1887

Abstract

Two previously undescribed, Gram-stain-positive, rod-shaped strains, 410 and 553, were isolated from faeces of the Tibetan antelope () from the Tibet-Qinghai Plateau, PR China. The optimum growth conditions of the two novel strains were 1 % (w/v) NaCl, 37 °C and pH 7. The end products from glucose fermentation included ethanol and lactic acid. Based on results of 16S rRNA gene sequence comparison and phylogenetic and phylogenomic analyses, strains 410 and 553 were classified into the genus , and were closely related to (97.6 %), (93.5 %) and (90.8 %). The genomic G+C content of strain 410 was 67.4 mol%. Digital DNA–DNA hybridization values between strain 410 and each of the closely related species were under 70 %. The respiratory quinones were MK-10 (68 %) and MK-9 (32 %). The main cellular fatty acids of the isolates were C, followed by C 9. The major polar lipids were diphosphatidylglycerol and phosphatidylinositol-mannoside. The whole-cell sugars contained rhamnose, ribose and glucose. The diagnostic amino acids of cell-wall peptidoglycan included alanine, glutamic acid, lysine and ornithine. The results of biochemical, chemotaxonomic and genotypic analyses revealed that the two novel strains represent a novel species of genus , for which the name s sp. nov. is proposed. The type strain is 410 (=CGMCC 1.16361= DSM 106201).

Funding
This study was supported by the:
  • National Key R&D Program of China (Award 2018YFC1200102)
    • Principle Award Recipient: Dong Jin
  • National Science and Technology Major Project of China (Award 2018ZX10305409-003)
    • Principle Award Recipient: Zhihong Ren
  • National Science and Technology Major Project of China (Award 2018ZX10712001-007)
    • Principle Award Recipient: Jing Yang
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
    • Principle Award Recipient: Jianguo Xu
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2019-10-14
2024-12-03
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References

  1. Schaal KP, Yassin AA, Genus I. Actinomyces. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology 5, 2nd ed. Part A New York: Springer; 2012 pp 42–109
    [Google Scholar]
  2. Funke G, Alvarez N, Pascual C, Falsen E, Akervall E et al. Actinomyces europaeus sp. nov., isolated from human clinical specimens. Int J Syst Bacteriol 1997; 47:687–692 [View Article]
    [Google Scholar]
  3. Ramos CP, Falsen E, Alvarez N, Akervall E, Sjödén B et al. Actinomyces graevenitzii sp. nov., isolated from human clinical specimens. Int J Syst Bacteriol 1997; 47:885–888 [View Article]
    [Google Scholar]
  4. 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]
    [Google Scholar]
  5. Hoyles L, Grainger JM, Collins MD, Foster G, Falsen E et al. Actinomyces marimammalium sp. nov., from marine mammals. Int J Syst Evol Microbiol 2001; 51:151–156 [View Article]
    [Google Scholar]
  6. 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]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. Meng X, Lu S, Wang Y, Lai XH, Wen Y et al. Actinomyces vulturis sp. nov., isolated from Gyps himalayensis . Int J Syst Evol Microbiol 2017; 67:1720–1726 [View Article]
    [Google Scholar]
  9. Meng X, Lai XH, 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]
    [Google Scholar]
  10. Ma L, Shao X, Wang Y, Yang Y, Bai Z et al. Molecular cloning, characterization and expression of myoglobin in Tibetan antelope (Pantholops hodgsonii), a species with hypoxic tolerance. Gene 2014; 533:532–537 [View Article]
    [Google Scholar]
  11. 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]
    [Google Scholar]
  12. 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]
    [Google Scholar]
  13. An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043–2048 [View Article]
    [Google Scholar]
  14. Lane DJ. 16s/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 125–175
    [Google Scholar]
  15. Vela AI, Casas-Díaz E, Lavín S, Domínguez L, Fernández-Garayzábal JF. Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits. Int J Syst Evol Microbiol 2015; 65:2903–2907 [View Article]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [View Article]
    [Google Scholar]
  19. 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]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  21. 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]
    [Google Scholar]
  22. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article]
    [Google Scholar]
  23. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  26. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article]
    [Google Scholar]
  27. Ventosa A, Marquez MC, Kocur M, Tindall BJ. Comparative study of "Micrococcus sp." strains CCM 168 and CCM 1405 and members of the genus Salinicoccus . Int J Syst Bacteriol 1993; 43:245–248 [View Article]
    [Google Scholar]
  28. Watanabe M, Aoyagi Y, Ohta A, Minnikin DE. Structures of phenolic glycolipids from Mycobacterium kansasii . Eur J Biochem 1997; 248:93–98 [View Article]
    [Google Scholar]
  29. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria . J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  31. 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]
  32. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156
    [Google Scholar]
  33. Yoon MH, Ten LN, Im WT, Lee ST. Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost. Int J Syst Evol Microbiol 2008; 58:1878–1884 [View Article]
    [Google Scholar]
  34. 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]
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