Genome-based reclassification of as a later heterotypic synonym of Free

Abstract

The present study was carried out to clarify the taxonomic relationship between two closely related species, Li . 2002 and (ex Boyer 1973) Nielsen 1995. The maximum-likelihood tree based on the 16S rRNA gene sequence and the phylogenomic tree based on concatenation of 16 protein-marker genes showed that these species were similar. Average nucleotide identity (ANIm 99.25 %, ANIb 98.2 %) and digital DNA–DNA hybridization values (93.5 %) between DSM 13666 and DSM 497 were greater than the threshold values for bacterial species delineation, indicating that they belong to the same species. Therefore, Li 2002 should be reclassified as a later heterotypic synonym of (ex Boyer 1973) Nielsen 1995.

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2019-11-01
2024-03-28
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References

  1. Cohn F. Untersuchungen über bakterien. Beitr Biol Pflanz Heft 1872; 1:127–224
    [Google Scholar]
  2. Li Z, Kawamura Y, Shida O, Yamagata S, Deguchi T et al. Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan. Int J Syst Evol Microbiol 2002; 52:1205–1209 [View Article][PubMed]
    [Google Scholar]
  3. Wayne LG, 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]
  4. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria?. Syst Appl Microbiol 2010; 33:175–182 [View Article][PubMed]
    [Google Scholar]
  5. Teng JL, Tang Y, Huang Y, Guo FB, Wei W et al. Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era. Front Microbiol 2016; 7:1137 [View Article][PubMed]
    [Google Scholar]
  6. Liu Y, Lai Q, Shao Z. Genome analysis-based reclassification of Bacillus weihenstephanensis as a later heterotypic synonym of Bacillus mycoides . Int J Syst Evol Microbiol 2018; 68:106–112 [View Article][PubMed]
    [Google Scholar]
  7. Stropko SJ, Pipes SE, Newman JD. Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus . Int J Syst Evol Microbiol 2014; 64:3804–3809 [View Article][PubMed]
    [Google Scholar]
  8. Möller EM, Bahnweg G, Sandermann H, Geiger HH. A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissues. Nucleic Acids Res 1992; 20:6115–6116 [View Article][PubMed]
    [Google Scholar]
  9. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  10. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  12. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  13. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  15. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article][PubMed]
    [Google Scholar]
  16. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  17. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
    [Google Scholar]
  18. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  19. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12–2483 [View Article][PubMed]
    [Google Scholar]
  22. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  23. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article]
    [Google Scholar]
  24. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  25. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
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