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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 6

Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus and emended descriptions of , , , , , and Free

Abstract

Phylogenetic analysis based on 16S rRNA gene sequences of the genus showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95–96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: as a later heterotypic synonym of ; as a later heterotypic synonym of ; as a later heterotypic synonym of ; as a later heterotypic synonym of ; as a later heterotypic synonym of ; and as a later heterotypic synonym of .

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  • Accepted:
  • Published Online:
Keyword(s): Actinobacteria , actinomycetes , genome indices , genome-based phylogeny and Streptomycetaceae
© 2020 The Authors
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2020-05-22
2024-05-06
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References

  1. Lechevalier MP. The taxonomy of the genus Nocardia: Some light at the end of the tunnel?. In Goodfellow M, Brownell GH, Serrano JA. (editors) The Biology of the Nocardiae London: Academic press; 1976 pp 1–38
     [Google Scholar]
  2. Labeda DP, Hatano K, Kroppenstedt RM, Tamura T. Revival of the genus Lentzea and proposal for Lechevalieria gen. nov. Int J Syst Evol Microbiol 2001; 51:1045–1050 [View Article][PubMed]
     [Google Scholar]
  3. Yassin AF, Rainey FA, Brzezinka H, Jahnke KD, Weissbrodt H et al. Lentzea gen. nov., a new genus of the order Actinomycetales . Int J Syst Bacteriol 1995; 45:357–363 [View Article][PubMed]
     [Google Scholar]
  4. 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]
  5. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Highly parallelized inference of large genome-based phylogenies. Concurr Computat Pract Exper 2014; 26:1715–1729 [View Article]
     [Google Scholar]
  6. Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J et al. Next-Generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 2016; 6:38392 [View Article][PubMed]
     [Google Scholar]
  7. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article][PubMed]
     [Google Scholar]
  9. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2007; 2018:9
     [Google Scholar]
  10. 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]
  11. Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA et al. Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves. Int J Syst Evol Microbiol 2016; 66:4204–4210 [View Article][PubMed]
     [Google Scholar]
  12. Mavromatis K, Ivanova NN, Chen I-MA, Szeto E, Markowitz VM et al. The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 2009; 1:63–67 [View Article][PubMed]
     [Google Scholar]
  13. 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]
  14. Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2018; 46:e5 [View Article][PubMed]
     [Google Scholar]
  15. Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol Biol Evol 2020; 37:291–294 [View Article][PubMed]
     [Google Scholar]
  16. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019; 35:4453–4455 [View Article][PubMed]
     [Google Scholar]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [View Article][PubMed]
     [Google Scholar]
  19. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  20. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article][PubMed]
     [Google Scholar]
  21. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc Committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed]
     [Google Scholar]
  22. Bouchek-Mechiche K, Gardan L, Normand P, Jouan B. DNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab. Int J Syst Evol Microbiol 2000; 50:91–99 [View Article][PubMed]
     [Google Scholar]
  23. Waksman SA. The Actinomycetes. Vol. II. Classification, Identification and Descriptions of Genera and Species Baltimore: The Williams and Wilkins Co; 1961
     [Google Scholar]
  24. Kämpfer P, Glaeser SP, Parkes L, Van Keulen G, Dyson P. The family Streptomycetaceae . In Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes Berlin: Springer Berlin Heidelberg; 2014 pp 889–1010
     [Google Scholar]
  25. Hamada M, Kinoshita N, Hattori S, Yoshida A, Okami Y et al. Streptomyces kasugaensis sp. nov.: a new species of the genus Streptomyces . Actinomycetologica 1995; 9:27–36
     [Google Scholar]
  26. Nishimura H, Kimura T, Kuroya M. [On a yellow crystalline antibiotic, identical with aureothricin isolated from a new species of streptomyces, 39a, and its taxonomic study]. J Antibiot 1953; 6:57–65[PubMed]
     [Google Scholar]
  27. Park DH, Kim JS, Kwon SW, Wilson C, Yu YM et al. Streptomyces luridiscabiei sp. nov., Streptomyces puniciscabiei sp. nov. and Streptomyces niveiscabiei sp. nov., which cause potato common scab disease in Korea. Int J Syst Evol Microbiol 2003; 53:2049–2054 [View Article][PubMed]
     [Google Scholar]
  28. Jensen HL. Actinomycetes in Danish soils. Soil Sci 1930; 30:59–77 [View Article]
     [Google Scholar]
  29. Waksman SA, Henrici AT. Family III. Streptomycetaceae . 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]
  30. Le Roes M, Meyers PR. Streptomyces pharetrae sp. nov., isolated from soil from the semi-arid Karoo region. Syst Appl Microbiol 2005; 28:488–493
     [Google Scholar]
  31. Preobrazhenskaya TP et al. Streptomyces glaucescens. In Gauze GF, Preobrazhenskaya TP, Kudrina ES, Blinov NO, Ryabova ID et al. (editors) Problems of Classification of Actinomycetes-antagonists Medgiz, Moscow: Government Publishing House of Medical Literature; 1957 pp 1–398
     [Google Scholar]
  32. 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]
  33. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
     [Google Scholar]
  34. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943,339AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology 4 Baltimore: Williams & Wilkins Co; 1989 pp 2452–2492
     [Google Scholar]
  35. Sakamoto JM, Kondo SI, Yumoto H, Arishima M, Bundlins A. and B, two antibiotics produced by Streptomyces griseofuscus nov. sp. J Antibiot 1962; 15:98–102
     [Google Scholar]
  36. Frommer W. Zur Systematik Der actinomycin bildenden Streptomyceten. Archiv. Mikrobiol. 1959; 32:187–206 [View Article]
     [Google Scholar]
  37. Gause GF, Preobrazhenskaya TP, Sveshnikova MA, Terekhova LP, Maximova TS. A guide for the determination of actinomycetes. Genera Streptomyces, Streptoverticillium, and Chainia . Nauka, Moscow, USSR 1983
     [Google Scholar]
  38. Krassiľnikov NA, Korenyako AI, Nikitina NI. Actinomycetes of the Yellow Group. Biology of Selected Groups of Actinomycetes (in Russian) Moscow: Publishing Firm Nauka; 1965 pp 1–372
     [Google Scholar]
  39. Zhang R, Han X, Xia Z, Luo X, Wan C et al. Streptomyces luozhongensis sp. nov., a novel actinomycete with antifungal activity and antibacterial activity. Antonie van Leeuwenhoek 2017; 110:195–203 [View Article][PubMed]
     [Google Scholar]
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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 70, 3924 (2020); https://doi.org/10.1099/ijsem.0.004217
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