1887

Abstract

A novel actinomycete, designated strain ASG 168, was isolated from cave rock collected from Stegodon Sea Cave in Thailand. Long chains of non-motile spores that were oval or spherical in shape with a smooth surface developed on aerial mycelia. Substrate mycelia fragmented into irregular rod-shaped elements. A polyphasic taxonomic study showed that strain ASG 168 had typical characteristics of members of the genus . 16S rRNA gene sequence analysis indicated that strain ASG 168 shared 97.5 % similarity with MS498 and 96.7 % with SCSIO 11529. Average nucleotide identity values with SCSIO 11529 and MS498 were 82.98 and 76.08 %, respectively. The cell-wall peptidoglycan contained -diaminopimelic acid. The whole-cell sugars contained ribose, arabinose and galactose. The predominant menaquinone was MK-9(H). The predominant fatty acids were iso-C, C and summed feature 3 (C 7/C 6). The phospholipid profile consisted of phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 70.6 mol%. Differentiation of strain ASG 168 from closely related species was evident from digital DNA–DNA hybridization values of 29.2 and 21.3 % with and , respectively. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, the novel actinomycete strain ASG 168 (=TBRC 13679=NBRC 114887) is proposed to be the type strain of a novel species, sp. nov.

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2021-11-22
2021-12-03
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References

  1. Kim SB, Goodfellow M. Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:507–512 [View Article]
    [Google Scholar]
  2. Wang J, Li Y, Bian J, Tang S-K, Ren B et al. Prauserella marina sp. nov., isolated from ocean sediment of the South China Sea. Int J Syst Evol Microbiol 2010; 60:985–989 [View Article] [PubMed]
    [Google Scholar]
  3. Suriyachadkun C, Chunhametha S, Thawai C, Tamura T, Potacharoen W et al. Planotetraspora thailandica sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol 2009; 59:992–997 [View Article] [PubMed]
    [Google Scholar]
  4. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  5. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article] [PubMed]
    [Google Scholar]
  6. Pootakham W, Mhuantong W, Yoocha T, Putchim L, Sonthirod C et al. High resolution profiling of coral-associated bacterial communities using full-length 16s rrna sequence data from Pacbio SMRT Sequencing System. Sci Rep 2017; 7:2774 [View Article] [PubMed]
    [Google Scholar]
  7. 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]
  8. 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]
  9. Hall TA. Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  10. 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]
  11. Felsenstein J. Parsimony in systematics: Biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  15. Chen S, Zhou Y, Chen Y, Gu J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:884–890
    [Google Scholar]
  16. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article] [PubMed]
    [Google Scholar]
  17. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. Spades: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  18. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. Jspeciesws: A web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  19. Rodriguez-R LM, Konstantinidis KT. The Enveomics collection: A toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Preprints 2016e1900v1
    [Google Scholar]
  20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  21. Lefort V, Desper R, Gascuel O. Fastme 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Kanehisa M, Sato Y, Morishima K. Blastkoala and Ghostkoala: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  24. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. Antismash 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
    [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article] [PubMed]
    [Google Scholar]
  26. Luo C, Rodriguez-R LM, Konstantinidis KT. Mytaxa: An advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  27. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the AD Hoc committee on Reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  28. Kelly KL. Inter-Society Color Council – National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  29. 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]
  30. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan (in Japanese); 1975
    [Google Scholar]
  31. Williams ST, Cross T. Actinomycetes. Methods Microbiol 1971; 4:295–334
    [Google Scholar]
  32. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  33. Uchida K, Aida K. An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 1984; 30:131–134 [View Article]
    [Google Scholar]
  34. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  35. 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]
  36. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 2001; 101:
    [Google Scholar]
  37. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol 1982; 151:828–837 [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176
    [Google Scholar]
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