1887

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Volume 70, Issue 10

sp. nov. and sp. nov., two new members of the genus Free

Abstract

Four unknown strains belonging to the genus were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785 and 208) had the greatest 16S rRNA gene sequence similarity to (98.6 and 98.7 %, respectively), (98.0 and 98.1%, respectively), (97.9 and 98.0 %, respectively) and (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391 and J915) had the highest sequence similarity to (98.6 and 98.3 %, respectively) and (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785 and J391, represented two separate novel species that are distinct from all currently recognized species in the genus . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785 and J391 were in line with those of the genus : anteiso-C(79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H) (65.8 %) or MK-9(H) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3 or A4 as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus are proposed, namely sp. nov. (type strain, 785=CGMCC 1.16725=GDMCC 1.1592=JCM 33491) and sp. nov. (type strain, J391=CGMCC 1.17382=GDMCC 1.1667=JCM 33841).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): wild animals , arthrobacter , novel species and Qinghai-Tibet Plateau
Funding
This study was supported by the:
  • National Key R&D Program of China (Award 2019YFC1200505)
    • Principle Award Recipient: Jing Yang
  • National Key R&D Program of China (Award 2019YFC1200500)
    • Principle Award Recipient: Jing Yang
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: Jianguo Xu
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
    • Principle Award Recipient: Jianguo Xu
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: Shan Lu
  • National Science and Technology Major Project of China (Award 2018ZX10712001-007)
    • Principle Award Recipient: Jing Yang
© 2020 The Authors
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2020-08-25
2024-12-02
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References

