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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 3

Polyphasic taxonomic description of sp. nov. and sp. nov. and their biotechnological potential Open Access

Abstract

strains DSM 116494 and DSM 116496 were isolated from sediment samples of the River Oker in Braunschweig, Germany, and subjected to a polyphasic taxonomic study and genome mining for specialized secondary metabolites. Phenotypic, genetic and genomic data confirmed the assignment of these strains to the genus. Pairwise 16S rRNA gene sequence similarity values between the strains and validly named species reached 99.5 and 99.7% for strains DSM 116494 and DSM 116496, respectively. Genome-based phylogeny demonstrated that and species were the close relatives to strain DSM 116494, while species was the nearest neighbour to strain DSM 116496. Digital DNA–DNA hybridization and average nucleotide identity comparisons of the genomic sequence of the strains and their close phylogenomic relatives revealed that values were below the determined threshold of 70 and 95–96% for prokaryotic species demarcation, respectively. The strains were distinguished from their close neighbours based on biochemical, chemotaxonomic and enzymatic data. Given these results, the strains merit being affiliated to novel species within the genus , for which the names sp. nov. (=OG2.3=DSM 116494=KCTC 59408) and sp. nov. (=OG3.14=DSM 116496=KCTC 59410) are proposed. Strains DSM 116494 and DSM 116496 harboured several biosynthetic gene clusters encoding potentially novel antimicrobial and anticancer compounds. Crude extracts of strains DSM 116494 and DSM 116496 inhibited the growth of Gram-negative bacteria ( ΔtolC, ) and a multi-drug-resistant Gram-positive, .

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Keyword(s): Actinomycetota , diversity , ecology and systematics
Funding
This study was supported by the:
  • Leibniz Association (Award K445/2022)
    • Principal Award Recipient: NotApplicable
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-03-14
2026-02-09

