1887

Abstract

We investigated the taxonomic relationships among , and . These type strains shared the same 16S rRNA gene sequence. Digital DNA–DNA relatedness and average nucleotide identity analyses using whole genome sequences suggested that and belong to the same genomospecies, whereas does not. In addition to previously reported phenotypic data, the presence of almost the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides also supported the synonymy between and . Therefore, should be reclassified as a later heterotypic synonym of .

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2020-08-18
2020-10-29
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References

  1. Kämpfer P, Genus I et al. 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 et al. (editors) Bergey's Manual of Systematic Bacteriology: The Actinobacteria, Part A New York: Springer; 2012 pp 1455–1781
    [Google Scholar]
  2. Shirling EB, Gottlieb D. Cooperative description of type cultures of Streptomyces III. Additional species descriptions from first and second studies. Int J Syst Bacteriol 1968; 18:279–392 [CrossRef]
    [Google Scholar]
  3. Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M et al. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol 2008; 190:4050–4060 [CrossRef][PubMed]
    [Google Scholar]
  4. 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]
  5. 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]
  6. 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]
  7. Kim K-O, Shin K-S, Kim MN, Shin K-S, Labeda DP et al. Reassessment of the status of Streptomyces setonii and reclassification of Streptomyces fimicarius as a later synonym of Streptomyces setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus based on combined 16S rRNA/gyrB gene sequence analysis. Int J Syst Evol Microbiol 2012; 62:2978–2985 [CrossRef][PubMed]
    [Google Scholar]
  8. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006; 33:152–155
    [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Waksman SA, Henrici AT. Family III. Streptomycetaceae Waksman and Henrici. In Breed RS, Murray EGD, Hitchens AP. (editors) Bergey's Manual of Determinative Bacteriology, 6th ed. Baltimore: The Williams & Wilkins Co; 1948 pp 929–980
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. Jensen HL. Actinomycetes in Danish soils. Soil Sci 1930; 30:59–77 [CrossRef]
    [Google Scholar]
  15. Gauze GF, Preobrazhenskaya TP, Sveshnikova MA, Terekhova LP, Maximova TS. A guide for the determination of actinomycetes. Genera Streptomyces, Streptoverticillium, and Chainia . Nauka, Moscow, URSS 1983
    [Google Scholar]
  16. Validation list no. 22 Validation of publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1986; 36:573–576 [CrossRef]
    [Google Scholar]
  17. Yoon S-H, Ha S-M, 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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Yoon S-H, Ha S-M, 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]
  21. 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]
  22. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef][PubMed]
    [Google Scholar]
  23. Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y et al. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains. Sci Rep 2018; 8:6888 [CrossRef][PubMed]
    [Google Scholar]
  24. Komaki H, Sakurai K, Hosoyama A, Kimura A, Trujilo ME et al. Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor. J Antibiot 2020; 73:141–151 [CrossRef][PubMed]
    [Google Scholar]
  25. 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]
  26. Fischbach MA, Walsh CT. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 2006; 106:3468–3496 [CrossRef][PubMed]
    [Google Scholar]
  27. Paulus C, Rebets Y, Zapp J, Rückert C, Kalinowski J et al. New alpiniamides from Streptomyces sp. IB2014/011-12 assembled by an unusual hybrid non-ribosomal peptide synthetase trans-AT polyketide synthase enzyme. Front Microbiol 2018; 9:1959 [CrossRef][PubMed]
    [Google Scholar]
  28. Patzer SI, Braun V. Gene cluster involved in the biosynthesis of griseobactin, a catechol-peptide siderophore of Streptomyces sp. ATCC 700974. J Bacteriol 2010; 192:426–435 [CrossRef][PubMed]
    [Google Scholar]
  29. Challis GL. Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 2008; 154:1555–1569 [CrossRef][PubMed]
    [Google Scholar]
  30. Álvarez-Álvarez R, Botas A, Albillos SM, Rumbero A, Martín JF et al. Molecular genetics of naringenin biosynthesis, a typical plant secondary metabolite produced by Streptomyces clavuligerus . Microb Cell Fact 2015; 14:178 [CrossRef][PubMed]
    [Google Scholar]
  31. Shiraishi T, Nishiyama M, Kuzuyama T. Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway. Org Biomol Chem 2019; 17:461–466 [CrossRef][PubMed]
    [Google Scholar]
  32. Hong ST, Carney JR, Gould SJ. Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016. J Bacteriol 1997; 179:470–476 [CrossRef][PubMed]
    [Google Scholar]
  33. Ohno S, Katsuyama Y, Tajima Y, Izumikawa M, Takagi M et al. Identification and characterization of the streptazone E biosynthetic gene cluster in Streptomyces sp. MSC090213JE08. ChemBioChem 2015; 16:2385–2391 [CrossRef][PubMed]
    [Google Scholar]
  34. Luo Y, Huang H, Liang J, Wang M, Lu L et al. Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster. Nat Commun 2013; 4:2894 [CrossRef][PubMed]
    [Google Scholar]
  35. Cheng Y-Q. Deciphering the biosynthetic codes for the potent anti-SARS-CoV cyclodepsipeptide valinomycin in Streptomyces tsusimaensis ATCC 15141. Chembiochem 2006; 7:471–477 [CrossRef][PubMed]
    [Google Scholar]
  36. Funabashi M, Funa N, Horinouchi S. Phenolic lipids synthesized by type III polyketide synthase confer penicillin resistance on Streptomyces griseus . J Biol Chem 2008; 283:13983–13991 [CrossRef][PubMed]
    [Google Scholar]
  37. Oja T, Palmu K, Lehmussola H, Leppäranta O, Hännikäinen K et al. Characterization of the alnumycin gene cluster reveals unusual gene products for pyran ring formation and dioxan biosynthesis. Chem Biol 2008; 15:1046–1057 [CrossRef][PubMed]
    [Google Scholar]
  38. Brautaset T, Sekurova ON, Sletta H, Ellingsen TE, StrŁm AR et al. Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway. Chem Biol 2000; 7:395–403 [CrossRef][PubMed]
    [Google Scholar]
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