1887

Abstract

In the present study, the taxonomic position of YSP-3 was evaluated using phylogenetic and genome-based comparison. YSP-3 showed the highest 16S rRNA gene sequence similarity to M30 (98.4 %), followed by K1-5 (97.5 %) and FJAT-45347 (97.2 %). In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 71 bacterial single-copy genes) trees, YSP-3 clustered with the members of the genus . The amino acid identity (AAI) values between YSP-3 and the members of the genus were >65 %, which is above the cut-off level (65–95 %) for genus delineation. The average nucleotide identity (ANI) values between YSP-3 and the members of the genus were <95 %, which is lower than the threshold value (95–96 %) for bacterial species delineation. The AAI value suggested that YSP-3 was a member of the genus while the ANIb value suggested it as a novel species of the genus . Based on the results, we propose to transfer to the genus as comb. nov.

Funding
This study was supported by the:
  • Guizhou Provincial Academician Workstation of Microbiology and Health (Award [2020]4004)
    • Principle Award Recipient: Ying-QianKang
  • Talent Base Project of Guizhou Province, China (Award FCJD2018-22)
    • Principle Award Recipient: Ying-QianKang
  • Guizhou Scientific Plan Project (Award (2019) 2873)
    • Principle Award Recipient: Ying-QianKang
  • Guizhou Scientific Plan Project (Award [2020]4Y220)
    • Principle Award Recipient: Ying-QianKang
  • International Science and Technology Cooperation Base of Guizhou Province (Award [2020]4101)
    • Principle Award Recipient: Ying-QianKang
  • National Natural Science Foundation of China (Award 32060034)
    • Principle Award Recipient: Ying-QianKang
  • 111 Project (Award D20009)
    • Principle Award Recipient: Ying-QianKang
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/content/journal/ijsem/10.1099/ijsem.0.005502
2022-09-14
2024-05-01
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References

  1. Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article] [PubMed]
    [Google Scholar]
  2. 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; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  3. Borsodi AK, Márialigeti K, Szabó G, Palatinszky M, Pollák B et al. Bacillus aurantiacus sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from Hungarian soda lakes. Int J Syst Evol Microbiol 2008; 58:845–851 [View Article] [PubMed]
    [Google Scholar]
  4. Menes RJ, Machin EV, Iriarte A, Langleib M. Bacillus natronophilus sp. nov., an alkaliphilic bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2020; 70:562–568 [View Article] [PubMed]
    [Google Scholar]
  5. Liu B, Liu G-H, Wang X-Y, Wang J-P, Zhu Y-J et al. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155–159 [View Article] [PubMed]
    [Google Scholar]
  6. Wang S, Sun L, Narsing Rao MP, Liu G-H, Jin P-J et al. Alteribacter salitolerans sp. nov., isolated from a saline-alkaline soil. Arch Microbiol 2021; 204:53 [View Article] [PubMed]
    [Google Scholar]
  7. Dong L, Wang S, Cao H, Zhao B, Zhang X et al. Bacillus lacisalsi sp. nov., a moderately haloalkaliphilic bacterium isolated from a saline-alkaline lake. Antonie van Leeuwenhoek 2020; 113:127–136 [View Article] [PubMed]
    [Google Scholar]
  8. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71:005096
    [Google Scholar]
  9. 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]
  10. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, 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. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  16. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  19. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
    [Google Scholar]
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  21. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  22. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article] [PubMed]
    [Google Scholar]
  23. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  24. 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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