1887

Abstract

A novel acid-tolerant actinobacterium (strain LPG 2), which formed fragmented substrate mycelia, was isolated from bio-fertiliser of spp. collected from Lampang Province, Thailand. Its morphological and chemotaxonomic properties, e.g., the presence of mycolic acid and MK-8 (H) in the cells, showed that strain LPG 2 was a member of the genus . 16S rRNA gene sequence analysis revealed that this strain was closely related to NBRC 14405 (98.7 %). The low average nucleotide identity– and digital DNA–DNA hybridization values (<78.6 and <24.0 %, respectively), and several phenotypic differences between strain LPG 2 and its related type strains, indicated that the strain merits classification as representing a novel species of the genus , for which we propose the name sp. nov. The type strain is LPG 2 (=TBRC 11242=NBRC 114293).

Funding
This study was supported by the:
  • King Mongkut’s Institute of Technology Ladkrabang Research Fund (Award RE-KRIS/005/64)
    • Principle Award Recipient: ChittiThawai
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005170
2021-12-20
2024-12-05
Loading full text...

Full text loading...

References

  1. Goodfellow M, Jones AL, Order V et al. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. eds Bergey’s Manual of Systematic Bacteriology, 2nd ed. edn vol. 5 New York: Springer; 2012 pp 232–243
    [Google Scholar]
  2. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article] [PubMed]
    [Google Scholar]
  3. Goodfellow M, Lechevalier MP. Genus Nocardia Trevisan 1889, 9AL. In Williams ST, Sharpe ME, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams &Wilkins; 1989 pp 2348–2361
    [Google Scholar]
  4. Li S, Ming H, Duan Y-Y, Huang J-R, Zhao Z-L et al. Nocardia tengchongensis sp. nov., isolated from a soil sample. Antonie van Leeuwenhoek 2017; 110:1149–1155 [View Article] [PubMed]
    [Google Scholar]
  5. Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W et al. Nocardia terrae sp. nov., an actinomycete isolated from soil in Thailand. Arch Microbiol 2021; 203:1071–1077 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang J-X, Ming H, Zhao Z-L, Ji W-L, Chang X-L et al. Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample. Int J Syst Evol Microbiol 2019; 69:3116–3120 [View Article] [PubMed]
    [Google Scholar]
  7. Orchard VA. Effect of sewage sludge additions on Nocardia in soil. Soil Biol Biochem 1979; 11:217–220 [View Article]
    [Google Scholar]
  8. Orchard VA. The ecology of Nocardia and related taxa. Zentralbl Bakteriol Supp 1981; 11:167–180
    [Google Scholar]
  9. Kämpfer P, Huber B, Buczolits S, Thummes K, Grün-Wollny I et al. Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli. Int J Syst Evol Microbiol 2007; 57:1183–1187 [View Article] [PubMed]
    [Google Scholar]
  10. Golinska P, Wang D, Goodfellow M. Nocardia aciditolerans sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013; 103:1079–1088 [View Article] [PubMed]
    [Google Scholar]
  11. Cui Q, Wang L, Huang Y, Liu Z, Goodfellow M. Nocardia jiangxiensis sp. nov. and Nocardia miyunensis sp. nov., isolated from acidic soils. Int J Syst Evol Microbiol 2005; 55:1921–1925 [View Article] [PubMed]
    [Google Scholar]
  12. Eroksuz Y, Gursoy NC, Karapinar T, Karabulut B, Incili CA et al. Systemic nocardiosis in a dog caused by Nocardia cyriacigeorgica. BMC Vet Res 2017; 13:30–35 [View Article] [PubMed]
    [Google Scholar]
  13. Zhou T, Wang X-Y, Deng D-Q, Xu L-H, Li X-L et al. Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis. Int J Syst Evol Microbiol 2020; 70:2981–2987 [View Article] [PubMed]
    [Google Scholar]
  14. Lotte R, Chevalier A, Dantas S, Degand N, Gaudart A et al. Nocardia takedensis: a newly recognized pathogen responsible for skin and soft tissue infections. Ann Clin Microbiol Antimicrob 2020; 19:38–45 [View Article] [PubMed]
    [Google Scholar]
  15. Moniuszko-Malinowska A, Czupryna P, Swiecicka I, Grześ H, Siemieniako A et al. Nocardia farcinica as a cause of chronic meningitis - case report. BMC Infect Dis 2020; 20:56–61 [View Article] [PubMed]
    [Google Scholar]
  16. Goodfellow M, Maldonado LA. Genus I. Nocardia Trevisan 1889. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I. eds Bergey’s Manual of Systematic Bacteriology, the Actinobacteria, 2nd edn. New York: Springer; 2012 pp 376–419
    [Google Scholar]
  17. Tay ST, Wong PL, Chiu C-K, Tang SN, Lee JL et al. Nocardia kroppenstedtii: a rare pathogen isolated from the spinal vertebral abscess of a patient on long-term immunosuppressive therapy. Eur Rev Med Pharmacol Sci 2021; 25:605–608 [View Article] [PubMed]
    [Google Scholar]
  18. Dhakal D, Rayamajhi V, Mishra R, Sohng JK. Bioactive molecules from Nocardia: diversity, bioactivities and biosynthesis. J Ind Microbiol Biotechnol 2019; 46:385–407 [View Article] [PubMed]
    [Google Scholar]
