1887

Abstract

Two Gram-stain-positive, irregular rod-shaped (0.2–0.5×1.3–2.5 um) strains, HY056 and HY057, were isolated from the faeces of (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056 and HY057 belong to the genus by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with JCM 16608, 78, Ka25 and XZ17. The digital DNA–DNA hybridization value of strain HY056 was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H) was the predominant (91.6 %) respiratory quinone. The cell wall contained -2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were Cω9 and -C The DNA G+C contents of strains HY056 and HY057 were 68.9 and 69.1 mol%, respectively. -Glucosidase expression was positive, and acid was produced from -fructose. Strain HY056 (=CGMCC 4.7563=JCM 33399) is assigned as the type strain of a novel species within the genus , for which the name sp. nov is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003674
2019-11-01
2021-08-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/11/3629.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003674&mimeType=html&fmt=ahah

References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 1976; 26:58–65 [View Article]
    [Google Scholar]
  2. Wu S, Xia X, Zhou Z, Wang D, Wang G. Nocardioides gansuensis sp. nov., isolated from geopark soil. Int J Syst Evol Microbiol 2019; 69:390–396 [View Article][PubMed]
    [Google Scholar]
  3. Lee KC, Kim KK, Kim JS, Kim DS, Ko SH 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]
  4. Lee KC, Kim KK, Kim JS, Kim DS, Ko SH et al. Paenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake. Int J Syst Evol Microbiol 2016; 66:4231–4235 [View Article][PubMed]
    [Google Scholar]
  5. Singh H, du J, Trinh H, Won K, Yang JE et al. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371–378 [View Article][PubMed]
    [Google Scholar]
  6. Wang Y, Xu D, Luo A, Wang G, Zheng S et al. Nocardioides litorisoli sp. nov., isolated from lakeside soil. Int J Syst Evol Microbiol 2017; 67:4216–4220 [View Article][PubMed]
    [Google Scholar]
  7. du HJ, Wei YZ, Su J, Liu HY, Ma BP et al. Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens. Int J Syst Evol Microbiol 2013; 63:1068–1072 [View Article][PubMed]
    [Google Scholar]
  8. Han JH, Kim TS, Joung Y, Kim MN, Shin KS et al. Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Syst Evol Microbiol 2013; 63:4730–4734 [View Article][PubMed]
    [Google Scholar]
  9. Chou JH, Cho NT, Arun AB, Young CC, Chen WM. Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water. Int J Syst Evol Microbiol 2008; 58:1864–1868 [View Article][PubMed]
    [Google Scholar]
  10. 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][PubMed]
    [Google Scholar]
  11. Wang X, Yang J, Lu S, Lai XH, 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]
  12. St-Louis A, Côté SD. Equus kiang (Perissodactyla: Equidae). Mammalian Species 2009; 835:1–11 [View Article]
    [Google Scholar]
  13. Schaller GB. Wildlife of the Tibetan steppe; 1998
  14. Shah N, St Louis A, Huibin Z, Bleisch W, van Gruissen J et al. Equus kiang. The IUCN Red List of Threatened Species 2015; 723:
    [Google Scholar]
  15. Luo Y, Chen Y, Liu F, Jiang C, Gao Y. Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang). Mitochondrial DNA 2011; 22:6–8 [View Article][PubMed]
    [Google Scholar]
  16. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcuspantholopis 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]
  17. Yoon SH, Ha SM, 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]
  18. 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]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  21. Roy Chaudhuri S, Bhattacharya S, Chakraborty M, Bhattacharjee K. Serum ferritin: a backstage weapon in diagnosis of dengue fever. Interdiscip Perspect Infect Dis 2017; 2017:1–6 [View Article][PubMed]
    [Google Scholar]
  22. Wang X, Jiang WK, Cui MD, Yang ZG, 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]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Berlin K, Koren S, Chin CS, 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]
  27. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article][PubMed]
    [Google Scholar]
  28. Yoon JH, Lee CH, Tk O, Sp N. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 2006; 200656:271271–275275
    [Google Scholar]
  29. de Ley J. Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 1970; 101:738–754[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. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  33. Florentino AP, Stams AJ, Sánchez-Andrea I. Genome sequence of Desulfurella amilsii strain TR1 and comparative genomics of Desulfurellaceae Family. Front Microbiol 2017; 8:222 [View Article][PubMed]
    [Google Scholar]
  34. Teng JL, Tang Y, Huang Y, Guo FB, Wei W et al. Phylogenomic analyses and reclassification of species within the genus Tsukamurella: insights to species definition in the post-genomic Era. Front Microbiol 2016; 7:1137 [View Article][PubMed]
    [Google Scholar]
  35. Auch AF, von Jan M, Klenk HP, 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. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 1990
    [Google Scholar]
  37. 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]
  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. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003674
Loading
/content/journal/ijsem/10.1099/ijsem.0.003674
Loading

Data & Media loading...

Supplements

Supplementary File 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