1887

Abstract

The taxonomic relationships and genome features of the type strains in the clade, including , , , , , and , were investigated. Type strains of these species shared high 16S rRNA gene sequence similarity to each other. Multilocus sequence analysis (MLSA) based on , , , and genes revealed that and belong to the same species. Also, and belong to the same species, but the remaining species are not closely related to each other. MLSA results were verified by the results average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses; while the ANI and dDDH values between and are 98.1 and 85.4 %, respectively, these values between and are 98.9 and 90.7 %, respectively. The presence of almost the same set of biosynthetic gene clusters and highly consistent phenotypic test results also supported the synonymy between and , as well as between and . Therefore, should be reclassified as a later heterotypic synonym of and should be reclassified as a later heterotypic synonym of .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004797
2021-05-17
2024-04-25
Loading full text...

Full text loading...

References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article][PubMed]
    [Google Scholar]
  2. Salam N, Jiao J-Y, Zhang X-T, Li W-J. 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]
  3. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev 2016; 80:1–43 [View Article][PubMed]
    [Google Scholar]
  4. Burg RW, Miller BM, Baker EE, Birnbaum J, Currie SA et al. Avermectins, new family of potent anthelmintic agents: producing organism and fermentation. Antimicrob Agents Chemother 1979; 15:361–367 [View Article][PubMed]
    [Google Scholar]
  5. Vino S, Lokesh K. Borrelidin: a promising anticancer agent from Streptomyces species. Adv Biotech 2008; 6:22–26
    [Google Scholar]
  6. Shih H-D, Liu Y-C, Hsu F-L, Mulabagal V, Dodda R et al. Fungichromin: a substance from Streptomyces padanus with inhibitory effects on Rhizoctonia solani . J Agric Food Chem 2003; 51:95–99 [View Article][PubMed]
    [Google Scholar]
  7. Tomita F, Tamaoki T, Tetrocarcins TT. Tetrocarcins, novel antitumor antibiotics. I. producing organism, fermentation and antimicrobial activity. J Antibiot 1980; 33:940–945 [View Article][PubMed]
    [Google Scholar]
  8. Aoyagi T, Yagisawa M, Kumagai M, Hamada M, Okami Y. An enzyme inhibitor, panosialin, produced by Streptomyces. I. biological activity, isolation and characterization of panosialin. J Antibiot 1971; 24:860–869 [View Article][PubMed]
    [Google Scholar]
  9. Omura S, Iwai Y, Takahashi Y, Sadakane N, Nakagawa A et al. Herbimycin, a new antibiotic produced by a strain of Streptomyces . J Antibiot 1979; 32:255–261 [View Article][PubMed]
    [Google Scholar]
  10. Box SJ, Cole M, Yeoman GH. Prasinons A and B: potent insecticides from Streptomyces prasinus . Appl Microbiol 1973; 26:699–704 [View Article][PubMed]
    [Google Scholar]
  11. Uyeda M, Mizukami M, Yokomizo K, Suzuki K. Pentalenolactone I and hygromycin A, immunosuppressants produced by Streptomyces filipinensis and Streptomyces hygroscopicus . Biosci Biotechnol Biochem 2001; 65:1252–1254 [View Article][PubMed]
    [Google Scholar]
  12. Kämpfer P. Genus I. Streptomyces Waksman and Henrici 1943, 339AL emend. Witt and Stackebrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K. (editors) Bergey’s Manual of Systematic Bacteriology 5 2012 pp 1455–1467
    [Google Scholar]
  13. Huang X, Kong F, Zhou S, Huang D, Zheng J et al. Streptomyces tirandamycinicus sp. nov., a novel marine sponge-derived actinobacterium with antibacterial potential against Streptococcus agalactiae . Front Microbiol 2019; 10:482 [View Article][PubMed]
    [Google Scholar]
  14. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:688–695 [View Article][PubMed]
    [Google Scholar]
  15. Law JW-F, Ser H-L, Ab Mutalib N-S, Saokaew S, Duangjai A et al. Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential. Sci Rep 2019; 9:3056 [View Article][PubMed]
    [Google Scholar]
  16. Piao C, Zheng W, Li Y, Liu C, Jin L et al. Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr. Arch Microbiol 2017; 199:963–970 [View Article][PubMed]
    [Google Scholar]
  17. Sun B, Yuan L, Xia Z, Wan C, Zhang L. Streptomyces albicerus sp. nov., a novel actinomycete isolated from the sediments of the Tailan river in Xinjiang, China. Arch Microbiol 2020; 202:1639–1646 [View Article][PubMed]
    [Google Scholar]
  18. Clarridge JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004; 17:840–862 [View Article][PubMed]
    [Google Scholar]
  19. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K et al. Polyphasic taxonomy, a consensus approach to bacterial Systematics. Microbiol Rev 1996; 60:407–438 [View Article][PubMed]
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. 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 [View Article][PubMed]
    [Google Scholar]
  27. Saygin H, Ay H, Guven K, Cetin D, Sahin N. Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili . Int J Syst Evol Microbiol 2020; 70:2750–2759 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. 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]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  33. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  35. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  36. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  37. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  38. 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]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  40. 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]
  41. 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]
  42. 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 [View Article][PubMed]
    [Google Scholar]
  43. Bosi E, Donati B, Galardini M, Brunetti S, Sagot M-F et al. Medusa: a multi-draft based scaffolder. Bioinformatics 2015; 31:2443–2451 [View Article][PubMed]
    [Google Scholar]
  44. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article][PubMed]
    [Google Scholar]
  45. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  46. Kelly K. Color-name Charts Illustrated with Centroid Colors Chicago: Inter-Society Color Council-National Bureau of Standards; 1964
    [Google Scholar]
  47. Saygin H, Ay H, Guven K, Cetin D, Sahin N. Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family Streptosporangiaceae isolated from the Karakum Desert. Antonie van Leeuwenhoek 2019; 112:409–423 [View Article][PubMed]
    [Google Scholar]
  48. Goodfellow M. Numerical taxonomy of some nocardioform bacteria. J Gen Microbiol 1971; 69:33–80 [View Article][PubMed]
    [Google Scholar]
  49. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  50. Küster E, Williams ST. Selection of media for isolation of streptomycetes. Nature 1964; 202:928–929 [View Article][PubMed]
    [Google Scholar]
  51. Nash P, Krent M. M. Culture media. In Ballows AHW, Herrmann KL, Isenberg HD, Shadomy HJ. (editors) Manual of Clinical Microbiology, 5th ed. Washington, DC: American Society for Microbiology; 1991 pp 1268–1270
    [Google Scholar]
  52. 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]
  53. 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]
  54. 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 [View Article]
    [Google Scholar]
  55. 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]
  56. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  57. 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]
  58. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004797
Loading
/content/journal/ijsem/10.1099/ijsem.0.004797
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