  19. Kavitha A, Prabhakar P, Vijayalakshmi M, Venkateswarlu Y. Production of bioactive metabolites by Nocardia levis MK-VL_113. Lett Appl Microbiol 2009; 49:484–490 [View Article] [PubMed]
    [Google Scholar]
  20. Kavitha A, Prabhakar P, Narasimhulu M, Vijayalakshmi M, Venkateswarlu Y et al. Isolation, characterization and biological evaluation of bioactive metabolites from Nocardia levis MK-VL_113. Microbiol Res 2010; 165:199–210 [View Article] [PubMed]
    [Google Scholar]
  21. Kawada M, Inoue H, Ohba S, Hatano M, Amemiya M et al. Intervenolin, a new antitumor compound with anti-Helicobacter pylori activity, from Nocardia sp. ML96-86F2. J Antibiot 2013; 66:543–548 [View Article]
    [Google Scholar]
  22. Hara S, Ishikawa N, Hara Y, Nehira T, Sakai K et al. Nabscessins A and B, aminocyclitol derivatives from Nocardia abscessus IFM 10029T. J Nat Prod 2017; 80:565–568 [View Article] [PubMed]
    [Google Scholar]
  23. Zhang J, Zhang L. Improvement of an isolation medium for Actinomycetes. MAS 2011; 5:124–127 [View Article]
    [Google Scholar]
  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  25. 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]
  26. Chapin KC, Murray PR. Stains. In Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH. eds Manual of Clinical Microbiology Washington, DC: American Society for Microbiology; 1999 p 1678
    [Google Scholar]
  27. Waksman SA. The Actinomycetes, vol. 2, Classification, Identification and Description of Genera and Species Baltimore: Williams & Wilkins; 1961
    [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. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
    [Google Scholar]
  30. Williams ST, Cross T. Actinomycetes. In Booth C. eds Methods in Microbiology vol. 4 London: Academic Press; 1971 pp 295–334
    [Google Scholar]
  31. 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]
  32. 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]
  33. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  34. 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]
  35. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  36. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  37. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [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. 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]
  40. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatog A 1980; 188:221–233 [View Article]
    [Google Scholar]
  41. Tamaoka J. Determination of DNA Base Composition. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 463–470
    [Google Scholar]
  42. Thawai C. Micromonospora costi sp. nov., isolated from a leaf of Costus speciosus. Int J Syst Evol Microbiol 2015; 65:1456–1461 [View Article]
    [Google Scholar]
  43. 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]
  44. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. 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]
  48. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  49. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  50. 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]
  51. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  52. 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]
  53. 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]
  54. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article] [PubMed]
    [Google Scholar]
  55. 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]
  56. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  57. Goodfellow M. Nocardia and related genera. In Topley and Wilson’s Microbiology and Microbial Infections, 9th Edn, Vol. 2, Systematic Bacteriology London: Arnold; 1998 pp 463–489
    [Google Scholar]
  58. Goodfellow M, Isik K, Yates E. Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold 1999; 80:47–82
    [Google Scholar]
  59. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  60. Kageyama A, Yazawa K, Taniguchi H, Chibana H, Nishimura K et al. Nocardia concava sp. nov., isolated from Japanese patients. Int J Syst Evol Microbiol 2005; 55:2081–2083 [View Article] [PubMed]
    [Google Scholar]
  61. Kudo T, Hatai K, Seino A. Nocardia seriolae sp. nov. causing nocardiosis of cultured fish. Int J Syst Bacteriol 1988; 38:173–178 [View Article]
    [Google Scholar]
  62. 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]
  63. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. 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]
  64. 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]
  65. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
    [Google Scholar]
  66. Kageyama A, Yazawa K, Nishimura K, Mikami Y. Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 2004; 54:563–569 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005170
Loading
/content/journal/ijsem/10.1099/ijsem.0.005170
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