Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand

Abstract

A novel actinomycete strain CYP1-5T was isolated from the mountain soil sample collected from Chaiyaphum province, Thailand and its taxonomic position was clarified by using a polyphasic taxonomic approach. The chemotaxonomic properties of strain CYP1-5T were consistent within the genus Actinomadura. Cell-wall peptidoglycan of this strain contained meso-diaminopimelic acid. Galactose, madurose, and ribose were presented as the diagnostic sugars in whole-cell hydrolysates. The major menaquinone was MK-9(H6). Major cellular fatty acids were iso-C16:0 and C16:0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside were observed as predominant phospholipids. Based on the results of phylogenetic analyses of 16S rRNA gene sequence, strain CYP1-5T was constituent with the genus Actinomadura and was closely related to Actinomadura syzygii GKU157T (99.5%) and Actinomadura chibensis IFM 10266T (= JCM 14158T) (98.2%). The draft genome size of strain CYP1-5T was 9.30 Mb with 72.2 mol% of G + C content. Strain CYP1-5T showed ANIb values of 94.9% with A. syzygii GKU157T and 93.2% with A. chibensis JCM 14158T. Phenotypic characteristics, phylogenetic analysis and genome data support that strain CYP1-5T could be discriminated from its closest relatives, representing a novel species of the genus Actinomadura, for which the name Actinomadura decatromicini sp. nov. is proposed. The type strain is CYP1-5T (= JCM 16996T = KCTC 19916T = TISTR 2901T).

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol. 1970;20:435–43.

    CAS  Google Scholar 

  2. Kroppenstedt RM, Stackebrandt E, Goodfellow M. Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol. 1990;13:148–60.

    CAS  Google Scholar 

  3. Kroppenstedt RM, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E, editors. The Prokaryotes, Archaea and Bacteria: Firmicutes, Actinomycetes.3rd ed, vol. 3. New York: Springer; 2006. pp. 682–724.

  4. Parte AC. List of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol. 2018;68:1825–9.

    PubMed  Google Scholar 

  5. Ara I, Matsumoto A, Bakir M, Kudo T, Omura S, Takahashi Y. Actinomadura maheshkhaliensis sp. nov., a novel actinomycete isolated from mangrove rhizosphere soil of Maheshkhali, Bangladesh. J Gen Appl Microbiol. 2008;54:335–42.

    CAS  PubMed  Google Scholar 

  6. He J, Xu Y, Sahu M, Tian XP, Nie GX, Xie Q, et al. Actinomadura sediminis sp. Nov., a marine actinomycete isolated from mangrove sediment. Int J Syst Bacteriol. 2011;62:1110–16.

    Google Scholar 

  7. Qin S, Zhao GZ, Li J, Zhu WY, Xu LH, Li WJ. Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis. Int J Syst Evol Microbiol. 2009;95:2453–7.

    Google Scholar 

  8. Qin S, Chen HH, Zhao GZ, Li J, Zhu WY, Xu LH, et al. Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods. Environ Microbiol Rep. 2012;4:522–31.

    PubMed  Google Scholar 

  9. Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y, Thamchaipenet A. Actinomadura syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels). Int J Syst Evol Microbiol. 2015;65:1946–9.

    CAS  PubMed  Google Scholar 

  10. Han XX, Cui CB, Gu QQ, Zhu W, Liu H, Gu JY, et al. ZHD-0501, a novel naturally occurring staurosporine analog from Actinomadura sp. 007. Tetrahedron Lett. 2005;46:6137–40.

    CAS  Google Scholar 

  11. Shaaban KA, Elshahawi SI, Wang X, Horn J, Kharel MK, Leggas M, et al. Cytotoxic indolocarbazoles from Actinomadura melliaura ATCC 39691. J Nat Prod. 2015;78:1723–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Takagi M, Motohashi K, Khan ST, Hashimoto J, Shin-ya K. JBIR-65, a new diterpene, isolated from a sponge-derived Actinomadura sp. SpB081030SC-15. J Antibiot. 2010;63:401–3.

    CAS  Google Scholar 

  13. Simmons L, Kaufmann K, Garcia R, Schwӓr G, Huch V, Muller R. Bendigoles D-F, bioactive sterols from the marine sponge-derived Actinomadura sp. SBMs009. Bioorg Med Chem. 2011;19:6570–75.

    CAS  PubMed  Google Scholar 

  14. Mazzei E, Iorio M, Maffioli F, Sosio M, Donadio S. Characterization of madurastatin C1, a novel siderophore from Actinomadura sp. J Antibiot. 2012;65:267–9.

    CAS  Google Scholar 

  15. Igarashi Y, Iida T, Oku N, Watanabe H, Furihata K, Miyanouchi K. Nomimicin, a new spirotetronate-class polyketide from an actinomycete of the genus Actinomadura. J Antibiot. 2012;65:355–9.

    CAS  Google Scholar 

  16. Kornsakulkarn J, Saepua S, Boonruangprapa T, Suphothina S, Thongpanchang C. New β-carboline and indole alkaloids from actinomycete Actinomadura sp. BCC 24717. Phytochem Lett. 2013;6:491–4.

    CAS  Google Scholar 

  17. Intaraudom C, Dramae A, Supothina S, Konwijit S, Pittayakhajonwut P. 3-Oxyanthranilic acid derivatives from Actinomadura sp. BCC 27169. Tetrahedron. 2014;70:2711–6.

