1887

Abstract

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus . Gene sequences of and are generally used in MLSA for species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of gene sequences was not necessarily able to distinguish closely related species. In contrast, gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that and are synonyms of .

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2022-05-13
2024-10-03
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References

  1. Kämpfer P. Genus I. Streptomyces Waksman and Henrici 1943, 399AL emend. Witt and Stackbrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Whitman WB, Parte A, Goodfellow M, Kämpfer P, Busse H. eds Bergey’s Manual of Systematic Bacteriology: The Actinobacteria, Part B New York: Springer; 2012 pp 1455–1767
    [Google Scholar]
  2. Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B et al. Phylogenetic study of the species within the family Streptomycetaceae. Antonie van Leeuwenhoek 2012; 101:73–104 [View Article] [PubMed]
    [Google Scholar]
  3. Komaki H. Reclassification of 15 Streptomyces species as synonyms of Streptomyces albogriseolus, Streptomyces althioticus, Streptomyces anthocyanicus, Streptomyces calvus, Streptomyces griseoincarnatus, Streptomyces mutabilis, Streptomyces pilosus or Streptomyces rochei. Int J Syst Evol Microbiol 2021; 71:004718
    [Google Scholar]
  4. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article] [PubMed]
    [Google Scholar]
  5. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  6. Anderson AS, Wellington EM. The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 2001; 51:797–814 [View Article] [PubMed]
    [Google Scholar]
  7. Hatano K, Nishii T, Kasai H. Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev. Int J Syst Evol Microbiol 2003; 53:1519–1529 [View Article] [PubMed]
    [Google Scholar]
  8. Rong X, Guo Y, Huang Y. Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Syst Appl Microbiol 2009; 32:314–322 [View Article] [PubMed]
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  10. Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res 2013; 41:W29–33 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Guo Y, Zheng W, Rong X, Huang Y. A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 2008; 58:149–159 [View Article] [PubMed]
    [Google Scholar]
  14. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 2010; 60:696–703 [View Article] [PubMed]
    [Google Scholar]
  15. Lanoot B, Vancanneyt M, Dawyndt P, Cnockaert M, Zhang J et al. BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus. Syst Appl Microbiol 2004; 27:84–92 [View Article]
    [Google Scholar]
  16. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
    [Google Scholar]
  17. Yoon S, Ha S, 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]
  18. Goodfellow M, Williams ST, Alderson G. Transfer of Actinosporangium violaceum Krasil’nikov and Yuan, Actinosporangium vitaminophilum Shomura et al. and Actinopycnidium caeruleum Krasil’nikov to the genus Streptomyces, with amended descriptions of the species. Syst Appl Microbiol 1986; 8:61–64 [View Article]
    [Google Scholar]
  19. Pridham TG. New names and new combinations in the order Actinomycetales Buchanan 1917. Bull US Dept Agri 1970; 1424:1–55
    [Google Scholar]
  20. Waksman SA. Classification, identification and descriptions of genera and species. In The Actinomycetes Vol 2 Baltimore: The Williams & Wilkins Co; 1961
    [Google Scholar]
  21. Waksman SA, Henrici AT. Family III. Streptomycetaceae Waksman and Henrici. In Breed RS, Murray EGD, Hitchens AP. eds Bergey’s Manual of Determinative Bacteriology, 6th ed. Baltimore: The Williams & Wilkins Co; 1948 pp 929–980
    [Google Scholar]
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