for generic boundaries in Burkholderia sensu lato. Front Microbiol 2017; 8:1154 [CrossRef][PubMed]
    [Google Scholar]
  35. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [CrossRef][PubMed]
    [Google Scholar]
  36. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [CrossRef][PubMed]
    [Google Scholar]
  37. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [CrossRef][PubMed]
    [Google Scholar]
  38. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  39. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [CrossRef][PubMed]
    [Google Scholar]
  40. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  41. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  42. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  43. Hájek V, Meugnier H, Bes M, Brun Y, Fiedler F et al. Staphylococcus saprophyticus subsp. bovis subsp. nov., isolated from bovine nostrils. Int J Syst Bacteriol 1996; 46:792–796 [CrossRef][PubMed]
    [Google Scholar]
  44. De Bel A, Švec P, Petráš P, Sedláček I, Pantůček R et al. Reclassification of Staphylococcus jettensis de Bel et al. 2013 as Staphylococcus petrasii subsp. jettensis subsp. nov. and emended description of Staphylococcus petrasii Pantucek et al. 2013. Int J Syst Evol Microbiol 2014; 64:4198–4201 [CrossRef][PubMed]
    [Google Scholar]
  45. Probst AJ, Hertel C, Richter L, Wassill L, Ludwig W et al. Staphylococcus condimenti sp. nov., from soy sauce mash, and Staphylococcus carnosus (Schleifer and Fischer 1982) subsp. utilis subsp. nov. Int J Syst Bacteriol 1998; 48 Pt 3:651–658 [CrossRef][PubMed]
    [Google Scholar]
  46. Pantůcek R, Sedlácek I, Doškař J, Rosypal S. Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans. Int J Syst Bacteriol 1999; 49 Pt 3:941–951 [CrossRef][PubMed]
    [Google Scholar]
  47. de la Fuente R, Suarez G, Schleifer KH. Staphylococcus aureus subsp. anaerobius subsp. nov., the causal agent of abscess disease of sheep. Int J Syst Bacteriol 1985; 35:99–102 [CrossRef]
    [Google Scholar]
  48. Kloos WE, Schleifer KH, Smith RF. Characterization of Staphylococcus sciuri sp.nov. and its subspecies. Int J Syst Bacteriol 1976; 26:22–37 [CrossRef]
    [Google Scholar]
  49. Schleifer KH, Geyer U, Kilpper-Bälz R, Devriese LA. Elevation of Staphylococcus sciuri subsp. lentus (Kloos et al.) to species status: Staphylococcus lentus (Kloos et al.) comb. nov. Syst Appl Microbiol 1983; 4:382–387 [CrossRef][PubMed]
    [Google Scholar]
  50. Vernozy-Rozand C, Mazuy C, Meugnier H, Bes M, Lasne Y et al. Staphylococcus fleurettii sp. nov., isolated from goat's milk cheeses. Int J Syst Evol Microbiol 2000; 50:1521–1527 [CrossRef][PubMed]
    [Google Scholar]
  51. Chesneau O, Morvan A, Aubert S, el Solh N. The value of rRNA gene restriction site polymorphism analysis for delineating taxa in the genus Staphylococcus. Int J Syst Evol Microbiol 2000; 50 Pt 2:689–697 [CrossRef][PubMed]
    [Google Scholar]
  52. Hauschild T, Stepanović S, Zakrzewska-Czerwińska J. Staphylococcus stepanovicii sp. nov., a novel novobiocin-resistant oxidase-positive staphylococcal species isolated from wild small mammals. Syst Appl Microbiol 2010; 33:183–187 [CrossRef]
    [Google Scholar]
  53. Webster JA, Bannerman TL, Hubner RJ, Ballard DN, Cole EM et al. Identification of the Staphylococcus sciuri species group with EcoRI fragments containing rRNA sequences and description of Staphylococcus vitulus sp. nov. Int J Syst Bacteriol 1994; 44:454–460 [CrossRef][PubMed]
    [Google Scholar]
  54. Place RB, Hiestand D, Burri S, Teuber M. Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese. Syst Appl Microbiol 2002; 25:353–359 [CrossRef][PubMed]
    [Google Scholar]
  55. Igimi S, Takahashi E, Mitsuoka T. Staphylococcus schleiferi subsp. coagulans subsp. nov., isolated from the external auditory meatus of dogs with external ear otitis. Int J Syst Bacteriol 1990; 40:409–411 [CrossRef][PubMed]
    [Google Scholar]
  56. Pantůček R, Švec P, Dajcs JJ, Machová I, Černohlávková J et al. Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections. Syst Appl Microbiol 2013; 36:90–95 [CrossRef][PubMed]
    [Google Scholar]
  57. Švec P, Bel AD, Sedláček I, Petráš P, Gelbíčová T et al. Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material. Int J Syst Evol Microbiol 2015; 65:2071–2077 [CrossRef][PubMed]
    [Google Scholar]
  58. Kloos WE, Wolfshohl JF. Staphylococcus cohnii subspecies: Staphylococcus cohnii subsp. cohnii subsp. nov. and Staphylococcus cohnii subsp. urealyticum subsp. nov. Int J Syst Bacteriol 1991; 41:284–289 [CrossRef][PubMed]
    [Google Scholar]
  59. Rosenbach FJ. Microorganismen bei den Wund-Infections-Krankheiten des Menschen. J.F Wiesbaden: Bergmann; 1884 pp 1–122
    [Google Scholar]
  60. De La Fuente R, Suarez G, Schleifer KH. Staphylococcus aureus subsp. anaerobius subsp. nov., the causal agent of abscess disease of sheep. Int J Syst Bacteriol 1985; 35:99–102 [CrossRef]
    [Google Scholar]
  61. Schleifer KH, Fischer U. Description of a new species of the genus Staphylococcus: Staphylococcus carnosus. Int J Syst Bacteriol 1982; 32:153–156 [CrossRef]
    [Google Scholar]
  62. De Bel A, Van Hoorde K, Wybo I, Vandoorslaer K, Echahidi F et al. Staphylococcus jettensis sp. nov., a coagulase-negative staphylococcal species isolated from human clinical specimens. Int J Syst Evol Microbiol 2013; 63:3250–3256 [CrossRef][PubMed]
    [Google Scholar]
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