1887

Abstract

Four mesophilic and Gram-stain-positive strains (zg-686/zg-691 and HY186/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4–68.3 mol% and low DNA relatedness (19.2–27.6 %) with all available genomes in the genus . Strains zg-686/zg-691 and HY186/HY189 had Cω9, C 10-methyl, C 7/Cω6 and C as major cellular fatty acids. The polar lipids detected in strains zg-686 and HY186 included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H) (10.8 %) and MK9(H) (89.2 %) for strain zg-686, and MK6 (7.7 %), MK8(H) (8.4 %), MK8(H) (3.1 %) and MK9(H) (80.8 %) for strain HY186. Optimal growth conditions were pH 7.0, 35–37 °C and 0.5–1.5 % NaCl (w/v) for strains pair zg-686/zg-691, and pH 7.0, 28 °C and 1.5 % (w/v) NaCl for strains pair HY186/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are zg-686 (=GDMCC 1.1715 =JCM 33890) and HY186 (=CGMCC 4.7607 =JCM 33466), respectively.

Funding
This study was supported by the:
  • National Major Science and Technology Projects of China (Award 2017ZX10303405-005-002)
    • Principle Award Recipient: DongJin
  • National Major Science and Technology Projects of China (Award 2017ZX10303405-002)
    • Principle Award Recipient: DongJin
  • National Major Science and Technology Projects of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: ShanLu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004897
2021-07-19
2021-08-04
Loading full text...

Full text loading...

References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971; 68:15–26 [View Article] [PubMed]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
    [Google Scholar]
  3. Kageyama A, Iida S, Yazawa K, Kudo T, Suzuki SI et al. Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 2006; 56:1817–1821 [View Article] [PubMed]
    [Google Scholar]
  4. Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H et al. Gordonia otitidis sp. nov., isolated from a patient with external otitis. Int J Syst Evol Microbiol 2005; 55:1871–1876 [View Article] [PubMed]
    [Google Scholar]
  5. Tsang CC, Xiong L, Poon RWS, Chen JHK, Leung KW et al. Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong. Int J Syst Evol Microbiol 2016; 66:3942–3950 [View Article] [PubMed]
    [Google Scholar]
  6. Liu Y, Ge F, Chen G, Li W, Ma P et al. Gordonia neofelifaecis sp. nov., a cholesterol side-chain-cleaving actinomycete isolated from the faeces of Neofelis nebulosa. Int J Syst Evol Microbiol 2011; 61:165–169 [View Article] [PubMed]
    [Google Scholar]
  7. Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal K. Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L. Int J Syst Evol Microbiol 2019; 69:1621–1627 [View Article] [PubMed]
    [Google Scholar]
  8. Park S, Kang SJ, Kim W, Yoon JH. Gordonia hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:3172–3175 [View Article] [PubMed]
    [Google Scholar]
  9. Shen FT, Goodfellow M, Jones AL, Chen YP, Arun AB et al. Gordonia soli sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 2006; 56:2597–2601 [View Article] [PubMed]
    [Google Scholar]
  10. le Roes M, Goodwin CM, Meyers PR. Gordonia lacunae sp. nov., isolated from an estuary. Syst Appl Microbiol 2008; 31:17–23 [View Article] [PubMed]
    [Google Scholar]
  11. Huang Y, Wang X, Yang J, Lu S, Lai XH 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]
  12. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii. Int J Syst Evol Microbiol 2016; 66:3281–3286 [View Article] [PubMed]
    [Google Scholar]
  13. Dong K, Yang J, Lu S, Pu J, Lai XH et al. Microbacterium wangchenii sp. nov., isolated from faeces of Tibetan gazelles (Procapra picticaudata) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2020; 70:1307–1314 [View Article] [PubMed]
    [Google Scholar]
  14. Meng X, Lu S, Lai XH, Wang Y, Wen Y et al. Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus. Int J Syst Evol Microbiol 2017; 67:1873–1879 [View Article] [PubMed]
    [Google Scholar]
  15. Zhang G, Lai XH, Yang J, Jin D, Pu J et al. Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae. Int J Syst Evol Microbiol 2020; 70:3186–3193 [View Article] [PubMed]
    [Google Scholar]
  16. Meng J, Jin D, Yang J, Lai XH, Pu J et al. Lactobacillus xujianguonis sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2020; 70:11–15 [View Article] [PubMed]
    [Google Scholar]
  17. Ge Y, Yang J, Lai XH, Zhang G, Jin D et al. Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content. Int J Syst Evol Microbiol 2020; 70:2493–2498 [View Article] [PubMed]
    [Google Scholar]
  18. Kim YS, Kim SJ, Jang YH, Kim KH. Pukyongia salina gen. nov., sp. nov., a novel genus in the family Flavobacteriaceae. J Microbiol 2020; 58:456–462 [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
    [Google Scholar]
  20. 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]
  21. 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]
  22. Felsenstein J. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  23. McCarthy A. Third generation DNA sequencing: pacific biosciences’ single molecule real time technology. Chem Biol 2010; 17:675–676 [View Article] [PubMed]
    [Google Scholar]
  24. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  27. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. Contest16s: An algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057
    [Google Scholar]
  28. Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2018; 44:393–413 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Wayne LG. International Committee on Systematic Bacteriology: Announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434
    [Google Scholar]
  34. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. Kampfer P, Young CC, Chu JN, Frischmann A, Busse HJ et al. Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:65–70 [View Article] [PubMed]
    [Google Scholar]
  37. Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y et al. Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:3718–3723 [View Article] [PubMed]
    [Google Scholar]
  38. Yassin AF, Shen FT, Hupfer H, Arun AB, Lai WA et al. Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2007; 57:1065–1068 [View Article] [PubMed]
    [Google Scholar]
  39. Luo H, Gu Q, Xie J, Hu C, Liu Z et al. Gordonia shandongensis sp. nov., isolated from soil in China. Int J Syst Evol Microbiol 2007; 57:605–608 [View Article] [PubMed]
    [Google Scholar]
  40. Linos A, Berekaa MM, Steinbüchel A, Kim KK, Sproer C et al. Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. Int J Syst Evol Microbiol 2002; 52:1133–1139 [View Article] [PubMed]
    [Google Scholar]
  41. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50:2031–2036 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004897
Loading
/content/journal/ijsem/10.1099/ijsem.0.004897
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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