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Abstract

A novel Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile, rod-shaped bacterium, designated strain YIM M12148, was isolated from a marine sediment sample collected from the Indian Ocean. The strain grew optimally at 28 °C, pH 8.0 and in the presence of 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M12148 belongs to the genus , with the highest sequence similarity to NBRC 15706 (96.12 %). The cell-wall sugars of strain YIM M12148 were rhamnose, ribose, glucose and mannose. The predominant isoprenoid quinones were MK-8 and MK-9. The polar lipids consisted of major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown lipid. Major fatty acids (>5 % of the total) of the novel isolate were anteiso-C, iso-C, iso-C and anteiso-C. The genomic DNA G+C content of strain YIM M12148 was 67.15 mol%. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M12148 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM M12148 (=KCTC 29660=DSM 29154).

Funding
This study was supported by the:
  • Natural Science Foundation of Xizang (Tibet) Autonomous Region (Award XZ202001ZR0018G)
    • Principle Award Recipient: ZhaoJiang
  • Research Program of Xizang Minzu University (Award 19MDX01)
    • Principle Award Recipient: ZhaoJiang
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2021-07-22
2021-07-29
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References

  1. Manaia CM, Nogales B, Weiss N, Nunes OC. Gulosibacter molinativorax gen. nov. sp. nov. a molinate-degrading bacterium, and classification of “Brevibacterium helvolum” DSM 20419 as Pseudoclavibacter helvolus gen. nov. sp. nov. Int J Syst Evol Microbiol 2004; 54:783–789 [View Article] [PubMed]
    [Google Scholar]
  2. Park MH, Traiwan J, Jung MY, Kim W. Gulosibacter chungangensis sp. nov. an actinomycete isolated from a marine sediment, and emended description of the genus Gulosibacter. Int J Syst Evol Microbiol 2012; 62:1055–1060 [View Article] [PubMed]
    [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; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  4. Li GD, Li QY, Chen X, Jiang LQ, Zhang K et al. Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces. Int J Syst Evol Microbiol 2020; 70:5115–5122 [View Article]
    [Google Scholar]
  5. Jiang Y, Tang SK, Wiese J, Xu LH, Imhoff J et al. Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces. Int J Syst Evol Microbiol 2007; 57:2694–2698 [View Article]
    [Google Scholar]
  6. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428
    [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxoni-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  8. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  12. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011; 28:2731–2739 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [View Article]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  16. 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 [View Article] [PubMed]
    [Google Scholar]
  17. Hyatt D, Chen GL, 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]
  18. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
    [Google Scholar]
  19. Katoh K, Misawa K, Kuma K, Miyata T. Mafft: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
    [Google Scholar]
  20. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
    [Google Scholar]
  21. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Skerman VBD. A guide to the identification of the genera of bacteria ED. 2. Quarterly Review of Biology 1967; 36:870
    [Google Scholar]
  26. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family Oxalobacteraceae isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153
    [Google Scholar]
  27. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. Williams S, Sharpe M, Holt J. eds In Bergey’s Manual of Systematic Bacteriology Vol 4 Baltimore, MD: Williams and Willkins; 1989 pp 2453–2492
    [Google Scholar]
  28. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  29. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycani based on 2,4-diaminobutyric acid. Appl Bacteriol 1980; 48:459–470
    [Google Scholar]
  30. 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]
  31. 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]
  32. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  33. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  34. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article] [PubMed]
    [Google Scholar]
  35. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
  36. Kim MK, Jung HY. Pseudoclavibacter soli sp. nov. a β-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2009; 59:835–838 [View Article] [PubMed]
    [Google Scholar]
  37. Cho SL, Jung MY, Park MH, Chang YH, Yoon JH et al. Pseudoclavibacter chungangensis sp. nov. isolated from activated sludge. Int J Syst Evol Microbiol 2010; 60:1672–1677 [View Article] [PubMed]
    [Google Scholar]
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