1887

Abstract

This study aimed to clarify the taxonomic relationships among , and . These strains share the same 16S rRNA gene sequence. Multilocus sequence analysis revealed that , and belong to the same species, but does not. Digital DNA–DNA relatedness and average nucleotide identity among and were 70.9–74.6% and 96.5–97.0 %, respectively. In addition to the previously reported phenotypic data, the presence of a similar set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides supported the similarity among the three species. Therefore, and should be reclassified as later heterotypic synonyms of .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004638
2021-01-20
2021-02-26
Loading full text...

Full text loading...

References

  1. Goodfellow M, Kumar Y, Labeda DP, Sembiring L. The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores. Antonie van Leeuwenhoek 2007; 92: 173 199 [CrossRef] [PubMed]
    [Google Scholar]
  2. 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 [CrossRef] [PubMed]
    [Google Scholar]
  3. Komaki H, Tamura T. Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov. Int J Syst Evol Microbiol 2019; 69: 2577 2583 [CrossRef] [PubMed]
    [Google Scholar]
  4. Kumar Y, Goodfellow M. Reclassification of Streptomyces hygroscopicus strains as Streptomyces aldersoniae sp. nov., Streptomyces angustmyceticus sp. nov., comb. nov., Streptomyces ascomycinicus sp. nov., Streptomyces decoyicus sp. nov., comb. nov., Streptomyces milbemycinicus sp. nov. and Streptomyces wellingtoniae sp. nov. Int J Syst Evol Microbiol 2010; 60: 769 775 [CrossRef] [PubMed]
    [Google Scholar]
  5. Labeda DP, Doroghazi JR, Ju K-S, Metcalf WW. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. Int J Syst Evol Microbiol 2014; 64: 894 900 [CrossRef] [PubMed]
    [Google Scholar]
  6. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110: 563 583 [CrossRef] [PubMed]
    [Google Scholar]
  7. Liu Z, Shi Y, Zhang Y, Zhou Z, Lu Z et al. Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of 'Microstreptospora cinerea' to the genus Streptomyces as Streptomyces yanii sp. nov. Int J Syst Evol Microbiol 2005; 55: 1605 1610 [CrossRef] [PubMed]
    [Google Scholar]
  8. 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 [CrossRef] [PubMed]
    [Google Scholar]
  9. 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 [CrossRef] [PubMed]
    [Google Scholar]
  10. Komaki H, Ichikawa N, Oguchi A, Hamada M, Tamura T et al. Genome analysis-based reclassification of Streptomyces endus and Streptomyces sporocinereus as later heterotypic synonyms of Streptomyces hygroscopicus subsp. hygroscopicus . Int J Syst Evol Microbiol 2017; 67: 343 345 [CrossRef] [PubMed]
    [Google Scholar]
  11. Komaki H, Tamura T. Reclassification of Streptomyces fulvissimus as a later heterotypic synonym of Streptomyces microflavus . Int J Syst Evol Microbiol 2020; 70: 5156 5162 [CrossRef] [PubMed]
    [Google Scholar]
  12. Komaki H, Tamura T. Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis . Int J Syst Evol Microbiol 2020; 70: 4291 4297 [CrossRef] [PubMed]
    [Google Scholar]
  13. Komaki H, Tamura T. Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis . Int J Syst Evol Microbiol 2020; 70: 4398 4405 [CrossRef] [PubMed]
    [Google Scholar]
  14. Komaki H, Tamura T. Reclassification of Streptomyces castelarensis and Streptomyces sporoclivatus as later heterotypic synonyms of Streptomyces antimycoticus . Int J Syst Evol Microbiol 2020; 70: 1099 1105 [CrossRef] [PubMed]
    [Google Scholar]
  15. Madhaiyan M, Saravanan VS, See-Too W. Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus . Int J Syst Evol Microbiol 2020; 70: 3924 3929 [CrossRef] [PubMed]
    [Google Scholar]
  16. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9: 2007 [CrossRef] [PubMed]
    [Google Scholar]
  17. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006; 33: 152 155
    [Google Scholar]
  18. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37: 463 464 [CrossRef]
    [Google Scholar]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60 [CrossRef] [PubMed]
    [Google Scholar]
  20. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106: 19126 19131 [CrossRef] [PubMed]
    [Google Scholar]
  21. Frommer W. [Systematology of actinomycin-forming Streptomyces]. Arch Mikrobiol 1959; 32: 187 206 [PubMed]
    [Google Scholar]
  22. Oren A, Garrity GM. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2019; 69: 13 32 [CrossRef] [PubMed]
    [Google Scholar]
  23. Sakamoto JMJ, Kondo S, Yumoto H, Arishima M. Bundlins A and B, two antibiotics produced by Streptomyces griseofuscus nov. sp. J Antibiot 1962; 15: 98 102
    [Google Scholar]
  24. Gauze G, Preobrazhenskaya T, Sveshnikova M, Terekhova L, Maximova T. A guide for the determination of actinomycetes. Genera Streptomyces, Streptoverticillium, and Chainia . Nauka, Moscow, URSS 1983
    [Google Scholar]
  25. Validation list no. 22 Validation of the publication of new names and new combinations previously effectively published outside the IJSB: list no. 22. Int J Syst Bacteriol 1986; 36: 573 576 [CrossRef]
    [Google Scholar]
  26. Esnard J, Potter TL, Zuckerman BM. Streptomyces costaricanus sp. nov., isolated from nematode-suppressive soil. Int J Syst Bacteriol 1995; 45: 775 779 [CrossRef] [PubMed]
    [Google Scholar]
  27. Euzeby J, no Vlist. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2008; 58: 1 2 [CrossRef] [PubMed]
    [Google Scholar]
  28. 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 [CrossRef] [PubMed]
    [Google Scholar]
  29. Yoon S, Ha S, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110: 1281 1286 [CrossRef] [PubMed]
    [Google Scholar]
  30. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10: 2182 [CrossRef] [PubMed]
    [Google Scholar]
  31. 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 [CrossRef] [PubMed]
    [Google Scholar]
  32. 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. (editors) Bergey’s Manual of Systematic Bacteriology: The Actinobacteria, Part B New York: Springer; 2012 pp 1455 1767
    [Google Scholar]
  33. Nindita Y, Cao Z, Fauzi AA, Teshima A, Misaki Y et al. The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids. Sci Rep 2019; 9: 10973 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004638
Loading
/content/journal/ijsem/10.1099/ijsem.0.004638
Loading

Data & Media loading...

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