1887

Abstract

A novel mycelium-forming actinomycete strain, designated A-F 0318, was isolated from a yellow-ringed grass moth () collected from Phitsanulok Province, Thailand. Long chains of non-motile cylindrical spores with a smooth surface developed on aerial mycelia. The polyphasic taxonomic study suggested that strain A-F 0318 belonged to the genus . The 16S rRNA gene sequence analysis indicated that strain A-F 0318 was closely related to LL-DO5139 with 97.94 % sequence similarity. The average nucleotide identity (ANI) based on , ANI based on the MUMmer algorithm and average amino acid identity values of strain A-F 0318 with LL-DO5139 were 86.9, 89.1 and 84.24 %, respectively. The digital DNA–DNA hybridization value between A-F 0318 and its closest relative, LL-DO5139 was 33.8 %. The digital G+C content of the genomic DNA was 71.7 mol%. The cell-wall peptidoglycan contained -diaminopimelic acid. The whole-cell sugars contained ribose, xylose, glucose and galactose. The predominant menaquinone was MK-10(H). The predominant fatty acids were iso-C, anteiso-C, anteiso-C and iso-C G. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phosphoglycolipids and one unknown phospholipid. Based on comparative analysis of genotypic, phenotypic and chemotaxonomic data, the novel actinomycete strain A-F 0318 (=TBRC 13612=NBRC 115417) represents the type strain of a novel species, for which the name sp. nov. is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005604
2022-11-09
2024-02-27
Loading full text...

Full text loading...

References

  1. Labeda DP, Testa RT, Lechevalier MP, Lechevalier HA, Glycomyces LHA. Glycomyces, a new genus of the Actinomycetales. Int J Syst Bacteriol 1985; 35:417–421 [View Article]
    [Google Scholar]
  2. Labeda DP, Kroppenstedt RM. Emended description of the genus Glycomyces and description of Glycomyces algeriensis sp. nov., Glycomyces arizonensis sp. nov. and Glycomyces lechevalierae sp. nov. Int J Syst Evol Microbiol 2004; 54:2343–2346 [View Article]
    [Google Scholar]
  3. Li W, Liu C, Guo X, Song W, Sun T et al. Glycomyces tritici sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Glycomyces. Antonie van Leeuwenhoek 2018; 111:1087–1093 [View Article]
    [Google Scholar]
  4. Mu S, Sun T, Li Y, Jiang S, Guo X et al. Glycomyces dulcitolivorans sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2018; 68:3034–3039 [View Article]
    [Google Scholar]
  5. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  6. Santamaría RI, Martínez-Carrasco A, Sánchez de la Nieta R, Torres-Vila LM, Bonal R et al. Characterization of actinomycetes strains isolated from the intestinal tract and feces of the larvae of the longhorn beetle Cerambyx welensii. Microorganisms 2020; 8(12):E2013 [View Article]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  9. SAITO H, MIURA KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article]
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. 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]
    [Google Scholar]
  12. 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]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. 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]
  19. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  20. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985; 22:160–174
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  22. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article]
    [Google Scholar]
  23. 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]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. 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]
    [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 e1900v1 [View Article]
    [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  28. 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]
    [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]
    [Google Scholar]
  30. 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]
    [Google Scholar]
  31. 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]
  32. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  33. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 e73 [View Article]
    [Google Scholar]
  34. 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 [View Article]
    [Google Scholar]
  35. Itoh T, Kudo T, Parenti F, Seino A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 1989; 39:168–173 [View Article]
    [Google Scholar]
  36. 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]
  37. 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]
  38. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
    [Google Scholar]
  39. Williams ST, Cross T. Actinomycetes. Methods Microbiol 1971; 4:295–334
    [Google Scholar]
  40. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
    [Google Scholar]
  41. 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]
  42. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  43. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  44. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology (English translation of Mikrobiologiia) 1989; 16:176–178
    [Google Scholar]
  45. 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]
  46. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids. MIDI; 2001
  47. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol 1982; 151:828–837 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005604
Loading
/content/journal/ijsem/10.1099/ijsem.0.005604
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error