1887

Abstract

Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512 and dk508) were isolated from the faeces of Tibetan gazelle () collected from the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed the highest identity to K-1 (98.0 and 97.9 % similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512 and dk508 were members of the genus , and most closely related to strains M4-8 and FCC-01. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0 % (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0 % (w/v) NaCl. The genome of type strain dk512 was 3.8 Mb with a G+C content of 70.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain dk512 and previously characterized species were <95 and <70 %, respectively. In strain dk512, the detected primary cellular fatty acids were anteiso-C and anteiso-C, the main respiratory quinones were MK-9 (37.9 %) and MK-10 (35.7 %), and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. The major cell-wall sugars were rhamnose, ribose and galactose. Alanine, glutamic acid, glycine and ornithine were in the cell-wall peptidoglycan. Based on phenotypic data and phylogenetic inference, these two strains represent a novel species of the genus , named here as sp. nov, where dk512 is designated the type strain (=CGMCC 1.16590=JCM 33494=KCTC 49313).

Funding
This study was supported by the:
  • Chinese Academy of Medical Sciences the Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
  • National Key R&D Program of China (Award 2018YFC1200102)
  • the National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: Shan Lu
  • the National Science and Technology Major Project of China (Award 2018ZX10712001-007)
    • Principle Award Recipient: Jing Yang
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2019-12-12
2024-12-10
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References

  1. Orla-Jensen S. The lactic acid bacteria, Copenhagen. Andr Fred Host and Sons imp 1919
    [Google Scholar]
  2. 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; 48:739–747 [View Article]
    [Google Scholar]
  3. Ling L, Zhao J, Li X, Zhang X, Jiang H et al. Microbacterium bovistercoris sp. nov., a novel actinomycete isolated from cow dung. Int J Syst Evol Microbiol 2019; 69:2703–2708 [View Article]
    [Google Scholar]
  4. Zhu ZN, Li YR, Li YQ, Xiao M, Han MX et al. Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica. Int J Syst Evol Microbiol 2019; 69:411–416 [View Article]
    [Google Scholar]
  5. Kim YJ, Roh SW, Jung MJ, Kim MS, Park EJ et al. Microbacterium mitrae sp. nov., isolated from salted turban shell. Int J Syst Evol Microbiol 2011; 61:399–403 [View Article]
    [Google Scholar]
  6. Kim KK, Lee KC, Oh HM, Lee JS. Microbacterium aquimaris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:1616–1620 [View Article]
    [Google Scholar]
  7. Kook M, Son HM, Yi TH. Microbacterium kyungheense sp. nov. and Microbacterium jejuense sp. nov., isolated from salty soil. Int J Syst Evol Microbiol 2014; 64:2267–2273 [View Article]
    [Google Scholar]
  8. Wu YH, Wu M, Wang CS, Wang XG, Yang JY et al. Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments. Int J Syst Evol Microbiol 2008; 58:2930–2934 [View Article]
    [Google Scholar]
  9. Gao JL, Sun P, Wang XM, Lv FY, Sun JG. Microbacterium zeae sp. nov., an endophytic bacterium isolated from maize stem. Antonie van Leeuwenhoek 2017; 110:697–704 [View Article]
    [Google Scholar]
  10. Kämpfer P, Rekha PD, Schumann P, Arun AB, Young CC et al. Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems. Int J Syst Evol Microbiol 2011; 61:1334–1337 [View Article]
    [Google Scholar]
  11. Chen X, Li GD, Li QY, Xu FJ, Jiang CL et al. Microbacterium faecale sp. nov., isolated from the faeces of Columba livia. Int J Syst Evol Microbiol 2016; 66:4445–4450 [View Article]
    [Google Scholar]
  12. Chen X, Li QY, Li GD, Xu FJ, Jiang Y et al. Microbacterium gilvum sp. nov., isolated from civet faeces. Antonie van Leeuwenhoek 2016; 109:1177–1183 [View Article]
    [Google Scholar]
  13. 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]
  14. 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]
  15. 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]
  16. Li J, Lu S, Jin D, Yang J, Lai XH 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 [View Article]
    [Google Scholar]
  17. Yoon SH, Ha SM, 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]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  20. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [View Article]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  22. 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]
    [Google Scholar]
  23. Ohta Y, Ito T, Mori K, Nishi S, Shimane Y et al. Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory. Int J Syst Evol Microbiol 2013; 63:2765–2769 [View Article]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. Zheng H, Ji S, Lan R, Liu Z, Bai X et al. Population analysis of Streptococcus suis isolates from slaughtered swine by use of minimum core genome sequence typing. J Clin Microbiol 2014; 52:3568–3572 [View Article]
    [Google Scholar]
  26. Chin C-S, 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]
  27. 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]
  28. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article]
    [Google Scholar]
  29. Cheng LJ, Ming H, Zhao ZL, Ji WL, Zhang LY et al. Microbacterium ureisolvens sp. nov., isolated from a Yellow River sample. Int J Syst Evol Microbiol 2019; 69:560–566 [View Article]
    [Google Scholar]
  30. 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]
  31. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article]
    [Google Scholar]
  32. 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]
  33. 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 [View Article]
    [Google Scholar]
  34. 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 [View Article]
    [Google Scholar]
  35. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386–2392 [View Article]
    [Google Scholar]
  36. Anandham R, Tamura T, Hamada M, Weon HY, Kim SJ et al. Microbacterium suwonense sp. nov., isolated from cow dung. J Microbiol 2011; 49:852–856 [View Article]
    [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990; 101:1–7
    [Google Scholar]
  38. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  39. Collins M, Pirouz T, Goodfellow M, Minnikin D. Distribution of menaquinones in actinomycetes and corynebacteria. Microbiology 1977; 100:221–230
    [Google Scholar]
  40. 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]
  41. Lechevalier M. The chemotaxonomy of Actinomycetes . Actinomycete Taxonomy 1980227–291
    [Google Scholar]
  42. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407
    [Google Scholar]
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