1887

Abstract

The 16S-23S internally transcribed spacer (ITS) sequences were analysed to clarify inter-and intraspecific relationships among strains of the genus and the relationship between two species. The 16S-23S ITS regions from 33 strains, two species and were sequenced directly after polymerase chain reaction (PCR) amplification and λ exonuclease treatment. The genomes of some strains included two types of 16S-23S ITS sequences. The sizes of the 16S-23S ITS sequences of strains ranged from 328 to 539 bp. The 16S-23S ITS sequences of NSP37, NSP38and NSP39were 349, 355 and 386 bp long, respectively. Nucleotide similarity among 16S-23S ITS sequences of strains and of strains was 84·1-100% and 97·7-100%, respectively. The 16S-23S ITS sequence of was identical to that of NSP32and was only 1 bp different from that of strains. However, the 16S-23S ITS sequences of NSP32showed only a low degree of similarity to NSP32(54·8%). The degree of 16S-23S ITS similarity between NSP20and strains ranged from 85 to 93%. The mean nucleotide similarity values between the type strains of validly described species were highly divergent at 68·1±16·8%. The two species showed a level of 16S-23S ITS similarity of 71·2%. In this study, 16S-23S ITS sequences of the members of the genera and were useful for inferring the relationships between closely related strains and species. However, they were not found to be appropriate for elucidating the phylogenetic relationships between distantly related organisms at the genus level.

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1998-07-01
2022-12-06
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References

