1887

Abstract

Two novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod-shaped bacteria (strains 2129 and 2119) were isolated from the faeces of Tibetan antelopes () on the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed highest similarity values to DSM 23838 (92.9 and 92.8 %, respectively), and phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that strains 2129 and 2119 represent a new lineage. Strains 2129 and 2119 could ferment -adonitol and -xylose, but were unable to utilize -mannose and -melibiose nor produce esterase (C4) and proline arylamidase. The G+C contents of the two strains were both 69.0 mol%. Their genomes exhibited less than 40.4 % relatedness in DNA–DNA hybridization tests (below 70 % as the recommended threshold for new species) with all available genomes of the genus in the NCBI database. The major fatty acids of the two strains were Cω9 and C, and the major polar lipids were diphosphatidylglycerol, glycolipid, phosphatidylinositol, phosphatidyl inositol mannoside and phosphoglycolipid. Based on the results of genotypic, phenotypic and biochemical analyses, it is proposed that the two unidentified bacteria be classified as representing a novel species, sp. nov. The type strain is 2129 (=CGMCC 4.7483=DSM 106426).

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2019-08-28
2019-10-18
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References

  1. Harz K. Actinomyces bovis ein neuer schimmel in den geweben des rindes. Deutsche Zeitschrift für Thiermedizin 1879;5:125–140
    [Google Scholar]
  2. Schaal KP. Genus Actinomyces. In Sneath PHA. (editor) Bergey’s Manual of Systematic Bacteriologyvol. 2 Baltimore: Williams & Wilkins Press; 1986; pp.1383–1418
    [Google Scholar]
  3. 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;9:9 [CrossRef][PubMed]
    [Google Scholar]
  4. Acevedo F, Baudrand R, Letelier LM, Gaete P. Actinomycosis: a great pretender. Case reports of unusual presentations and a review of the literature. Int J Infect Dis 2008;12:358–362 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  11. Tippmann HF. Analysis for free: comparing programs for sequence analysis. Brief Bioinform 2004;5:82–87 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 [CrossRef][PubMed]
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Chen C, Zhang W, Zheng H, Lan R, Wang H et al. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013;51:2582–2591 [CrossRef][PubMed]
    [Google Scholar]
  16. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012;61:1061–1067 [CrossRef][PubMed]
    [Google Scholar]
  17. Hall V, Collins MD, Lawson PA, Falsen E, Duerden BI. Actinomyces dentalis sp. nov., from a human dental abscess. Int J Syst Evol Microbiol 2005;55:427–431 [CrossRef][PubMed]
    [Google Scholar]
  18. Johnson JL, Moore LV, Kaneko B, Moore WE. Actinomyces georgiae sp. nov., Actinomyces gerencseriae sp. nov., designation of two genospecies of Actinomyces naeslundii, and inclusion of A. naeslundii serotypes II and III and Actinomyces viscosus serotype II in A. naeslundii genospecies 2. Int J Syst Bacteriol 1990;40:273–286 [CrossRef][PubMed]
    [Google Scholar]
  19. Dent VE, Williams RAD. Actinomyces slackii sp. nov. from Dental Plaque of Dairy Cattle. Int J Syst Bacteriol 1986;36:392–395 [CrossRef]
    [Google Scholar]
  20. Renvoise A, Raoult D, Roux V. Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample. Int J Syst Evol Microbiol 2010;60:1516–1521 [CrossRef][PubMed]
    [Google Scholar]
  21. Pascual C, Foster G, Falsen E, Bergström K, Greko C et al. Actinomyces bowdenii sp. nov., isolated from canine and feline clinical specimens. Int J Syst Bacteriol 1999;49 Pt 4:1873–1877 [CrossRef][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;14:60 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  26. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29:319–322 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef][PubMed]
    [Google Scholar]
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