    CAS  Google Scholar 

  18. Kusserow K, Gulder TAM. Complete genome sequence of Actinomadura parvosata subsp. kistnae, a rich source of novel natural product (Bio-) chemistry. J Genom. 2017;5:75–6.

    Google Scholar 

  19. Küster E, Williams ST. Selection of media for the isolation of Streptomycetes. Nature. 1964;202:928–9.

    Google Scholar 

  20. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol. 1966;16:313–40.

    Google Scholar 

  21. Kelly KL. Inter-Society Color Council—National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC: US Government Printing Office; 1964.

  22. Arai T. Culture media for Actinomycetes. Tokyo, Japan: The Society for Actinomycetes; 1975.

  23. Williams ST, Cross T. Actinomycetes. In: Methods in microbiology. London, Academic Press; 1971. p. 295–334.

  24. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol. 1974;28:226–31.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Mikami H, Ishida Y. Post-column fluorometric detection of reducing sugar in high-performance liquid chromatography using arginine. Bunseki Kagaku. 32: E207-E.2101983.

  26. 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;37:463–4.

    Google Scholar 

  27. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods. 1984;2:233–41.

    CAS  Google Scholar 

  28. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI, Inc; 1990.

  29. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroids. J Bacteriol. 1982;151:828–37.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol. 1977;100:221–30.

    CAS  PubMed  Google Scholar 

  31. Kudo T, Matsushima K, Itoh T, Sasaki J, Suzuki K. Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia. Int J Syst Bacteriol. 1998;48:1245–55.

    CAS  PubMed  Google Scholar 

  32. Suriyachadkun C, Chunhametha S, Thawai C, Tamura T, Potacharoen W, Kirtikara K, et al. Planotetraspora thailandica sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol. 2009;59:992–7.

    CAS  PubMed  Google Scholar 

  33. Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. New York, Wiley; 1991. p. 115–75.

  34. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98 NT. Nucleic acids Symp Ser. 1999;41:95–8.

    CAS  Google Scholar 

  35. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBiocloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–20.

    CAS  PubMed  Google Scholar 

  37. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

    CAS  PubMed  Google Scholar 

  38. Fitch WM. Toward defining the course of evolution: minimum change for specific tree topology. Syst Zool. 1971;20:406–16.

    Google Scholar 

  39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.

    CAS  PubMed  Google Scholar 

  40. Kumar S, Stecher G, Tamura K. MEGA 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

    PubMed  Google Scholar 

  42. 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;19:455–77.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, et al. The RAST Server: rapid annotations using subsystem technology. BMC Genom. 2008;9:75.

    Google Scholar 

  44. 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.

    PubMed  PubMed Central  Google Scholar 

  45. Ritcher M, Rosselló-Móra R. Shifting the genomics gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.

    Google Scholar 

  46. Ritcher M, Rosselló-Móra R, Glöckner FO, Peplies J. JspeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics. 2016;32:929–31.

    Google Scholar 

  47. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinforma. 2013;14:60.

    Google Scholar 

  48. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, et al. antiSMASH 5.0: update to the secondary metabolite genome mining pipeline. Nucleic Acid Res. 2019. https://doi.org/10.1093/nar/gkz310.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Goris J, Konstantinidis K, Klappenbach J, 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.

    CAS  PubMed  Google Scholar 

  50. Momose I, Iinuma H, Kinoshita N, Momose Y, Kunimoto S, Hamada M, et al. Decatromicins A and B, new antibiotics produced by Actinomadura sp. MK73-NF4. I. Taxonomy, isolation, physico-chemical properties and biological activities. J Antibiot. 1999;52:781–6.

    CAS  Google Scholar 

  51. Jørgensen H, Degnes KF, Sletta H, Fjaervik E, Dikiy A, Herfindal L, et al. Biosynthesis of macrolactam BE-14106 involves two distinct PKS systems and amino acid processing enzymes for generation of the aminoacyl starter unit. Chem Biol. 2009;16:1109–21.

    PubMed  Google Scholar 

  52. Mascaretti OA, Chang CJ, Hook D, Otsuka H, Kreutzer EF, Floss HG. Biosynthesis of the macrolide antibiotic chlorothricin. Biochemistry. 1981;20:919–24.

    CAS  PubMed  Google Scholar 

  53. Poralla K, Muth G, Härtner T. Hopanoids are formed during transition from substrate to aerial hyphae in Streptomyces coelicolor A3(2). FEMS Microbiol Lett. 2000;189:93–5.

    CAS  PubMed  Google Scholar 

  54. Gottardi EM, Krawczyk JM, von Suchodoletz H, et al. Abyssomicin biosynthesis: formation of an unusual polyketide, antibiotic-feeding studies and genetic analysis. Chembiochem. 2011;12:1401–10.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol. 2015;32:2798–800.

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat. 1972;106:645–67.

    Google Scholar 

Download references

Acknowledgements

This research is supported by Grant for International Research Integration: Research Pyramid, Ratchadaphiseksomphot Endowment Fund (GCURP_58_01_33_01). We also thank the Pharmaceutical Research Instrument Center, Faculty of Pharmaceutical Sciences, Chulalongkorn University, for providing research facilities.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Somboon Tanasupawat.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Songsumanus, A., Kuncharoen, N., Kudo, T. et al. Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand. J Antibiot 74, 51–58 (2021). https://doi.org/10.1038/s41429-020-0353-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41429-020-0353-y

Search

Quick links