  1. Conn HJ, Dimmick I. Soil bacteria similar in morphology to Mycobacterium and Corynebacterium . J Bacteriol 1947; 54:291–303 [View Article][PubMed]
     [Google Scholar]
  2. Busse H-J. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus . Int J Syst Evol Microbiol 2016; 66:9–37 [View Article][PubMed]
     [Google Scholar]
  3. Cheng J, Zhang M-Y, Zhao J-C, Xu H, Zhang Y et al. Arthrobacter ginkgonis sp. nov., an actinomycete isolated from rhizosphere of Ginkgo biloba L. Int J Syst Evol Microbiol 2017; 67:319–324 [View Article][PubMed]
     [Google Scholar]
  4. Wang H-F, Li L, Zhang Y-G, Hozzein WN, Zhou X-K et al. Arthrobacter endophyticus sp. nov., an endophytic actinobacterium isolated from root of Salsola affinis C. A. Mey. Int J Syst Evol Microbiol 2015; 65:2154–2160 [View Article][PubMed]
     [Google Scholar]
  5. Chen Y-G, Tang S-K, Zhang Y-Q, Li Z-Y, Yi L-B et al. Arthrobacter halodurans sp. nov., a new halotolerant bacterium isolated from sea water. Antonie van Leeuwenhoek 2009; 96:63–70 [View Article][PubMed]
     [Google Scholar]
  6. Storms V, Devriese LA, Coopman R, Schumann P, Vyncke F et al. Arthrobacter gandavensis sp. nov., for strains of veterinary origin. Int J Syst Evol Microbiol 2003; 53:1881–1884 [View Article][PubMed]
     [Google Scholar]
  7. Lee J-Y, Hyun D-W, Soo Kim P, Sik Kim H, Shin N-R et al. Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina . Int J Syst Evol Microbiol 2016; 66:1887–1893 [View Article][PubMed]
     [Google Scholar]
  8. Flegler A, Runzheimer K, Kombeitz V, Mänz AT, Heidler von Heilborn D et al. Arthrobacter bussei sp. nov., a pink-coloured organism isolated from cheese made of cow's milk. Int J Syst Evol Microbiol 20201–10
     [Google Scholar]
  9. Margesin R, Schumann P, Zhang D-C, Redzic M, Zhou Y-G et al. Arthrobacter cryoconiti sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:397–402 [View Article][PubMed]
     [Google Scholar]
  10. Liu Q, Xin Y-H, Chen X-L, Liu H-C, Zhou Y-G et al. Arthrobacter ruber sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2018; 68:1616–1621 [View Article][PubMed]
     [Google Scholar]
  11. Wauters G, Charlier J, Janssens M, Delmée M. Identification of Arthrobacter oxydans, Arthrobacter luteolus sp. nov., and Arthrobacter albus sp. nov., isolated from human clinical specimens. J Clin Microbiol 2000; 38:2412–2415 [View Article][PubMed]
     [Google Scholar]
  12. Funke G, Hutson RA, Bernard KA, Pfyffer GE, Wauters G et al. Isolation of Arthrobacter spp. from clinical specimens and description of Arthrobacter cumminsii sp. nov. and Arthrobacter woluwensis sp. nov. J Clin Microbiol 1996; 34:2356–2363 [View Article][PubMed]
     [Google Scholar]
  13. Huang Y, Zhao N, He L, Wang L, Liu Z et al. Arthrobacter scleromae sp. nov. isolated from human clinical specimens. J Clin Microbiol 2005; 43:1451–1455 [View Article][PubMed]
     [Google Scholar]
  14. Dastager SG, Liu Q, Qin L, Tang S-K, Krishnamurthi S et al. Arthrobacter enclensis sp. nov., isolated from sediment sample. Arch Microbiol 2014; 196:775–782 [View Article][PubMed]
     [Google Scholar]
  15. Hoang V-A, Kim Y-J, Nguyen N-L, Yang D-C. Arthrobacter gyeryongensis sp. nov., isolated from soil of a Gynostemma pentaphyllum field. Int J Syst Evol Microbiol 2014; 64:420–425 [View Article][PubMed]
     [Google Scholar]
  16. Meng X, Wang Y, Lu S, Lai X-H, Jin D et al. Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2017; 67:3363–3368 [View Article][PubMed]
     [Google Scholar]
  17. Zhang G, Yang J, Lai X-H, Lu S, Jin D et al. Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae). Antonie van Leeuwenhoek 2019; 112:1001–1010 [View Article][PubMed]
     [Google Scholar]
  18. Zhang G, Yang J, Lai X-H, Jin D, Pu J et al. Neisseria weixii sp. nov., isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2019; 69:2305–2311 [View Article][PubMed]
     [Google Scholar]
  19. Huang Y, Wang X, Yang J, Lu S, Lai X-H et al. Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. Int J Syst Evol Microbiol 2019; 69:3629–3635 [View Article][PubMed]
     [Google Scholar]
  20. Jin D, Yang J, Lu S, Lai X-H, Xiong Y et al. Enterococcus wangshanyuanii sp. nov., isolated from faeces of yaks (Bos grunniens). Int J Syst Evol Microbiol 2017; 67:5216–5221 [View Article][PubMed]
     [Google Scholar]
  21. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  27. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article][PubMed]
     [Google Scholar]
  28. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
     [Google Scholar]
  29. Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015; 33:623–630 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Chen C, Zhang W, Zheng H, Lan R, Wang H et al. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013; 51:2582–2591 [View Article][PubMed]
     [Google Scholar]
  34. Borsodi AK, Tóth E, Aszalós JM, Bárány Ágnes, Schumann P et al. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil. Int J Syst Evol Microbiol 2017; 67:3490–3495 [View Article][PubMed]
     [Google Scholar]
  35. Austrian R. The Gram stain and the etiology of lobar pneumonia, an historical note. Bacteriol Rev 1960; 24:261–265 [View Article][PubMed]
     [Google Scholar]
  36. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article][PubMed]
     [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
     [Google Scholar]
  38. 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]
  39. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  40. 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]
  41. Koch C, Schumann P, Stackebrandt E. Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter . Int J Syst Bacteriol 1995; 45:837–839 [View Article][PubMed]
     [Google Scholar]
  42. Lee J-S, Lee KC, Pyun Y-R, Bae KS. Arthrobacter koreensis sp. nov., a novel alkalitolerant bacterium from soil. Int J Syst Evol Microbiol 2003; 53:1277–1280 [View Article][PubMed]
     [Google Scholar]
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Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter
Int J Syst Evol Microbiol 70, 5287 (2020); https://doi.org/10.1099/ijsem.0.004414
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