1887

Abstract

Four novel bacterial strains (ST-M6, L-033, L-031 and Z-333) were isolated from the intestinal contents of plateau pikas () collected on the QinghaiTibet Plateau, PR China. Cells were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, capsuled and short-rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequences and 387 core genes indicated that the four isolates belong in the genus and clearly separate from recognized species. The two type strains (ST-M6 and L-031) shared low 16S rRNA similarity, average nucleotide identity values and digital DNA–DNA hybridization relatedness with their phylogenetic neighbours ( DSM 18659, DSM 19179, JCM 30598, CCTCC M208212, DSM 16091 and DSM 20754). The genomic DNA G+C contents of strains ST-M6 and L-031 were 70.4 and 70.7 mol%, respectively. The major cellular fatty acids of strain ST-M6 were anteiso-C, anteiso-C and iso-C, in contrast to anteiso-C, anteiso-C and anteiso-C 9 of strain L-031. Both type strains (ST-M6 and L-031) were glycolate test positive and shared the following common features: MK-11 and MK-12 as major menaquinones; rhamnose, ribose, mannose and galactose as major cell-wall sugars; diphosphatidylglycerol, phosphatidylglycerol and two glycolipids as polar lipids; and ornithine, alanine, glycine and glutamic acid as cell-wall amino acids. Comparing the phenotypic, phylogenetic and chemotaxonomic features of the four strains and their related taxa, strains ST-M6 and L-031 represent two novel species of the genus , for which the names sp. nov. (type strain ST-M6=CGMCC 1.16364=DSM 104058) and sp. nov. (type strain L-031 =CGMCC 1.16363=DSM 106170) are proposed.

Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
    • Principle Award Recipient: JianguoXu
  • National Key R&D Program of China (Award 2018YFC1200102)
    • Principle Award Recipient: DongJin
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: NotApplicable
  • National Science and Technology Major Project of China (Award 2018ZX10712001-007)
    • Principle Award Recipient: JingYang
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2021-01-27
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References

  1. Orla-Jensen S. The Lactic Acid Bacteria Høst: Copenhagen; 1919 pp 1–196
    [Google Scholar]
  2. Collins MD, Jones D, Kroppenstedt RM. Reclassification of Brevibacterium imperiale (Steinhaus) and "Corynebacterium laevaniformans" (Dias and Bhat) in a redefined genus Microbacterium (Orla-Jensen), as Microbacterium imperiale comb. nov. and Microbacterium laevaniformans nom. rev.; comb. nov. Syst Appl Microbiol 1983; 4:65–78 [View Article][PubMed]
    [Google Scholar]
  3. Takeuchi M, Hatano K. Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 1998; 48 Pt 3:739–747 [View Article][PubMed]
    [Google Scholar]
  4. Fidalgo C, Riesco R, Henriques I, Trujillo ME, Alves A. Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2016; 66:4492–4500 [View Article][PubMed]
    [Google Scholar]
  5. Alves A, Riesco R, Correia A, Trujillo ME. Microbacterium proteolyticum sp. nov. isolated from roots of Halimione portulacoides. Int J Syst Evol Microbiol 2015; 65:1794–1798 [View Article][PubMed]
    [Google Scholar]
  6. Hoang V-A, Kim Y-J, Nguyen NL, Kang CH, Kang J-P et al. Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng. Int J Syst Evol Microbiol 2015; 65:3196–3202 [View Article][PubMed]
    [Google Scholar]
  7. Park M-J, Kim MK, Kim H-B, Im W-T, Yi T-H et al. Microbacterium ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:429–433 [View Article][PubMed]
    [Google Scholar]
  8. Zhang W, Zhu H-H, Yuan M, Yao Q, Tang R et al. Microbacterium radiodurans sp. nov., a UV radiation-resistant bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:2665–2670 [View Article][PubMed]
    [Google Scholar]
  9. Kageyama A, Takahashi Y, Matsuo Y, Adachi K, Kasai H et al. Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments. Actinomycetologica 2007; 21:53–58 [View Article]
    [Google Scholar]
  10. Schippers A, Bosecker K, Spröer C, Schumann P. Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria. Int J Syst Evol Microbiol 2005; 55:655–660 [View Article][PubMed]
    [Google Scholar]
  11. Bakir MA, Kudo T, Benno Y. Microbacterium hatanonis sp. nov., isolated as a contaminant of hairspray. Int J Syst Evol Microbiol 2008; 58:654–658 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. Zhang G, Yang J, Lai X-H, Lu S, Jin D et al. Neisseria chenwenguii sp. nov. isolated from the rectal contents of a plateau pika (Ochotona curzoniae). Antonie van Leeuwenhoek 2019; 112:1001–1010 [View Article][PubMed]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. 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 [View Article][PubMed]
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. 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 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  25. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article][PubMed]
    [Google Scholar]
  26. 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 [View Article][PubMed]
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. 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]
  32. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  33. Austrian R. The gram stain and the etiology of lobar pneumonia, an historical note. Bacteriol Rev 1960; 24:261–265 [View Article][PubMed]
    [Google Scholar]
  34. 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 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [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. 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]
  39. 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]
  40. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
    [Google Scholar]
  41. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  42. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  43. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article][PubMed]
    [Google Scholar]
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