1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 6

sp. nov.,isolated from faeces of Tibetan gazelle () Free

Abstract

Two novel Gram-stain-positive, irregular rod-shaped bacterial strains, dk3136 and dk3543, were isolated from the faeces of Tibetan gazelle () in the Qinghai–Tibet Plateau of PR China. The cells were aerobic, oxidase-negative and catalase-positive. Colonies were yellowish, circular without any observable aerial mycelium after culturing at 28 ℃ for 3 days on brain–heart infusion (BHI) agar with 5 % sheep blood. The cells grew optimally at 28 °C, pH 7.5 and with 1 % (w/v) NaCl on BHI agar supplemented with 5 % sheep blood. Phylogenetic analysis of the 16S rRNA gene sequences revealed that their nearest phylogenetic relative was Ka25 (97.9 % similarity). The results of 16S rRNA gene sequence and phylogenetic/phylogenomic analyses illustrated that Ka25, XZ17, 78 and D287 were their nearest phylogenetic neighbours. The DNA G+C contents of strains dk3136 and dk3543 were 70.3 mol% and 70.4 mol%, respectively. Their genomes exhibit lower than threshold (95–96 %) average nucleotide identity to known species of the genus . -2,6-diaminopimelic acid was the diagnostic diamino acid and MK-8(H) was the predominant respiratory quinone. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The two strains had C 9, -C and C 8 as the major fatty acids, and rhamnose and galactose as the main whole-cell sugars. On the basis of the results of our genotypic, phenotypic and biochemical analyses, we conclude that strains dk3136 and dk3543 represent a novel species in genus , for which the name sp. nov. is proposed. The type strain is dk3136 (=CGMCC 4.7570=JCM 33496=KCTC 49314).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Nocardioides , novel species , Qinghai–Tibet Plateau and Tibetan gazelle
Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function Chinese Academy of Medical Sciences. (Award 2018RU010)
    • Principle Award Recipient: Jianguo Xu
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
    • Principle Award Recipient: Jianguo Xu
  • National Key R&D Program of China (Award 2018YFC1200102)
    • Principle Award Recipient: Dong Jin
  • the National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: Shan Lu
  • National Major Science and Technology Projects of China (CN) (Award 2018ZX10712001-007)
    • Principle Award Recipient: Jing Yang
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004218
2020-05-14
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/6/3665.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004218&mimeType=html&fmt=ahah

References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales . International Journal of Systematic and Evolutionary Microbiology 1976; 26:58–65
     [Google Scholar]
  2. Lee DW, Lee S-Y, Yoon J-H, Lee SD. Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil. Int J Syst Evol Microbiol 2011; 61:1933–1937 [View Article][PubMed]
     [Google Scholar]
  3. Lee SD, Seong CN. Nocardioides opuntiae sp. nov., isolated from soil of a cactus. Int J Syst Evol Microbiol 2014; 64:2094–2099 [View Article][PubMed]
     [Google Scholar]
  4. Wang X, Jiang W-K, Cui M-D, Yang Z-G, Yu X et al. Nocardioides agrisoli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2017; 67:3722–3727 [View Article][PubMed]
     [Google Scholar]
  5. Lee KC, Kim KK, Kim J-S, Kim D-S, Ko S-H et al. Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake. Int J Syst Evol Microbiol 2016; 66:4231–4235 [View Article][PubMed]
     [Google Scholar]
  6. Cho Y, Jang GI, Cho BC. Nocardioides marinquilinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2594–2599 [View Article][PubMed]
     [Google Scholar]
  7. Tuo L, Dong Y-P, Habden X, Liu J-M, Guo L et al. Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015; 65:1604–1610 [View Article][PubMed]
     [Google Scholar]
  8. Glaeser SP, McInroy JA, Busse H-J, Kämpfer P. Nocardioides zeae sp. nov., isolated from the stem of Zea mays . Int J Syst Evol Microbiol 2014; 64:2491–2496 [View Article][PubMed]
     [Google Scholar]
  9. Kämpfer P, Glaeser SP, McInroy JA, Busse H-J. Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize. Int J Syst Evol Microbiol 2016; 66:1869–1874 [View Article][PubMed]
     [Google Scholar]
  10. Xu H, Zhang S, Cheng J, Asem MD, Zhang M-Y et al. Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L. Int J Syst Evol Microbiol 2016; 66:2013–2018 [View Article][PubMed]
     [Google Scholar]
  11. Zhang H-X, Wang K, Xu Z-X, Chen G-J, Du Z-J. Nocardioides gilvus sp. nov., isolated from Namtso Lake. Antonie van Leeuwenhoek 2016; 109:1367–1374 [View Article][PubMed]
     [Google Scholar]
  12. Tóth EM, Kéki Z, Homonnay ZG, Borsodi AK, Márialigeti K et al. Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera). Int J Syst Evol Microbiol 2008; 58:78–83 [View Article]
     [Google Scholar]
  13. 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]
  14. 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]
  15. Meng X, Lai X-H, Lu S, Liu S, Chen C et al. Actinomyces tangfeifanii sp. nov., isolated from the vulture Aegypius monachus . Int J Syst Evol Microbiol 2018; 68:3701–3706 [View Article][PubMed]
     [Google Scholar]
  16. Meng X, Lu S, Wang Y, Lai X-H, Wen Y et al. Actinomyces vulturis sp. nov., isolated from Gyps himalayensis . Int J Syst Evol Microbiol 2017; 67:1720–1726 [View Article][PubMed]
     [Google Scholar]
  17. Jin D, Chen C, Li L, Lu S, Li Z et al. Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis . BMC Microbiol 2013; 13:141 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Sultanpuram VR, Mothe T, Mohammed F. Nocardioides solisilvae sp. nov., isolated from a forest soil. Antonie van Leeuwenhoek 2015; 107:1599–1606 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  23. Telles GP, Araújo GS, Walter MEMT, Brigido MM, Almeida NF. Live neighbor-joining. BMC Bioinformatics 2018; 19:172 [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. Zheng H, Ji S, Lan R, Liu Z, Bai X et al. Population analysis of Streptococcus suis isolates from slaughtered swine by use of minimum core genome sequence typing. J Clin Microbiol 2014; 52:3568–3572 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. 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]
  30. 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]
  31. Borsodi AK, Tóth E, Aszalós JM, Bárány Á, 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]
  32. Yoon J-H, Kim I-G, Kang KH, Oh T-K, Park Y-H. Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int J Syst Evol Microbiol 2004; 54:71–75 [View Article][PubMed]
     [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
     [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  35. 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]
  36. 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]
  37. Tamaoka J. Analysis of Bacterial Menaquinone Mixtures by Reverse-Phase High-Performance Liquid Chromatography Methods in enzymology: Elsevier; 1986 pp 251–256
     [Google Scholar]
  38. Hu Q-W, Chu X, Xiao M, Li C-T, Yan Z-F et al. Arthrobacter deserti sp. nov., isolated from a desert soil sample. Int J Syst Evol Microbiol 2016; 66:2035–2040 [View Article][PubMed]
     [Google Scholar]
  39. Komagata K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  40. Lechevalier MP. The chemotaxonomy of actinomycetes. Actinomycete taxonomy 1980227–291
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004218
Loading
Nocardioides jishulii sp. nov.,isolated from faeces of Tibetan gazelle (Procapra picticaudata)
Int J Syst Evol Microbiol 70, 3665 (2020); https://doi.org/10.1099/ijsem.0.004218
/content/journal/ijsem/10.1099/ijsem.0.004218
/content/journal/ijsem/10.1099/ijsem.0.004218
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