1887

Abstract

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350 and Z527) were isolated from intestinal contents of plateau pika () from the Qinghai–Tibet Plateau, PR China. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Z350 belongs to the genus (family ) but clearly differs from the currently recognized species DSM 101040 (98.4 % similarity) and DSM 27763 (97.4 %). Strain Z350 had a DNA G+C content of 70.7 mol% and shared 80.4 and 76.7 % average nucleotide identity values and 23.4 and 20.6 % DNA–DNA hybridization relatedness with DSM 101040 and DSM 27763, respectively. Further phylogenetic analyses based on 497 core genes indicated that our isolates were members of the genus but separated from all existing genera within the family . The major cellular fatty acids were C ω9 and 10-methyl C. The cell wall contained -diaminopimelic acid as the diamino acid, and rhamnose, ribose and glucose as whole cell-wall sugars. MK-9(H) was detected as the major menaquinone. Polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phospholipid. Based on distinct differences in the genotypic and phenotypic data from the two species, a novel species, sp. nov., is proposed. The type strain is Z350 (=CGMCC 4.7464=DSM 106288).

Funding
This study was supported by the:
  • Jianguo Xu , Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences and Peking Union Medical College (CN) , (Award SZSM201811071)
  • Jianguo Xu , National Center of Competence in Research Materials’ Revolution: Computational Design and Discovery of Novel Materials (CH) , (Award 2018RU010)
  • Zhihong Ren , Science and Technology Service Network Plan (CN) , (Award 2018ZX10305409-003)
  • Jing Yang , National Science and Technology Major Project of China , (Award 2018ZX10712001-007)
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2020-02-25
2020-06-02
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References

  1. Lee L-H, Zainal N, Azman A-S, Mutalib N-SA, Hong K et al. Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae . Int J Syst Evol Microbiol 2014; 64:1461–1467 [CrossRef]
    [Google Scholar]
  2. Zhou S, Jia F, Liu C, Fan J, Li J et al. Mumia xiangluensis sp. nov., isolated from the rhizosphere of Peucedanum praeruptorum Dunn. Antonie van Leeuwenhoek 2016; 109:827–832 [CrossRef]
    [Google Scholar]
  3. Smith AT, Foggin JM, Marcfoggin J. The plateau pika (Ochotona curzoniae) is a keystone species for biodiversity on the Tibetan Plateau. Anim Conserv 1999; 2:235–240 [CrossRef]
    [Google Scholar]
  4. Meng X, Wang Y, Lu S, Lai X-H, Jin D et al. Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2017; 67:3363–3368 [CrossRef]
    [Google Scholar]
  5. Zhang G, Yang J, Lai XH, Lu S, Jin D et al. Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae). Animal Conservation 20191–10
    [Google Scholar]
  6. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [CrossRef]
    [Google Scholar]
  7. Jin D, Chen C, Li L, Lu S, Li Z et al. Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis . BMC Microbiol 2013; 13:141 [CrossRef]
    [Google Scholar]
  8. Li J, Lu S, Jin D, Yang J, Lai X-H et al. Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2019; 69:1093–1098 [CrossRef]
    [Google Scholar]
  9. Yoon S-H, Ha S-M, 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 [CrossRef]
    [Google Scholar]
  10. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [CrossRef]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef]
    [Google Scholar]
  13. Guindon S, Gascuel O. . A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [CrossRef]
    [Google Scholar]
  14. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [CrossRef]
    [Google Scholar]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [Google Scholar]
  18. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [CrossRef]
    [Google Scholar]
  19. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef]
    [Google Scholar]
  21. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef]
    [Google Scholar]
  22. Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57 [CrossRef]
    [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef]
    [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M, Hans-Peter K. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  26. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [CrossRef]
    [Google Scholar]
  27. Austrian R. The Gram stain and the etiology of lobar pneumonia, an historical note. Bacteriol Rev 1960; 24:261–265
    [Google Scholar]
  28. 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:e64211 [CrossRef]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
    [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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  32. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes . In Dietz TDW. editor Actinomycete Taxonomy. Special Publication no. 6 Arlington, VA: Society for Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  33. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [CrossRef]
    [Google Scholar]
  34. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM, Seviour RJ et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30:178–182 [CrossRef]
    [Google Scholar]
  35. 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 [CrossRef]
    [Google Scholar]
  36. Póntigo F, Moraga M, Flores SV. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus . Genet Mol Res 2015; 14:10905–10918 [CrossRef]
    [Google Scholar]
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