  1. Baylis H. A., Bibb M. J. 1988; Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2). Mol Microbiol 2:569–579
    [Google Scholar]
  2. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. 1981; Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107–127
    [Google Scholar]
  3. Collins M. D., Stackebrandt E. 1989; Molecular taxonomic studies on some LL-diaminopimelic acid-containing coryneforms from herbage: description of Nocardioides fastidiosa sp. nov. FEMS Microbiol Lett 57:289–294
    [Google Scholar]
  4. Collins M. D., Dorsch M., Stackebrandt E. 1989; Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39:1–6
    [Google Scholar]
  5. Collins M. D., Cockcroft S., Wallbanks S. 1994; Phylogenetic analysis of a new LL-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov. Int J Syst Bacteriol 44:523–526
    [Google Scholar]
  6. Dolzani L., Tonin E., Lagatolla C., Monti-Bragadin C. 1994; Typing of Staphylococcus aureus by amplification of the 16S-23S rRNA intergenic spacer sequences. FEMS Microbiol Lett 119:167–174
    [Google Scholar]
  7. French J. C., Howells J. D., Anderson L. E. 1970; US patent 3 551 294.
    [Google Scholar]
  8. Goodfellow M. 1989; Genus Rhodococcus Zopf 1891, 28AL. In Bergey's Manual of Systematic Bacteriology vol 4 pp 2362–2371 Edited by Williams S. T., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  9. Gray P. H. H., Thornton H. G. 1928; Soil bacteria that decompose certain aromatic compounds. Zentbl Bakteriol Parasitenkd Infektkrankh Hyg Abt II 73:74–96
    [Google Scholar]
  10. Green C. J., Void B. S. 1983; Sequence analysis of a cluster of twenty-one tRNA genes in Bacillus subtilis. Nucleic Acids Res 11:5763–5774
    [Google Scholar]
  11. Green C. J., Stewart G. C., Hollis M. A., Void B. S., Bott K. F. 1985; Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB. Gene 37:261–266
    [Google Scholar]
  12. Gürtler V., Stanisich V. A. 1996; New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142:3–16
    [Google Scholar]
  13. Hain T., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E., Rainey F. A. 1997; Discrimination of Streptomyces albido- flavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers. Int J Syst Bacteriol 47:202–206
    [Google Scholar]
  14. Kim E., Kim H., Hong S.-P., Kang K. H., Kho Y. H., Park Y.-H. 1993; Gene organization and primary structure of a ribosomal RNA gene cluster from Streptomyces griseus subsp. griseus. Gene 132:21–31
    [Google Scholar]
  15. Kim S.-B., Yoon J.-H., Kim H., Lee S.T., Park Y.-H., Goodfellow M. 1995; A phylogenetic analysis of the genus Saccharomonospora conducted with 16S rRNA gene sequences. Int J Syst Bacteriol 45:351–356
    [Google Scholar]
  16. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L. 1985; Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959
    [Google Scholar]
  17. Leblond-Bourget N., Philippe H., Mangin I., Decaris B. 1996; 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phy- logeny. Int J Syst Bacteriol 46:102–111
    [Google Scholar]
  18. Lechevalier M. P., Lechevalier H. A. 1970; A critical evaluation of the genera of aerobic actinomycetes. In The Actino- mycetales pp 393405 Edited by Prauser H. Jena: Gustav Fischer Verlag;
    [Google Scholar]
  19. Lee S.-T., Rhee S.-K., Lee G. M. 1994; Biodegradation of pyridine by freely suspended and immobilized Pimelobacter sp. Appl Microbiol Biotechnol 41:652–657
    [Google Scholar]
  20. Lu Y., Yan X. 1983; Studies of the classification of thermophilic actinomycetes: determination of thermophilic members of Nocardiaceae . Acta Microbiol Sinica 23:220–228
    [Google Scholar]
  21. Miller E. S., Woese C. R., Brenner S. 1991; Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov. Int J Syst Bacteriol 41:363–368
    [Google Scholar]
  22. Navarro E., Simonet P., Normand P., Bardin R. 1992; Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol 157:107–115
    [Google Scholar]
  23. Normand P., Cournoyer B., Simonet P., Nazaret S. 1992; Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene 111:119–124
    [Google Scholar]
  24. O'Donnell A. G., Goodfellow M., Minnikin D. E. 1982; Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O’Donnell et al., as Nocardioides simplex comb. nov. Arch Microbiol 133:323–329
    [Google Scholar]
  25. Pernodet J.-L., Boccard F., Alegre M.-T., Gagnat J., Gubrineau M. 1989; Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens . Gene 79:336
    [Google Scholar]
  26. Prauser H. 1976; Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26:58–65
    [Google Scholar]
  27. Prauser H. 1984; Nocardioides luteus spec. nov. Z Allg Microbiol 24:647–648
    [Google Scholar]
  28. Prauser H. 1989; Genus Nocardioides Prauser 1976, 61AL. In Bergey's Manual of Systematic Bacteriology vol 4 pp 2371–2375 Edited by Williams S. T., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  29. Ruan J. S., Zhang Y. M. 1979; Two new species of Nocardioides. Acta Microbiol Sinica 19:347–352
    [Google Scholar]
  30. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406425
    [Google Scholar]
  31. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning a Laboratory Manual, 2nd edn. pp 6.286.29 Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  32. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849
    [Google Scholar]
  33. Stackebrandt E., Liesack W. 1993; Nucleic acids and classification. In Handbook of New Bacterial Systematics pp 152–189 Edited by Goodfellow M., O’Donnell A. G. London: Academic Press;
    [Google Scholar]
  34. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a new hierarchic classification system, Actino- bacteria classis nov. Int J Syst Bacteriol 47:479–491
    [Google Scholar]
  35. Suzuki K., Komagata K. 1983; Pimelobacter gen. nov., a new genus of coryneform bacteria with LL-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29:59–71
    [Google Scholar]
  36. Suzuki Y., Yamada T. 1988; The nucleotide sequence of 16S rRNA gene from Streptomyces lividans TK21. Nucleic Acids Res 16:370
    [Google Scholar]
  37. Suzuki Y., Ono Y., Nagata A., Yamada T. 1988; Molecular cloning and characterization of an rRNA operon in Streptomyces lividans TK21. J Bacteriol 170:1631–1636
    [Google Scholar]
  38. Tamura T., Yokota A. 1994; Transfer of Nocardioides fastidiosa Collins and Stackebrandt 1989 to the genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov. Int J Syst Bacteriol 44:608–611
    [Google Scholar]
  39. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
    [Google Scholar]
  40. Van Wezel G. P., Vijgenboom E., Bosch L. 1991; A com-parative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rrn A . Nucleic Acids Res 19:4399–4403
    [Google Scholar]
  41. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
  42. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
    [Google Scholar]
  43. Yoon J.-H., Kim H., Kim S.-B., Kim H.-J., Kim W. Y., Lee S. T., Goodfellow M., Park Y.-H. 1996; Identification of Saccharo- monospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46:502–505
    [Google Scholar]
  44. Yoon J.-H., Rhee S.-K., Lee J.-S., Park Y.-H., Lee S. T. 1997a; Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int J Syst Bacteriol 47:933–938
    [Google Scholar]
  45. Yoon J.-H., Lee S. T., Kim S.-B., Goodfellow M., Park Y.-H. 1997b; Inter- and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences. Int J Syst Bacteriol 47:661–669
    [Google Scholar]
  46. Yoon J.-H., Lee S. T., Kim S.-B., Kim W. Y., Goodfellow M., Park Y.-H. 1997c; Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 47:111–114
    [Google Scholar]
  47. Yoon J.-H., Lee J.-S., Shin Y. K., Park Y.-H., Lee S. T. 1997d; Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis . Int J Syst Bacteriol 47:904–907
    [Google Scholar]
  48. Yoon J.-H., Lee S. T., Park Y.-H. 1998; Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48:187–194
    [Google Scholar]
  49. Zavaleta A. I., Martfnez-Murcia A. J., Rodrfguez-Valera F. 1996; 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Micro-biology 142:2105–2114
    [Google Scholar]
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