Skip to content
1887

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

Volume 71, Issue 5

sp. nov., isolated from the respiratory tract of , and sp. nov., isolated from the lung tissue of Free

Abstract

Four Gram-stain-positive, non-motile and asporous bacilli (strains ZJ-599, ZJ-621, MC1420 and MC1482), isolated from animal tissue and environmental samples collected on the Qinghai-Tibet Plateau, PR China, were taxonomically characterized. Based on the results of 16S rRNA gene sequence analyses, the closest relatives of strains ZJ-599 and ZJ-621 were LMM-1653 (97.5 %), M408/89/1 (96.5 %) and OJ8 (96.3 %), whereas strains MC1420 and MC1482 were closest to CCUG 58655 (98.9 %), DSM 20632 (98.4 %) and DSM 44291 (97.9 %). The results of gene sequence similarity analysis indicated that M408/89/1 and CCUG 58655 were closest to strains ZJ-599/ZJ-621 (83.5 %) and MC1420/MC1482 (91.8 %), respectively. The two novel type strains shared a similarity of 95.2 % in 16S rRNA and 81.3 % in gene sequences. The TAP-PCR DNA fingerprint and MALDI-TOF MS spectrum patterns clearly differentiated the novel isolates within and between each pair of strains. Strain ZJ-599 had 21.9–22.4 % digital DNA–DNA hybridization (dDDH) scores with LMM-1653, M408/89/1 and OJ8, and 72.3–72.9 % of average nucleotide identity (ANI) with them. Similarly, strain MC1420 had 22.9–23.7 % dDDH values with CCUG 58655, DSM 20632 and DSM 44291, and 80.4–81.3 % ANI scores with them. Strain ZJ-599 had a 23.1 % dDDH value and 70.5 % ANI score with strain MC1420, both below the corresponding thresholds for species delineation. Strains ZJ-599 and MC1420 both contain mycolic acids and have MK-8(H) and MK-9(H) as the predominant respiratory quinones, -diaminopimelic acid as the diagnostic diamino acid, and C 9 as the main fatty acid. C 8 and C 8 were predominant in strain ZJ-599 in contrast to C 7 being predominant in strain MC1420. The main polar lipids in strain ZJ-599 were diphosphatidylglycerol, phosphatidylinositol and one unidentified glycolipid, while strain MC1420 had diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid as the major components. Since the two pairs of novel strains (ZJ-599/ZJ-621, MC1420/MC1482) distinctly differ from each other and from their nearest relatives, two novel species of the genus are proposed, namely (type strain ZJ-599=GDMCC 1.1779=JCM 34341) and (type strain MC1420=GDMCC 1.1783=JCM 34340), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Corynebacterium lizhenjunii , Corynebacterium qintianiae , Marmota himalayana , Pseudois nayaur and Qinghai–Tibet Plateau
Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
  • National Key R&D Program of China (Award 2019YFC1200501)
    • Principle Award Recipient: JingYang
  • National Key R&D Program of China (Award 2019YFC1200500)
    • Principle Award Recipient: JingYang
  • National Science and Technology Major Project of China (Award 2017ZX10303405-005-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2017ZX10303405-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: ShanLu
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004803
2021-05-11
2025-05-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/5/ijsem004803.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004803&mimeType=html&fmt=ahah

