1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 7

sp. nov., isolated from the foliose lichen, (Nyl.) Hale No Access

Abstract

A novel actinomycete strain PM05-2 was isolated from the lichen (Nyl.) Hale collected from Chaiyaphum Province, Thailand. The taxonomic position of the strain was studied using the polyphasic approach. Based on the morphology and chemotaxonomic properties, strain PM05-2 was identified as a member of the genus . The whole-cell hydrolysate contained -diaminopimelic acid, rhamnose, ribose, xylose, madurose, glucose and galactose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phosphoglycolipid, four unidentified phospholipids and one unidentified lipid. The menaquinones were MK-9(H), MK-9(H), MK-9(H), MK-9(H) and MK-9(H). The major cellular fatty acids were C and C ω9. Strain PM05-2 showed the highest 16S rRNA gene similarity to NBRC 15177 (98.58%), NBRC 14229 (98.29 %) and DSM 44197 (98.14 %). The phylogenetic tree analysis revealed that strain PM05-2 was related to NBRC 15177, NBRC 14229, DSM 44197 and RB68. The genomic analysis revealed that average nucleotide identity values based on both and MUMmer between strain PM05-2 and the relative type strains ranged from 77.6 to 86.4%. The digital DNA–DNA hybridization values among the strains were lower than the threshold for assigning to the same species. The taxonomic results suggested that strain PM05-2 represented a novel species of the genus for which the name is proposed. The type strain is PM05-2 (=TBRC 15492=NBRC 115416).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinobacteria , lichen , Parmotrema and rare Actinobacteria
Funding
This study was supported by the:
  • Faculty of Pharmaceutical Sciences, Chulalongkorn University
    • Principle Award Recipient: PhongsopitanunWongsakorn
  • National Research Council of Thailand
    • Principle Award Recipient: VasunPeongsungnone
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005447
2022-07-11
2024-04-28
Loading full text...

Full text loading...

References

  1. Lechevalier HA, Lechevalier MP. A critical evaluation of the genera of aerobic actinomycetes. In Prauser H. eds The Actinomycetales Jena: VEB Gustav Fischer Verlag; 1970 pp 395–405
     [Google Scholar]
  2. Trujillo ME, Goodfellow M. Genus III. Actinomadura Lechevalier and Lechevalier 1970, 400AL emend. Kroppenstedt, Stackebrandt and Goodfellow 1990, 156. In Goodfellow M, Kämpfer P, Busse MJ, Trujillo ME, Suzuki KL. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 5 New York: Springer; 2012 pp 1940–1959
     [Google Scholar]
  3. Li L, Xu QH, Wang XT, Lin HW, Lu YH. Actinomadura craniellae sp. nov., isolated from a marine sponge in the South China Sea. Int J Syst Evol Microbiol 2019; 69:1207–1212 [View Article] [PubMed]
     [Google Scholar]
  4. He J, Xu Y, Sahu MK, Tian XP, Nie GX et al. Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2012; 62:1110–1116 [View Article] [PubMed]
     [Google Scholar]
  5. Rachniyom H, Matsumoto A, Inahashi Y, Take A, Takahashi Y et al. Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn. Int J Syst Evol Microbiol 2018; 68:1584–1590 [View Article] [PubMed]
     [Google Scholar]
  6. Benndorf R, Martin K, Küfner M, de Beer ZW, Vollmers J et al. Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis. Int J Syst Evol Microbiol 2020; 70:5255–5262 [View Article]
     [Google Scholar]
  7. Kanchanasin P, Phongsopitanun W, Yuki M, Kudo T, Ohkuma M et al. Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  8. Lichon V, Khachemoune A. Mycetoma: a review. Am J Clin Dermatol 2006; 7:315–321 [View Article] [PubMed]
     [Google Scholar]
  9. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  10. van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA et al. The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res 2022; 50:D1317–D1323 [View Article] [PubMed]
     [Google Scholar]
  11. Kimura T, Iwatsuki M, Asami Y, Ishiyama A, Hokari R et al. Anti-trypanosomal compound, sagamilactam, a new polyene macrocyclic lactam from Actinomadura sp. K13-0306. J Antibiot 2016; 69:818–824 [View Article] [PubMed]
     [Google Scholar]
  12. Mazzei E, Iorio M, Maffioli SI, Sosio M, Donadio S. Characterization of madurastatin C1, a novel siderophore from Actinomadura sp. J Antibiot 2012; 65:267–269 [View Article] [PubMed]
     [Google Scholar]
  13. Saepua S, Kornsakulkarn J, Choowong W, Suriyachadkun C, Boonlarppradab C et al. Antimicrobial and cytotoxic angucyclic quinones from Actinomadura miaoliensis. J Nat Prod 2021; 84:2775–2785 [View Article] [PubMed]
     [Google Scholar]
  14. Shin B, Kim B-Y, Cho E, Oh K-B, Shin J et al. Actinomadurol, an antibacterial norditerpenoid from a rare actinomycete, Actinomadura sp. KC 191. J Nat Prod 2016; 79:1886–1890 [View Article] [PubMed]
     [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt S, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–148
     [Google Scholar]
  17. 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]
  18. 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] [PubMed]
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  21. Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010 http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  22. Krueger F. Trim galore!: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files; 2015 http://www.bioinformatics.babraham.ac.uk/projects/trim_ galore/
  23. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  24. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. 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]
  27. Kelly KL. Inter-Society Color Council - National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  28. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  29. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
     [Google Scholar]
  30. Williams ST, Cross T. Chapter XI Actinomycetes. Methods Microbiol 1971; 4:295–334
     [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  35. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  36. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005447
Loading
Actinomadura parmotrematis sp. nov., isolated from the foliose lichen, Parmotrema praesorediosum (Nyl.) Hale
Int J Syst Evol Microbiol 72, 005447 (2022); https://doi.org/10.1099/ijsem.0.005447
/content/journal/ijsem/10.1099/ijsem.0.005447
/content/journal/ijsem/10.1099/ijsem.0.005447
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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