1887

Abstract

The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus has been debated due to the proposed split of this genus into five new genera (, , , and an emended ). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species does not cause confusion in clinical treatment as outlined by the rule (56a) of the Prokaryotic Code. In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera potentially used as sub-genus complex names.

Keyword(s): genome , genus and Mycobacterium
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-09-23
2021-10-24
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References

  1. Lehmann KB, Neumann R. Atlas und Grundriss der Bakeriologie und Lehrbuch der speziellen bakteriologischen Diagnositk, 1st edn. 1896
    [Google Scholar]
  2. Tortoli E, Fedrizzi T, Meehan CJ, Trovato A, Grottola A et al. The new phylogeny of the genus Mycobacterium: The old and the new. Infect Genet Evol 2017; 56:19–25 [View Article] [PubMed]
    [Google Scholar]
  3. Tortoli E, Meehan CJ, Grottola A, Serpini GF, Fabio A et al. Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium. Infect Genet Evol 2019; 103983:
    [Google Scholar]
  4. Fedrizzi T, Meehan CJ, Grottola A, Giacobazzi E, Fregni Serpini G et al. Genomic characterization of nontuberculous mycobacteria. Sci Rep 2017; 7:45258 [View Article] [PubMed]
    [Google Scholar]
  5. 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 [View Article] [PubMed]
    [Google Scholar]
  6. Tindall BJ. Misunderstanding the bacteriological code. Int J Syst Bacteriol 1999; 49 Pt 3:1313–1316 [View Article] [PubMed]
    [Google Scholar]
  7. Tortoli E, Brown-Elliott BA, Chalmers JD, Cirillo DM, Daley CL et al. Same meat, different gravy: ignore the new names of mycobacteria. Eur Respir J 2019; 54:1900795 [View Article] [PubMed]
    [Google Scholar]
  8. Armstrong DT, Parrish N. Current updates on mycobacterial taxonomy, 2018-2019. J Clin Microbiol 2021; 59:e0152820 [View Article] [PubMed]
    [Google Scholar]
  9. Gupta AK. Classification Springer Geology. Springer; 2015 pp 69–87
    [Google Scholar]
  10. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
    [Google Scholar]
  11. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  12. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME Journal 2017; 11:2399–2406 [View Article]
    [Google Scholar]
  13. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996 [View Article] [PubMed]
    [Google Scholar]
  14. Qin QL, Bin XB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  15. Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS et al. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie van Leeuwenhoek 2017; 110:727–736 [View Article]
    [Google Scholar]
  16. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: Proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article] [PubMed]
    [Google Scholar]
  17. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J et al. Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 2018; 111:55–72 [View Article]
    [Google Scholar]
  18. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475-19 [View Article] [PubMed]
    [Google Scholar]
  19. Gupta RS, Lo B, Son J. Corrigendum: Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 2019; 10:714 [View Article] [PubMed]
    [Google Scholar]
  20. Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 1–8:
    [Google Scholar]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  24. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  25. Parks DH. CompareM; 2014 https://github.com/dparks1134/CompareM
  26. Warnes GR, Bolker B, Lumley T. gplots: Various R programming tools for plotting data. R package version 2.6.0; 2012 http://cran.r-project.org/web/packages/gplots
  27. R Core Team R: A language and environment for statistical computing; 2017 http://www.r-project.org
  28. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article] [PubMed]
    [Google Scholar]
  29. Gagneux S. Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol 2018; 16:202–213 [View Article] [PubMed]
    [Google Scholar]
  30. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:
    [Google Scholar]
  31. Gupta RS. Commentary: Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2019; 10:206 [View Article] [PubMed]
    [Google Scholar]
  32. Gao B, Gupta RS. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 2012; 76:66–112 [View Article] [PubMed]
    [Google Scholar]
  33. Oren A, Trujillo ME. On the valid publication of names of mycobacteria. Eur Respir J 2019; 54: [View Article] [PubMed]
    [Google Scholar]
  34. Zopf W. Die Spaltpilze: Nachdem neuesten Standpunkte Breslau: Eduard Trewendt; 1883
    [Google Scholar]
  35. Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol 1980; 30:225–420
    [Google Scholar]
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