References

  1. Tauch A, Burkovski A. Molecular armory or niche factors: virulence determinants of Corynebacterium species. FEMS Microbiol Lett 2015; 362:fnv185 [View Article][PubMed]
     [Google Scholar]
  2. Bernard K. The genus Corynebacterium and other medically relevant coryneform-like bacteria. J Clin Microbiol 2012; 50:3152–3158 [View Article][PubMed]
     [Google Scholar]
  3. Murphy JR. Corynebacterium Diphtheriae (Chapter 32). In Baron S. editor Medical Microbiology, 4th ed. Galveston, Texas, USA: University of Texas Medical Branch at Galveston; 1996
     [Google Scholar]
  4. Frederick E. A bacteriologic study of the diphtheroid organisms with special reference to Hodgkin’s disease. J Infect Dis 1918; 23:1–43
     [Google Scholar]
  5. Riegel P, Ruimy R, de Briel D, Prévost G, Jehl F et al. Taxonomy of Corynebacterium diphtheriae and related taxa, with recognition of Corynebacterium ulcerans sp. nov. nom. rev. FEMS Microbiol Lett 1995; 126:271–276 [View Article][PubMed]
     [Google Scholar]
  6. Becker J, Gieelmann G, Hoffmann SL, Wittmann C. Corynebacterium glutamicum for sustainable bioproduction: from metabolic physiology to systems metabolic engineering. In Zhao H, Zeng AP. (editors) Advances in Biochemical Engineering/Biotechnology Cham: Springer; 2016 pp 217–263
     [Google Scholar]
  7. Villadangos AF, Ordóñez E, Pedre B, Messens J, Gil JA et al. Engineered coryneform bacteria as a bio-tool for arsenic remediation. Appl Microbiol Biotechnol 2014; 98:10143–10152 [View Article][PubMed]
     [Google Scholar]
  8. Zhang Y, Cai J, Shang X, Wang B, Liu S et al. A new genome-scale metabolic model of Corynebacterium glutamicum and its application. Biotechnol Biofuels 2017; 10:169 [View Article][PubMed]
     [Google Scholar]
  9. Shah A, Blombach B, Gauttam R, Eikmanns BJ. The RamA regulon: complex regulatory interactions in relation to central metabolism in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:5901–5910 [View Article][PubMed]
     [Google Scholar]
  10. Parise D, Teixeira Dornelles Parise M, Pinto Gomide AC, Figueira Aburjaile F, Bentes Kato R et al. The transcriptional regulatory network of Corynebacterium pseudotuberculosis. Microorganisms 2021; 9:415 17 02 2021 [View Article][PubMed]
     [Google Scholar]
  11. Funke G, Bernard KA et al. Coryneform Gram‐positive rods (Chapter 28). In Jorgensen JH, Carroll KC, Funke G, Pfaller MA, Landry ML. (editors) Manual of Clinical Microbiology, 11th ed. Washington, DC: American Society for Microbiology; 2015
     [Google Scholar]
  12. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article][PubMed]
     [Google Scholar]
  13. 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]
  14. Collins MD, Goodfellow M, Minnikin DE. A survey of the structures of mycolic acids in Corynebacterium and related taxa. J Gen Microbiol 1982; 128:129–149 [View Article][PubMed]
     [Google Scholar]
  15. Ge R-L, Cai Q, Shen Y-Y, San A, Ma L et al. Draft genome sequence of the Tibetan antelope. Nat Commun 2013; 4:4 [View Article][PubMed]
     [Google Scholar]
  16. Wang X, Yang J, Lu S, Lai X-H, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018; 68:3874–3880 [View Article][PubMed]
     [Google Scholar]
  17. Niu L, Lu S, Lai X-H, Hu S, Chen C et al. Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2017; 67:256–261 [View Article][PubMed]
     [Google Scholar]
  18. Xiong J, Sun H, Peng F, Zhang H, Xue X et al. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiol Ecol 2014; 89:281–292 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. Neilan BA, Wilton AN, Jacobs D. A universal procedure for primer labelling of amplicons. Nucleic Acids Res 1997; 25:2938–2939 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  23. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  27. Khamis A, Raoult D, La Scola B. rpoB gene sequencing for identification of Corynebacterium species. J Clin Microbiol 2004; 42:3925–3931 [View Article][PubMed]
     [Google Scholar]
  28. Cusick SM, O'Sullivan DJ. Use of a single, triplicate arbitrarily primed-PCR procedure for molecular fingerprinting of lactic acid bacteria. Appl Environ Microbiol 2000; 66:2227–2231 [View Article][PubMed]
     [Google Scholar]
