1887

Abstract

Two strains (pika_113 and pika_114) of a previously undescribed -like bacterium were recovered from the intestinal contents of plateau pika () on the Tibet-Qinghai Plateau, China. Results from biochemical characterization indicated that the two strains were phenotypically homogeneous and distinct from other previously described species of the genus . Based on the comparison of 16S rRNA gene sequences and genome analysis, the bacteria were determined to be a hitherto unknown subline within the genus , being most closely related to type strains of and with a respective 97.2 and 97.1 % similarity in their 16S rRNA gene sequences. Phylogenetic analyses confirmed that pika_113 was well separated from any other recognized species of the genus and within the cluster with and . The genome of strain pika_113 displayed less than 42 % relatedness in DNA–DNA hybridization with all the available genomes of existing species of the genus in the NCBI database. Collectively, based on the phenotypic characteristics and phylogenetic analyses results, we propose the novel isolates as representatives of sp. nov. The type strain of is pika_113 (=CGMCC 4.7372=DSM 104049), with a genomic DNA G+C content of 71 mol%.

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2017-09-01
2021-10-16
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References

  1. Schaal KP. Genus Actinomyces. In Sneath PHA. (editor) Bergey’s Manual of Systematic Bacteriology vol. 2 Baltimore: Williams & Wilkins Press; 1986 pp. 1383–1418
    [Google Scholar]
  2. Funke G, Englert R, Frodl R, Bernard KA, Stenger S. Actinomyces hominis sp. nov., isolated from a wound swab. Int J Syst Evol Microbiol 2010; 60:1678–1681 [View Article][PubMed]
    [Google Scholar]
  3. 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]
  4. Hoyles L, Pascual C, Falsen E, Foster G, Grainger JM et al. Actinomyces marimammalium sp. nov., from marine mammals. Int J Syst Evol Microbiol 2001; 51:151–156 [View Article][PubMed]
    [Google Scholar]
  5. Hyun DW, Shin NR, Kim MS, Kim PS, Kim JY et al. Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai. Int J Syst Evol Microbiol 2014; 64:456–461 [View Article][PubMed]
    [Google Scholar]
  6. Renvoise A, Raoult D, Roux V. Actinomyces massiliensis sp. nov., isolated from a patient blood culture. Int J Syst Evol Microbiol 2009; 59:540–544 [View Article][PubMed]
    [Google Scholar]
  7. Meng X, Lu S, Wang Y, Lai X-H, Wen Y et al. Actinomyces vulturis sp. nov., isolated from Gyps himalayensis in Qinghai Tibet Plateau China. Int J Syst Evol Microbiol 2017; 67:1720–1726 [CrossRef]
    [Google Scholar]
  8. Meng X, Lu S, Lai X-H, Wang Y, Wen Y et al. Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus in Qinghai Tibet Plateau China. Int J Syst Evol Microbiol 2017; 67:1873–1879 [CrossRef]
    [Google Scholar]
  9. Schaal KP, Lee HJ. Actinomycete infections in humans–a review. Gene 1992; 115:201–211 [View Article][PubMed]
    [Google Scholar]
  10. Smith AT, Foggin JM, Marcfoggin J. The plateau pika (Ochotona curzoniae) is a keystone species for biodiversity on the Tibetan plateau. Animal Conservation 1999; 2:235–240 [View Article]
    [Google Scholar]
  11. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. Diversity of the human intestinal microbial flora. Science 2005; 308:1635–1638 [View Article][PubMed]
    [Google Scholar]
  12. Xu Y, Xu X, Lan R, Xiong Y, Ye C et al. An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. PLoS One 2013; 8:e6421164219 [View Article][PubMed]
    [Google Scholar]
  13. MIDI Identification System Sherlock Microbial Identification System User Manual, Version 4.5 Newark, DE: MIDI Inc; 2002
    [Google Scholar]
  14. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
    [Google Scholar]
  15. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316[PubMed]
    [Google Scholar]
  16. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematic Chichester, UK: John Wiley & Sons; 1991 pp. 115–175
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Ikegami T, Inatsugi T, Kojima I, Umemura M, Hagiwara H et al. Hybrid de novo genome assembly using MiSeq and SOLiD short read data. PLoS One 2015; 10:e0126289 [View Article][PubMed]
    [Google Scholar]
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1 [View Article][PubMed]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  24. Henssge U, do T, Radford DR, Gilbert SC, Clark D et al. Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963. Int J Syst Evol Microbiol 2009; 59:509–516 [View Article][PubMed]
    [Google Scholar]
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