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

Volume 74, Issue 7

sp. nov. and sp. nov., isolated from soil and faeces of Tibetan antelope () on the Qinghai-Tibet Plateau No Access

Abstract

Two novel strain pairs (HM61/HM23 and S-34/S-58) were isolated from soil and the faeces of Tibetan antelope () collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus . Strains HM61 and HM23 were most closely related to THG T63 (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34 and S-58 were most closely related to MMS20-HV4-12 (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61 and S-34 were 70.6 and 72.5 mol%, respectively. Strains HM61, S-34 and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4–90.5 % as well as digital DNA–DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus . The chemotaxonomic characteristics of strains HM61 and S-34 were consistent with the genus . The major fatty acids of all four strains were -C, C 8 or C 9. For strains HM61 and S-34, MK-8(H) was the predominant respiratory quinone, -2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61 and S-34 represent two novel species of the genus , respectively, with the names sp. nov. and sp. nov. The type strains are HM61 (=GDMCC 4.343=JCM 36399) and S-34 (=CGMCC 4.7664=JCM 33792).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Nocardioides , novel species , polyphasic taxonomy , Qinghai-Tibet Plateau , soil and Tibetan antelope
Funding
This study was supported by the:
  • Guangdong Provincial Introduction of Innovative Research and Development Team (Award 2019YFC1200505)
    • Principle Award Recipient: JingYang
  • Guangdong Provincial Introduction of Innovative Research and Development Team (Award 2019YFC1200501)
    • Principle Award Recipient: JingYang
  • Tarimsal Araştirmalar ve Politikalar Genel Müdürlüğü, Türkiye Cumhuriyeti Tarim Ve Orman Bakanliği (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
© 2024 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006437
2024-07-02
2025-06-19
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References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Evol Bacteriol 1976; 26:58–65 [View Article]
     [Google Scholar]
  2. Nesterenko OA, Kvasnikov EI, Nogina TM. Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zhurnal 1985; 47:3–12
     [Google Scholar]
  3. 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]
  4. Zhang G, Liu Y, Cheng Y, Yang J, Jin D et al. Identification of Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., two new members of the genus Nocardioides. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  5. Dong K, Lu S, Yang J, Pu J, Lai X-H et al. Nocardioides jishulii sp. nov.,isolated from faeces of Tibetan gazelle (Procapra picticaudata). Int J Syst Evol Microbiol 2020; 70:3665–3672 [View Article]
     [Google Scholar]
  6. Liu L, Zhang Y, Chen Q, Shen Q, Li L et al. Nocardioides potassii sp. nov., isolated from weathered potash tailings soil. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  7. Park Y, Liu Q, Maeng S, Choi WJ, Chang Y et al. Nocardioides panacis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  8. So Y, Chhetri G, Kim I, Park S, Jung Y et al. Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  9. Zhang XM, Mo WT, Wei YQ, Li X, Ma G-M et al. Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  10. Wang W, Ding Y, Wei S, Yin M, Zhang G. Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  11. Wang S, Zhou Y, Zhang G. Nocardioides flavus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:5275–5280 [View Article] [PubMed]
     [Google Scholar]
  12. Shi SB, Cui LQ, Zeng Q, Long L-J, Tian X-P. Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  13. Mitzscherling J, MacLean J, Lipus D, Bartholomäus A, Mangelsdorf K et al. Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  14. Kim I, Chhetri G, Kim J et al. Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island.. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  15. Yoon JH, Park YH. The genus Nocardioides. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. eds The Prokaryotes: Archaea Bacteria: Firmicutes, Actinomycetes vol 3 Springer; 2006 pp 1099–1113 [View Article]
     [Google Scholar]
  16. Favre A, Päckert M, Pauls SU, Jähnig SC, Uhl D et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas. Biol Rev Camb Philos Soc 2015; 90:236–253 [View Article] [PubMed]
     [Google Scholar]
  17. Zhang S, Wang X, Yang J, Lu S, Lai X-H et al. Luteimonas yindakuii sp. nov. isolated from the leaves of dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:1007–1014 [View Article] [PubMed]
     [Google Scholar]
  18. Yang C, Zhao L, Zhou J, Cheng Y, Yang J et al. Neisseria lisongii sp. nov. and Neisseria yangbaofengii sp. nov., isolated from the respiratory tracts of marmots. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  19. Li J, Lu S, Jin D, Yang J, Lai X-H et al. Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2019; 69:1093–1098 [View Article] [PubMed]
     [Google Scholar]
  20. Ma C, Zhang G, Cheng Y, Lei W, Yang C et al. Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  21. 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]
     [Google Scholar]
  22. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Yoon SH, 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]
  25. Kim M, Oh HS, 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]
  26. 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]
  27. 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]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [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. 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]
  33. 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]
  34. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  35. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  36. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. 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]
  39. Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D et al. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 2021; 49:D274–D281 [View Article] [PubMed]
     [Google Scholar]
  40. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note, vol. 101 Newark, DE: MIDI Inc; 1990 pp 1–7
     [Google Scholar]
  42. 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]
  43. 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]
  44. Whiton RS, Lau P, Morgan SL, Gilbart J, Fox A. Modifications in the alditol acetate method for analysis of muramic acid and other neutral and amino sugars by capillary gas chromatography-mass spectrometry with selected ion monitoring. J Chromatogr 1985; 347:109–120 [View Article] [PubMed]
     [Google Scholar]
  45. Yan ZF, Lin P, Li C-T, Kook M, Yi T-H. Nocardioides pelophilus sp. nov., isolated from freshwater mud. Int J Syst Evol Microbiol 2018; 68:1942–1948 [View Article] [PubMed]
     [Google Scholar]
  46. Lu L, Cao M, Wang D, Yuan K, Zhuang W et al. Nocardioides immobilis sp. nov., isolated from iron mine soil. Int J Syst Evol Microbiol 2017; 67:5230–5234 [View Article] [PubMed]
     [Google Scholar]
  47. Roh SG, Lee C, Kim M-K, Kang H-J, Kim YS et al. Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2020; 70:2682–2689 [View Article]
     [Google Scholar]
  48. Kim JH, Ham YJ, Kim SB. Nocardioides okcheonensis sp. nov., isolated from riverside soil. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
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Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau
Int J Syst Evol Microbiol 74, 006437 (2024); https://doi.org/10.1099/ijsem.0.006437
/content/journal/ijsem/10.1099/ijsem.0.006437
/content/journal/ijsem/10.1099/ijsem.0.006437
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