1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 7

Genome-based reclassification of , and the genera , and No Access

Abstract

In the present study, the taxonomic positions of , and members of the genera , and were evaluated. The 16S rRNA gene sequence similarity between DSM 14745, DSM 23947 and members of the genera and were above the cut-off level (>95 %) for genus delineation. Amino acid identity (AAI) values and the results of phylogenomic analysis suggested that and the members of the genera , and belong to the same genus. Furthermore, the AAI and phylogenomic results also differentiate from and the members of the genera , and . Based on the results, we propose to transfer , and to the genus . We also propose the reclassification of into a new genus gen. nov., with the type species comb. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacillus acidicola , Bacillus pervagus , Oikeobacillus pervagus gen. nov., comb. nov and re-classification
Funding
This study was supported by the:
  • Kasetsart University (Award KU Reinventing University Program 2022)
    • Principle Award Recipient: ManikPrabhu Narsing Rao
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005961
2023-07-18
2024-04-30
Loading full text...

Full text loading...

References

  1. Gupta RS, Patel S, Saini N, Chen S. Erratum: Robust demarcation of seventeen distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for emended genus Bacillus limiting it only to the members of the subtilis and cereus clades of species. Int J Syst Evol Microbiol 2020; 70:6531–6533 [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. Niu L, Xiong M, Zhang J, Xiang Y, Song L et al. Bacillus camelliae sp. nov., isolated from Pu’er tea. Int J Syst Evol Microbiol 2018; 68:564–569 [View Article] [PubMed]
     [Google Scholar]
  4. Logan NA, Lebbe L, Verhelst A, Goris J, Forsyth G et al. Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago. Int J Syst Evol Microbiol 2004; 54:373–376 [View Article] [PubMed]
     [Google Scholar]
  5. Jung MY, Kim JS, Chang YH. Bacillus acidiproducens sp. nov., vineyard soil isolates that produce lactic acid. Int J Syst Evol Microbiol 2009; 59:2226–2231 [View Article] [PubMed]
     [Google Scholar]
  6. Hammer BW. Bacteriological studies on the coagulation of evaporated milk. Iowa Agr Expt Sta Res Bull 1915; 19:119–131
     [Google Scholar]
  7. Ten LN, Im WT, Baek SH, Lee JS, Oh HM et al. Bacillus ginsengihumi sp. nov., a novel species isolated from soil of a ginseng field in Pocheon province. South Korea J Microbiol Biotechnol 2006; 16:1554–1560
     [Google Scholar]
  8. Kuhnigk T, Borst EM, Breunig A, König H, Collins MD et al. Bacillus oleronius sp.nov., a member of the hindgut flora of the termite Reticulitermes santonensis (Feytaud). Can J Microbiol 1995; 41:699–706 [View Article] [PubMed]
     [Google Scholar]
  9. Pettersson B, Lembke F, Hammer P, Stackebrandt E, Priest FG. Bacillus sporothermodurans, a new species producing highly heat-resistant endospores. Int J Syst Bacteriol 1996; 46:759–764 [View Article] [PubMed]
     [Google Scholar]
  10. Ma K, Chen X, Guo X, Wang Y, Wang H et al. Bacillus vini sp. nov. isolated from alcohol fermentation pit mud. Arch Microbiol 2016; 198:559–564 [View Article] [PubMed]
     [Google Scholar]
  11. Kieu HT, Pham TPT, Lo CI, Alibar S, Bréchard L et al. Weizmannia faecalis sp. nov., isolated from a human stool sample. Arch Microbiol 2022; 204:612 [View Article] [PubMed]
     [Google Scholar]
  12. Albert RA, Archambault J, Rosselló-Mora R, Tindall BJ, Matheny M. Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Int J Syst Evol Microbiol 2005; 55:2125–2130 [View Article] [PubMed]
     [Google Scholar]
  13. Kosowski K, Schmidt M, Pukall R, Hause G, Kämpfer P et al. Bacillus pervagus sp. nov. and Bacillus andreesenii sp. nov., isolated from a composting reactor. Int J Syst Evol Microbiol 2014; 64:88–94 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
     [Google Scholar]
  29. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  30. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2020; 36:2251–2252 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005961
Loading
Genome-based reclassification of Bacillus acidicola, Bacillus pervagus and the genera Heyndrickxia, Margalitia and Weizmannia
Int J Syst Evol Microbiol 73, 005961 (2023); https://doi.org/10.1099/ijsem.0.005961
/content/journal/ijsem/10.1099/ijsem.0.005961
/content/journal/ijsem/10.1099/ijsem.0.005961
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error