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

Volume 71, Issue 8

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of sp. nov., sp. nov. and sp. nov. Free

Abstract

Three novel corynebacterial species were isolated from soil sampled at a paddock in Vilsendorf, North Rhine-Westphalia, Germany. The strains were coccoid or irregular rod-shaped, catalase-positive and pale white to yellow-orange in colour. By whole genome sequencing and comparison of the 16S rRNA genes as well as the whole genome structure, it was shown that all three strains represent novel species of the family , order , class . This project describes the isolation, identification, sequencing, and phenotypic characterization of the three novel species. We propose the names sp. nov. (DSM 110639=LMG 31801), sp. nov. (DSM 110640=LMG 31802), and sp. nov. (DSM 110642=LMG 31803).

  • Received:
  • Accepted:
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Keyword(s): Corynebacterium and soil
© 2021 The Authors
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2021-08-03
2025-12-10

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References

  1. Liebl W. Corynebacterium taxonomy. In Handbook of Corynebacterium glutamicum CRC Press; 2005 pp 9–34
     [Google Scholar]
  2. 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]
  3. Bernard K, Funke G. Corynebacterium. Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki K. eds In Bergey’s Manual of Systematics of Archae and Bacteria New York: Springer; 2012 pp 245–289
     [Google Scholar]
  4. Tauch A, Sandbote J. The family Corynebacteriaceae. In The Prokaryotes Berlin, Heidelberg: Springer Berlin Heidelberg; 2014 pp 239–277
     [Google Scholar]
  5. Sangal V, Hoskisson PA. Evolution, epidemiology and diversity of Corynebacterium diphtheriae: New perspectives on an old foe. Infect Gen Evol 2016; 43:364–370
     [Google Scholar]
  6. Silva-Santana G, Silva CMF, Olivella JGB, Silva IF, Fernandes LMO. Worldwide survey of Corynebacterium striatum increasingly associated with human invasive infections, nosocomial outbreak, and antimicrobial multidrug-resistance, 1976–2020. Arch Microbiol 2021; 203:1863–1880 [View Article] [PubMed]
     [Google Scholar]
  7. Ortiz-Pérez A, Martín-De-Hijas NZ, Esteban J, Fernández-Natal MI, García-Cía JI et al. High frequency of macrolide resistance mechanisms in clinical isolates of Corynebacterium species. Microb Drug Resist 2010; 16:273–277 [View Article] [PubMed]
     [Google Scholar]
  8. Becker J, Wittmann C. Industrial microorganisms: Corynebacterium glutamicum. In Industrial Biotechnology Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA; 2016 pp 183–220
     [Google Scholar]
  9. 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]
  10. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013; 41:e1 [View Article] [PubMed]
     [Google Scholar]
  11. Illumina Truseq DNA PCR-free reference guide; 2017 https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseq-dna-pcr-free-workflow/truseq-dna-pcr-free-workflow-reference-1000000039279-00.pdf
  12. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010; 95:315–327 [View Article] [PubMed]
     [Google Scholar]
  13. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
     [Google Scholar]
  14. Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 2017; 27:737–746 [View Article] [PubMed]
     [Google Scholar]
  15. Oxford Nanopore Technologies Nanoporetech/medaka: Sequence correction provided by ONT Research. https://github.com/nanoporetech/medaka accessed 04 Dec 2019
  16. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  17. Gordon D, Green P. Consed: a graphical editor for next-generation sequencing. Bioinformatics 2013; 29:2936–2937 [View Article] [PubMed]
     [Google Scholar]
  18. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  19. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  20. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. 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]
  23. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  24. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  25. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. blast+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Riegel P, Ruimy R, De Briel D, Prevost G, Jehl F et al. Corynebacterium argentoratense sp. nov., from the human throat. Int J Syst Bacteriol 1995; 45:533–537 [View Article] [PubMed]
     [Google Scholar]
  28. Bomholt C, Glaub A, Gravermann K, Albersmeier A, Brinkrolf K et al. Whole-genome sequence of the clinical strain Corynebacterium argentoratense DSM 44202, isolated from a human throat specimen. Genome Announc 2013; 1: [View Article] [PubMed]
     [Google Scholar]
  29. Du Z-J, Jordan EM, Rooney AP, Chen G-J, Austin B. Corynebacterium marinum sp. nov. isolated from coastal sediment. Int J Syst Evol Microbiol 2010; 60:1944–1947 [View Article] [PubMed]
     [Google Scholar]
  30. Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R et al. Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T. Stand Genomic Sci 2012; 7:284–293 [View Article] [PubMed]
     [Google Scholar]
  31. Chen H-H, Li W-J, Tang S-K, Kroppenstedt RM, Stackebrandt E et al. Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of China. Int J Syst Evol Microbiol 2004; 54:779–782 [View Article]
     [Google Scholar]
  32. Negi V, Singh Y, Schumann P, Lal R. Corynebacterium pollutisoli sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3531–3537 [View Article] [PubMed]
     [Google Scholar]
  33. Wu C-Y, Zhuang L, Zhou S-G, Li F-B, He J. Corynebacterium humireducens sp. nov., an alkaliphilic, humic acid-reducing bacterium isolated from a microbial fuel cell. Int J Syst Evol Microbiol 2011; 61:882–887 [View Article] [PubMed]
     [Google Scholar]
  34. Erko S, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  35. 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 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Mag 2014; 9:111–118
     [Google Scholar]
  38. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  39. Busse H-J, Kleinhagauer T, Glaeser SP, Spergser J, Kämpfer P et al. Classification of three corynebacterial strains isolated from the Northern Bald Ibis (Geronticus eremita): proposal of Corynebacterium choanae sp. nov., Corynebacterium pseudopelargi sp. nov., and Corynebacterium gerontici sp. Int J Syst Evol Microbiol 2019; 69:2928–2935 [View Article] [PubMed]
     [Google Scholar]
  40. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  41. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology Washington, DC, USA: ASM Press; 2007 pp 330–393
     [Google Scholar]
  42. Vilchèze C, Jacobs WR. Isolation and analysis of Mycobacterium tuberculosis mycolic acids. Curr Protoc Microbiol 2007; 5:
     [Google Scholar]
  43. Hsu F-F, Soehl K, Turk J, Haas A. Characterization of mycolic acids from the pathogen Rhodococcus equi by tandem mass spectrometry with electrospray ionization. Anal Biochem 2011; 409:112–122 [View Article] [PubMed]
     [Google Scholar]
  44. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
     [Google Scholar]
  45. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  46. 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]
  47. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
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Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
Int J Syst Evol Microbiol 71, 004933 (2021); https://doi.org/10.1099/ijsem.0.004933
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