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References

  1. 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]
  2. Baltz RH. Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 2017; 44:573–588 [View Article] [PubMed]
     [Google Scholar]
  3. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article] [PubMed]
     [Google Scholar]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  5. Rossi-Doria T. Su di alcune specie di ‘streptothrix’trovate nellaria studiate in rapporto a quelle già note e specialmente all’‘Actinomyces. Ann Inst Igiene Sperimentale, Univ Roma 1891; 1:399–438
     [Google Scholar]
  6. 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 H-J, Trujillo M-E, Suzuki K-I et al. eds Bergey’ s Manual of Systematic Bacteriology, 2nd Ed, The Actinobacteria Part A and B vol 5 1943 p 339AL
     [Google Scholar]
  7. Witt D, Stackebrandt E. Unification of the genera Streptoverticillum and Streptomyces, and amendation of Streptomyces Waksman and Henrici 1943, 339AL. Syst Appl Microbiol 1990; 13:361–371 [View Article]
     [Google Scholar]
  8. Pridham TG, Lyons JR AJ, Seckinger HL. Comparison of some dried holotype and neotype specimens of Streptomycetes with their living counterparts. Int J Syst Evol Microbiol 1965; 15:191–237 [View Article]
     [Google Scholar]
  9. Szabo I, Marton M. Comments on the first results of the international cooperative work on criteria used in characterization of Streptomycetes. Int J Syst Evol Microbiol 1964; 14:17–38 [View Article]
     [Google Scholar]
  10. 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]
  11. Labeda DP, Doroghazi JR, Ju KS, 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]
     [Google Scholar]
  12. 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]
     [Google Scholar]
  13. 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]
  14. Goodfellow M, Fiedler HP. A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010; 98:119–142 [View Article] [PubMed]
     [Google Scholar]
  15. Thumar JT, Dhulia K, Singh SP. Isolation and partial purification of an antimicrobial agent from halotolerant alkaliphilic Streptomyces aburaviensis strain Kut-8. World J Microbiol Biotechnol 2010; 26:2081–2087 [View Article]
     [Google Scholar]
  16. Khodamoradi S, Hahnke RL, Mast Y, Schumann P, Kämpfer P et al. Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach. Antonie van Leeuwenhoek 2021; 114:1483–1496 [View Article] [PubMed]
     [Google Scholar]
  17. Sanjivkumar M, Babu DR, Suganya AM, Silambarasan T, Balagurunathan R et al. Investigation on pharmacological activities of secondary metabolite extracted from a mangrove associated actinobacterium Streptomyces olivaceus (MSU3). Biocatal Agric Biotechnol 2016; 6:82–90 [View Article]
     [Google Scholar]
  18. Sanjivkumar M, Brindhashini A, Deivakumari M, Palavesam A, Immanuel G. Investigation on saccharification and bioethanol production from pretreated agro-residues using a mangrove associated actinobacterium Streptomyces variabilis (MAB3). Waste Biomass Valor 2018; 9:969–984 [View Article]
     [Google Scholar]
  19. Katz L, Baltz RH. Natural product discovery: past, present, and future. J Ind Microbiol Biotechnol 2016; 43:155–176 [View Article] [PubMed]
     [Google Scholar]
  20. Parashar D, Chauhan DS, Sharma VD, Chauhan A, Chauhan SVS et al. Optimization of procedures for isolation of mycobacteria from soil and water samples obtained in northern India. Appl Environ Microbiol 2004; 70:3751–3753 [View Article] [PubMed]
     [Google Scholar]
  21. McFarland J. The nephelometer: an instrument for estimating the number of bacteria in suspensions used for calculating the opsonic index and for vaccines. JAMA 1907; XLIX:1176 [View Article]
     [Google Scholar]
  22. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  23. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  24. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990
     [Google Scholar]
  25. Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M et al. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71:004631 [View Article]
     [Google Scholar]
  26. Moss CW, Lambert-Fair MA. Location of double bonds in monounsaturated fatty acids of Campylobacter cryaerophila with dimethyl disulfide derivatives and combined gas chromatography-mass spectrometry. J Clin Microbiol 1989; 27:1467–1470 [View Article] [PubMed]
     [Google Scholar]
  27. Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D et al. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter. Int J Syst Evol Microbiol 2021; 71:004769 [View Article]
     [Google Scholar]
  28. Wright L, Nouioui I, Mast Y, Bunk B, Spröer C et al. Nocardia australiensis sp. nov. and Nocardia spumae sp. nov., isolated from sea foam in Queensland, Australia. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  29. Yoon SH, Ha SM, 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]
  30. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article] [PubMed]
     [Google Scholar]
  31. Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R et al. Database indexing for production MegaBLAST searches. Bioinformatics 2008; 24:1757–1764 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  35. Kim M, Oh HS, Park SC, 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]
  36. Mahmoud FM, Pritsch K, Siani R, Benning S, Radl V et al. Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion. Microbiol Spectr 2024; 12:e0042224 [View Article] [PubMed]
     [Google Scholar]
  37. Fukasawa Y, Ermini L, Wang H, Carty K, Cheung M-S et al. LongQC: a quality control tool for third generation sequencing long read data. BMC Genomics 2020; 9: [View Article]
     [Google Scholar]
  38. 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
     [Google Scholar]
  39. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  40. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 2013; 14:1–4 [View Article] [PubMed]
     [Google Scholar]
  41. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article] [PubMed]
     [Google Scholar]
  42. Yoon SH, Ha SM, 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]
  43. Wayne LG, Brenner DJ, Colwell RR, Grimont PA, Kandler O 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]
  44. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  45. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  46. 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]
  47. Nouioui I, Zimmermann A, Hennrich O, Xia S, Rössler O et al. Challenging old microbiological treasures for natural compound biosynthesis capacity. Front Bioeng Biotechnol 2024; 12:1255151 [View Article] [PubMed]
     [Google Scholar]
  48. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  49. Goodfellow M, Nouioui I, Sanderson R, Xie F, Bull AT. Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils. Antonie van Leeuwenhoek 2018; 111:1315–1332 [View Article] [PubMed]
     [Google Scholar]
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Polyphasic taxonomic description of Streptomyces okerensis sp. nov. and Streptomyces stoeckheimensis sp. nov. and their biotechnological potential
Int J Syst Evol Microbiol 75, 006716 (2025); https://doi.org/10.1099/ijsem.0.006716
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