1887

Abstract

Six novel strains (ZJ34, ZJ561, ZJ750, ZJ1629, zg-993 and zg-987) isolated from faeces and respiratory tracts of from the Qinghai–Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus , and are closely related to DSM 15434 (16S rRNA gene sequences similarities, 94.9–98.7 %), CCUG 61299 (95.6–96.6 %), CCTCC AB2010168 (95.7 %) and DSM 15435 (95.2–96.4 %), with values of digital DNA–DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34/ZJ561, ZJ750/ZJ1629 and zg-993/zg-987). All the novel strains had C 9 and C as the two most abundant major fatty acids. MK-9(H) or MK-8(H) was the sole or predominant respiratory quinone of strains ZJ34, ZJ750 and zg-993 and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750 shared identical peptidoglycan amino acid profile with ZJ34 (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993 (glucose, rhamnose and ribose). Strain zg-993 contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34 was ribose. The DNA G+C contents of the novel strains were within the range of 65.8–70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus , for which the names sp. nov. [type strain ZJ34 (=GDMCC 1.1952=JCM 34355)] sp. nov. [type strain ZJ750 (=GDMCC 1.1950=JCM 34356)] and sp. nov. [type strain zg-993 (=GDMCC 1.1956=JCM 34357)] were proposed, respectively.

Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: ShanLu
  • National Key R&D Program of China (Award 2019YFC1200505)
    • Principle Award Recipient: LiyunLiu
  • National Key R&D Program of China (Award 2019YFC1200501)
    • Principle Award Recipient: JingYang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004875
2021-07-12
2021-08-02
Loading full text...

Full text loading...

References

  1. Schaal KP. Genus Actinomyces. Sneath P. eds In Bergey’s Manual of Systematic Bacteriology Baltimore: Williams & Wilkins Press; 1986 pp 1383–1418
    [Google Scholar]
  2. Ramos CP, Foster G, Collins MD. Phylogenetic analysis of the genus Actinomyces based on 16S rRNA gene sequences: description of Arcanobacterium phocae sp. nov., Arcanobacterium bernardiae comb. nov., and Arcanobacterium pyogenes comb. nov. Int J Syst Bacteriol 1997; 47:46–53 [View Article] [PubMed]
    [Google Scholar]
  3. Lawson PA, Falsen E, Åkervall E, Vandamme P, Collins MD. Characterization of some Actinomyces-like isolates from human clinical specimens: reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and description of Actinobaculum schaalii sp. nov. Int J Syst Evol Microbiol 1997; 47:899–903
    [Google Scholar]
  4. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  5. Nikolaitchouk N, Hoyles L, Falsen E, Grainger JM, Collins MD. Characterization of Actinomyces isolates from samples from the human urogenital tract: description of Actinomyces urogenitalis sp. nov. Int J Syst Evol Microbiol 2000; 50:1649–1654 [View Article]
    [Google Scholar]
  6. Collins MD, Hoyles L, Kalfas S, Sundquist G, Monsen T et al. Characterization of Actinomyces isolates from infected root canals of teeth: description of Actinomyces radicidentis sp. nov. J Clin Microbiol 2000; 38:3399–3403 [View Article] [PubMed]
    [Google Scholar]
  7. Pascual C, Foster G, Falsen E, Bergstrom K, Greko C et al. Actinomyces bowdenii sp. nov., isolated from canine and feline clinical specimens. Int J Syst Bacteriol 1999; 49:1873–1877
    [Google Scholar]
  8. Meng X, Wang Y, Lu S, Lai XH, 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]
  9. Li J, Lu S, Yang J, Pu J, Lai XH et al. Actinomyces lilanjuaniae sp. nov., isolated from the faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2019; 69:3485–3491 [View Article] [PubMed]
    [Google Scholar]
  10. Zhu W, Yang J, Lu S, Lai XH, Jin D et al. Actinomyces qiguomingii sp. nov., isolated from the Pantholops hodgsonii. Int J Syst Evol Microbiol 2020; 70:58–64 [View Article] [PubMed]
    [Google Scholar]
  11. Liu S, Jin D, Lan R, Wang Y, Meng Q et al. Escherichia marmotae sp. Nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2015; 65:2130–2134 [View Article] [PubMed]
    [Google Scholar]
  12. Hu S, Jin D, Lu S, Liu S, Zhang J et al. Helicobacter himalayensis sp. Nov. Isolated from gastric mucosa of Marmota himalayana. Int J Syst Evol Microbiol 2015; 65:1719–1725 [View Article] [PubMed]
    [Google Scholar]
  13. Niu L, Lu S, Hu S, Jin D, Lai X et al. Streptococcusmarmotae sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2016; 66:4315–4322 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 125–175
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Meier‐Kolthoff JP, Auch AF, Klenk HP, Göker M. Highly parallelized inference of large genome‐based phylogenies. Concurr Comput Pract Exp 2014; 26:1715–1729
    [Google Scholar]
  23. Chin CS, 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]
  24. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of standard operating procedures (SOPS) for (meta) annotatgenomic. OMICS 2008; 12:137–141 [View Article] [PubMed]
    [Google Scholar]
  25. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. 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
    [Google Scholar]
  28. 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]
  29. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386–2392 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Zhang S, Wang X, Yang J, Lu S, Lai X-H et al. Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2020; 70:3234–3240 [View Article] [PubMed]
    [Google Scholar]
  32. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  33. Minnikin D, O’donnell A, 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]
  34. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  35. Kunzler K, Eichenberger W. Betaine lipids and zwitterionic phospholipids in plants and fungi. Phytochemistry 1997; 46:883–892 [View Article] [PubMed]
    [Google Scholar]
  36. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4‐diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  37. 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]
  38. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Method Microbiol 1985; 18:123–156
    [Google Scholar]
  39. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16:1114–1116 [View Article]
    [Google Scholar]
  40. Hijazin M, Alber J, Lämmler C, Kämpfer P, Glaeser SP et al. Actinomyces weissii sp. nov., isolated from dogs. Int J Syst Evol Microbiol 2012; 62:1755–1760 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004875
Loading
/content/journal/ijsem/10.1099/ijsem.0.004875
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