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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

Reclassification of as a synonym of based on a polyphasic taxonomic approach No Access

Abstract

In the present work, the taxonomic relationship between and was reevaluated by a comprehensive comparison of phenotypic, chemotaxonomic and genomic characteristics, as well as phylogeny. Phylogenetic analysis based on 16S rRNA gene sequences and whole-genome sequences indicated that JCM 4385 was clustered together with JCM 4382, suggesting they were closely related to each other. However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between their genomes were 99.7 and 97.5 %, respectively, much larger than the recommended threshold values of 96.7 % ANI and 70 % dDDH for species delineation. In addition, the morphological, cultural, physio-biochemical and chemotaxonomic features of these two species further demonstrated that they belonged to the same genome species. Based on the above data and the principle of priority in nomenclature, it is proposed that (Preobrazhenskaya . 1957) Pridham . 1958 (Approved Lists 1980) is a later heterotypic synonym of (Preobrazhenskaya . 1957) Pridham . 1958 (Approved Lists 1980).

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  • Accepted:
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Keyword(s): polyphasic approach , reclassification , Streptomyces griseomycini , Streptomyces griseostramineus and synonym
Funding
This study was supported by the:
  • the Hunan Provincial Natural Science Foundation of China and Xiangtan Science and Technology Bureau (Award 2022JJ50125)
    • Principle Award Recipient: JianGao
  • Scientific Research Project of Hunan Province Department of Education (Award 20A200)
    • Principle Award Recipient: JianGao
© 2023 The Authors
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2023-09-15
2024-05-20
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References

  1. Dong L. The latest research progress of Streptomycetes. Acta Microbiologica Sinica 2023; 63:1815–1832
     [Google Scholar]
  2. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article] [PubMed]
     [Google Scholar]
  3. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:005056 [View Article]
     [Google Scholar]
  4. Gauze GF, Preobrazhenskaya TP, Kudrina ES, Blinov NO, Ryabova ID et al. Problems of Classification of Actinomycete-Antagonists American Institute of Biological Sciences; 1957
     [Google Scholar]
  5. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958; 6:52–79 [View Article] [PubMed]
     [Google Scholar]
  6. Sneath PHA, McGowan V, Skerman VBD. Approved lists of bacterial names. Int J Syst Bacteriol 1980; 30:225–420 [View Article]
     [Google Scholar]
  7. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  8. Atlas RM. Parks LC, Handbook of Microbiological Media Boca Raton: CRC Press; 1993
     [Google Scholar]
  9. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
     [Google Scholar]
  10. Ridgway R. Color standards and color nomenclature. Published by the author. Washington, DC; 1912
  11. Xu LH, Li WJ, Liu ZH, Jiang CL. Actinomycetes systematics: principles, methods and practices. Science Press, Beijing, China; 2007
  12. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  13. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  14. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  15. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London, England: Academic Press; 1985 pp 173–199
     [Google Scholar]
  16. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1987; 19:161–207
     [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 [View Article] [PubMed]
     [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  20. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1 [View Article]
     [Google Scholar]
  21. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Hu S, Li K, Zhang Y, Wang Y, Fu L et al. New insights into the threshold values of multi-locus sequence analysis, average nucleotide identity and digital DNA–DNA hybridization in delineating Streptomyces species. Front Microbiol 2022; 13:910277 [View Article]
     [Google Scholar]
  26. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  27. Garrity GM, Parker CT, Tindall BJ. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article] [PubMed]
     [Google Scholar]
  28. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  29. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
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Reclassification of Streptomyces griseostramineus as a synonym of Streptomyces griseomycini based on a polyphasic taxonomic approach
Int J Syst Evol Microbiol 73, 006021 (2023); https://doi.org/10.1099/ijsem.0.006021
/content/journal/ijsem/10.1099/ijsem.0.006021
/content/journal/ijsem/10.1099/ijsem.0.006021
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