1887

Abstract

The genus includes, at the time of writing, eight subspecies with validly published names. subsp. NBRC 15459 and subsp. NBRC 13045 show 16S rRNA gene sequence similarities of >99.7% to their parent species subsp. NBRC 13905 and subsp. NRRL B-2774, respectively. In contrast, the type strains of the remaining six subspecies, subsp. rubradiris and subsp. , do not show >99.0% 16S rRNA gene sequence similarity to that of each parent species. Although subsp. and subsp. were respectively reclassified to ‘’ and ‘’, these names have not been validly published yet. In this study, we investigated the taxonomic positions of subsp. , subsp. asoensis, subsp. and subsp. given that their whole genome sequences are available. Except for subsp. , these subspecies were discriminated from the parent and closely related species based on phylogenetic, genomic and phenotypic differences. Thus, we reclassify S. subsp. rubradiris and subsp. as sp. nov., sp. nov., sp. nov. and sp. nov., respectively. Multilocus sequence and 16S rRNA gene sequence analyses suggested that subsp. and subsp. may also be reclassified as independent species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005078
2021-11-17
2024-07-17
Loading full text...

Full text loading...

References

  1. Salam N, Jiao J, Zhang X, Li W. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
    [Google Scholar]
  2. Bérdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1–26 [View Article]
    [Google Scholar]
  3. 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 [View Article] [PubMed]
    [Google Scholar]
  4. Wellington EMH, Stackebrandt E, Sanders D, Wolstrup J, Jorgensen NOG. Taxonomic status of Kitasatosporia, and proposed unification with Streptomyces on the basis of phenotypic and 16S rRNA analysis and emendation of Streptomyces Waksman and Henrici 1943, 339al. Int J Syst Bacteriol 1992; 42:156–160 [View Article] [PubMed]
    [Google Scholar]
  5. Witt D, Stackebrandt E. Unification of the genera Streptoverticillium and Streptomyces, and amendation of Streptomyces Waksman and Henrici 1943, 339AL. Syst Appl Microbiol 1990; 13:361–371 [View Article]
    [Google Scholar]
  6. Zhang Z, Wang Y, Ruan J. A proposal to revive the genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982). Int J Syst Bacteriol 1997; 47:1048–1054 [View Article] [PubMed]
    [Google Scholar]
  7. Meier-Kolthoff JP, Goker M, Sproer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
    [Google Scholar]
  8. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR. 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]
  9. 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 2019; 71: [View Article] [PubMed]
    [Google Scholar]
  10. 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]
  11. 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]
  12. 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; 37:464463 [View Article]
    [Google Scholar]
  13. Wu L, Ma J. The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation. Int J Syst Evol Microbiol 2019; 69:895–898 [View Article] [PubMed]
    [Google Scholar]
  14. 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] [PubMed]
    [Google Scholar]
  15. 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 [View Article] [PubMed]
    [Google Scholar]
  16. Oren A, Garrity GM. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2019; 69:13–32 [View Article] [PubMed]
    [Google Scholar]
  17. Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 2009; 26:1362–1384 [View Article] [PubMed]
    [Google Scholar]
  18. Komaki H, Tamura T. Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis. Int J Syst Evol Microbiol 2020; 70:4291–4297 [View Article] [PubMed]
    [Google Scholar]
  19. 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 [View Article] [PubMed]
    [Google Scholar]
  20. 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 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Komaki H, Tamura T. Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov. Int J Syst Evol Microbiol 2019; 69:2577–2583 [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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 [View Article] [PubMed]
    [Google Scholar]
  25. 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 [View Article] [PubMed]
    [Google Scholar]