  29. Matsuda N, Matsuda M, Notake S, Yokokawa H, Kawamura Y et al. Evaluation of a simple protein extraction method for species identification of clinically relevant staphylococci by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 50:3862–3866 [View Article][PubMed]
     [Google Scholar]
  30. Ballas P, Rückert C, Wagener K, Drillich M, Kämpfer P et al. Corynebacterium endometrii sp. nov., isolated from the uterus of a cow with endometritis. Int J Syst Evol Microbiol 2020; 70:146–152 [View Article][PubMed]
     [Google Scholar]
  31. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  32. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  33. Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57 [View Article][PubMed]
     [Google Scholar]
  34. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M et al. Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999; 27:29–34 [View Article][PubMed]
     [Google Scholar]
  35. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article][PubMed]
     [Google Scholar]
  36. Sekiya M, Izumisawa S, Iwamoto-Kihara A, Fan Y, Shimoyama Y et al. Proton-pumping F-ATPase plays an important role in Streptococcus mutans under acidic conditions. Arch Biochem Biophys 2019; 666:46–51 [View Article][PubMed]
     [Google Scholar]
  37. 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]
  38. 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]
  39. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386–2392 [View Article][PubMed]
     [Google Scholar]
  40. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22:1658–1659 [View Article][PubMed]
     [Google Scholar]
  41. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article][PubMed]
     [Google Scholar]
  42. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article][PubMed]
     [Google Scholar]
  43. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16:1114–1116 [View Article]
     [Google Scholar]
  44. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251 [View Article][PubMed]
     [Google Scholar]
  45. Pascual C, Foster G, Alvarez N, Collins MD. Corynebacterium phocae sp. nov., isolated from the common seal (Phoca vitulina). Int J Syst Bacteriol 1998; 48 Pt 2:601–604 [View Article][PubMed]
     [Google Scholar]
  46. Barksdale L, Laneelle M-A, Pollice MC, Asselineau J, Welby M et al. Biological and chemical basis for the reclassification of Microbacterium flavum Orla-Jensen as Corynebacterium flavescens nom. nov. Int J Syst Bacteriol 1979; 29:222–233 [View Article]
     [Google Scholar]
  47. Funke G, Hutson RA, Hilleringmann M, Heizmann WR, Collins MD. Corynebacterium lipophiloflavum sp. nov. isolated from a patient with bacterial vaginosis. FEMS Microbiol Lett 1997; 150:219–224 [View Article][PubMed]
     [Google Scholar]
  48. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  49. 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]
  50. 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]
  51. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  52. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  53. Minnikin DE, Alshamaony L, Goodfellow M. Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 1975; 88:200–204 [View Article][PubMed]
     [Google Scholar]
  54. Zhang S, Wang X, Yang J, Lu S, Lai X-H et al. Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2020; 70:3234–3240 [View Article][PubMed]
     [Google Scholar]
  55. Jaén-Luchoro D, Gonzales-Siles L, Karlsson R, Svensson-Stadler L, Molin K et al. Corynebacterium sanguinis sp. nov., a clinical and environmental associated corynebacterium. Syst Appl Microbiol 2020; 43:126039 [View Article][PubMed]
     [Google Scholar]
  56. Collins MD. Corynebacterium mycetoides sp. nov., nom. rev. Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I Abt Originale C: Allgemeine, angewandte und ökologische. Mikrobiologie 1982; 3:399–400
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004803
Loading
Corynebacterium lizhenjunii sp. nov., isolated from the respiratory tract of Marmota himalayana, and Corynebacterium qintianiae sp. nov., isolated from the lung tissue of Pseudois nayaur
Int J Syst Evol Microbiol 71, 004803 (2021); https://doi.org/10.1099/ijsem.0.004803
/content/journal/ijsem/10.1099/ijsem.0.004803
/content/journal/ijsem/10.1099/ijsem.0.004803
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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