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Genome-based reclassification of Anoxybacillus kamchatkensis Kevbrin et al. 2005 as a later heterotypic synonym of Anoxybacillus ayderensis Dulger et al. 2004

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Abstract

In this study, we aimed to clarify the taxonomic positions of Anoxybacillus kamchatkensis DSM 14988T and Anoxybacillus ayderensis AB04T using whole-genome phylogenetic analysis, biochemical and chemotaxonomic characteristics. In phylogenetic trees drawn using whole-genome sequences and 16S rRNA gene sequences, A. kamchatkensis DSM 14988T and A. ayderensis AB04T clade together and showed high sequence similarity (99.6%) based on 16S rRNA gene. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between A. kamchatkensis DSM 14988T and A. ayderensis AB04T were found to be greater than the threshold values for species demarcation. Most phenotypic and chemotaxonomic features between both species were almost identical except for a few exceptions. The present results show that A. kamchatkensis DSM 14988T is a later heterotypic synonym of A. ayderensis AB04T.

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References

  • Collins MD (1985) Analysis of isoprenoid quinones. Methods Microbiol 18:329–366.

  • Deb S, Das L, Das SK (2020) Phylogenomic analysis reveals that Arthrobacter mysorens Nand and Rao 1972 (approved lists 1980) and Glutamicibacter mysorens Busse 2016 are later heterotypic synonyms of Arthrobacter nicotianae Giovannozzi-Sermanni 1959 (approved lists 1980) and Glutamicibacter nicotianae Busse 2016. Curr Microbiol 77:3793–3798

    Article  CAS  Google Scholar 

  • Dulger S, Demirbag Z, Belduzn AO (2004) Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov. Int J Syst Evol Microbiol 54:1499–1503

    Article  CAS  Google Scholar 

  • Euze´by J, (2016) Valid publication of new names and new combinations effectively published outside the IJSEM. validation list no. 109. Int J Syst Evol Microbiol 56:925–927

    Google Scholar 

  • Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106(951):645–667

    Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Kevbrin VV, Zengler K, Lysenko AM, Wiegel J (2005) Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad PH optimum from the Geyser valley Kamchatka. Extremophiles 9:391–398

    Article  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  • Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res 35:3100–3108

    Article  CAS  Google Scholar 

  • Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66(2):1100–1103

    Article  CAS  Google Scholar 

  • Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32:2798–2800

    Article  CAS  Google Scholar 

  • Liu GH, Rao MPN, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJ (2019) Genome-based reclassifcation of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995. Antonie Van Leeuwenhoek 112:1725–1730

    Article  CAS  Google Scholar 

  • Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucl Acids Res 42(8):e73

    Article  CAS  Google Scholar 

  • Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182

    Article  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY (2018) Phylogenomic analysis of the gammaproteobacterial methanotrophs (order methylococcales) calls for the reclassification of members at the genus and species levels. Front Microbiol 9:3162

    Article  Google Scholar 

  • Parker CT, Tindall BJ, Garrity GM (2019) International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69(1A):S1–S111

    Article  Google Scholar 

  • Pikuta E, Lysenko A, Chuvilskaya N, Mendrock U et al (2000) Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavithermus comb. nov. Int J Syst Evol Microbiol 50:2109–2117

    Article  CAS  Google Scholar 

  • Rao MPN, Xiao M, Liu D, Tang R, Liu G, Li W (2022) Genome-based reclassification of Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer of Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb nov. and Evansella tamaricis comb. Nov. Arch Microbiol 204:47. https://doi.org/10.1007/s00203-021-02720-w

    Article  CAS  Google Scholar 

  • Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 06(45):19126–19131

    Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    Article  CAS  PubMed  Google Scholar 

  • Tindall B.J. (1990) A Comparative Study of the Lipid Composition of Halobacterium saccharovorum from Various Sources. Syst Appl Microbiol 13(2):128–130

  • Tindall BJ (1990b) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202.

  • Tindall BJ, Sikorski J, Smibert RM, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. C. A. Reddy, T. J. Beveridge, J. A. Breznak, G. Marzluf, T. M. Schmidt, L. R. Snyder (Eds) Washington, DC:American Society for Microbiology.. In Methods for General and Molecular Microbiology, 3rd edn, pp. 330–393. 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680

    Article  CAS  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR et al (1987) International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing ezbiocloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  • Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–2128. https://doi.org/10.1007/s10482-017-0844-4

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This study was supported by Karadeniz Technical University (KTU BAP FAT-2019-7822).

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KIB designed the study. KIB, HIB and SC performed the genome analysis and analyzed the data. KIB, AN and AOB performed the phenotypic and chemotaxonomic analysis. KIB and AN wrote the manuscript. All the authors read and approved the final manuscript.

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Correspondence to Kadriye Inan Bektas.

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Communicated by Erko Stackebrandt.

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Inan Bektas, K., Nalcaoglu, A., Guler, H.İ. et al. Genome-based reclassification of Anoxybacillus kamchatkensis Kevbrin et al. 2005 as a later heterotypic synonym of Anoxybacillus ayderensis Dulger et al. 2004. Arch Microbiol 204, 613 (2022). https://doi.org/10.1007/s00203-022-03201-4

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