  26. Umezawa H, Takeuchi T, Okami Y, Tazaki T. On screening of antiviral substances produced by streptomyces and on an antiviral substance achromoviromycin. Jpn J Med Sci Biol 1953; 6:261–268 [View Article] [PubMed]
    [Google Scholar]
  27. Bhuyan BK, Owen SP, Dietz A. Rubradirin, a new antibiotic. I. fermentation and biological properties. Antimicrob Agents Chemother 1964; 10:91–96
    [Google Scholar]
  28. 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 Goodfellow M, Kämpfer P, Busse H, Trujillo ME, Suzuki K, Ludwig W, Whitman WB. eds Bergey’s Manual of Systematic Bacteriology, 2nd. edn Vol 5 New York: Springer; 2012 pp 1455–1767
    [Google Scholar]
  29. 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. edn Baltimore: The Williams & Wilkins Co; 1948 pp 929–980
    [Google Scholar]
  30. Isono K, Nagatsu J, Kawashima Y, Suzuki S. Studies on polyoxins, antifungal antibiotics. Part I. Isolation and characterization of polyoxins A and B. Agric Biol Chem 1965; 29:848–854
    [Google Scholar]
  31. Corbaz R, Ettlinger L, Kellerschierlein W, Zahner H. [Systematology of Actinomycetes. I. Streptomycetes with rhodomycin-like pigments]. Arch Mikrobiol 1957; 25:325–332 [PubMed]
    [Google Scholar]
  32. Schmitz H, Jubinski SD, Hooper IR, Crook KE, Price KE et al. Ossamycin, a new cytotoxic agent. J Antibiot 1965; 18:82–88
    [Google Scholar]
  33. Henssen A. [Morphology and system of thermophilic actinomycetes]. Arch Mikrobiol 1957; 26:373–414 [PubMed]
    [Google Scholar]
  34. Okami Y, Suzuki M, Umezawa H. Taxonomical studies on a Streptomyces strain producing labilomycin. J Antibiot 1963; 16:152–154
    [Google Scholar]
  35. Lanoot B, Vancanneyt M, Cleenwerck I, Wang L, Li W et al. The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus. Int J Syst Evol Microbiol 2002; 52:823–829 [View Article] [PubMed]
    [Google Scholar]
  36. Pridham TG. New names and new combinations in the order Actinomycetales Buchanan 1917. Bulletin of the United States Department of Agriculture 1970; 1424:1–55
    [Google Scholar]
  37. Labeda DP, Doroghazi JR, K Ju, 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 [View Article] [PubMed]
    [Google Scholar]
  38. Lanoot B, Vancanneyt M, Van Schoor A, Liu Z, Swings J. Reclassification of Streptomyces nigrifaciens as a later synonym of Streptomyces flavovirens; Streptomyces citreofluorescens, Streptomyces chrysomallus subsp. chrysomallus and Streptomyces fluorescens as later synonyms of Streptomyces anulatus; Streptomyces chibaensis as a later synonym of Streptomyces corchorusii; Streptomyces flaviscleroticus as a later synonym of Streptomyces minutiscleroticus; and Streptomyces lipmanii, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces willmorei as later synonyms of Streptomyces microflavus. Int J Syst Evol Microbiol 2005; 55:729–731 [View Article] [PubMed]
    [Google Scholar]
  39. 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 [View Article] [PubMed]
    [Google Scholar]
  40. 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]
  41. 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 [View Article] [PubMed]
    [Google Scholar]
  42. Kumar Y, Goodfellow M. Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp. nov., comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov. Int J Syst Evol Microbiol 2008; 58:1369–1378 [View Article]
    [Google Scholar]
  43. Dastager SG, Kim C, Lee J, Agasar D, Park D et al. Streptomyces deccanensis sp. nov., an alkaliphilic species isolated from soil. Int J Syst Evol Microbiol 2008; 58:1089–1093 [View Article] [PubMed]
    [Google Scholar]
  44. Jia F, Liu C, Zhao J, Zhang Y, Li L et al. Streptomyces vulcanius sp. nov., a novel actinomycete isolated from volcanic sediment. Antonie van Leeuwenhoek 2015; 107:15–21 [View Article] [PubMed]
    [Google Scholar]
  45. Jiang S, Piao C, Yu Y, Cao P, Li C et al. Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr. Int J Syst Evol Microbiol 2018; 68:118–124 [View Article] [PubMed]
    [Google Scholar]
  46. Kim B, Sahin N, Minnikin DE, Zakrzewska-Czerwinska J, Mordarski M. Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalcalitolerans sp. nov. Int J Syst Bacteriol 1999; 49:7–17 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005078
Loading
/content/journal/ijsem/10.1099/ijsem.0.005078
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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