1887

Abstract

The taxonomic position of an actinomycete, strain 1BDZ, isolated from a clinical human source was determined using a polyphasic approach. Phylogenetic analysis based on almost complete 16S rDNA sequences showed that this organism consistently formed a distinct line with the subclade within the genus , and shared moderately low 16S rDNA similarity (<96·5 %) with other species. The organism was also found to have chemical and morphological properties typical of members of the genus . A range of phenotypic characteristics readily distinguished this strain from representatives of all species of with validly published names. On the basis of these data, a novel species, sp. nov., is proposed to accommodate strain 1BDZ (=AS 4.1729=PCM 2600).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02685-0
2004-03-01
2020-01-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/2/ijs540359.html?itemId=/content/journal/ijsem/10.1099/ijs.0.02685-0&mimeType=html&fmt=ahah

References

  1. Al-Musallam, A. A., Al-Zarban, S. S., Fasasi, Y. A., Kroppenstedt, R. M. & Stackebrandt, E. ( 2003; ). Amycolatopsis keratiniphila sp. nov., a novel keratinolytic soil actinomycete from Kuwait. Int J Syst Evol Microbiol 53, 871–874.[CrossRef]
    [Google Scholar]
  2. Barreiro, C., Pisabarro, A. & Martin, J. F. ( 2000; ). Characterization of the ribosomal rrnD operon of the cephamycin-producer ‘Nocardia lactamdurans’ shows that this actinomycete belongs to the genus Amycolatopsis. Syst Appl Microbiol 23, 15–24.[CrossRef]
    [Google Scholar]
  3. Chun, J. & Goodfellow, M. ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.[CrossRef]
    [Google Scholar]
  4. Chun, J., Kim, S. B., Oh, Y. K. & 7 other authors ( 1999; ). Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China. Int J Syst Bacteriol 49, 1369–1373.[CrossRef]
    [Google Scholar]
  5. Collins, M. D. ( 1985; ). Isoprenoid quinone analyses in bacterial classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  6. de Boer, L., Dijkhuizen, L., Grobben, G., Goodfellow, M., Stackebrandt, E., Parlett, J. H., Whitehead, D. & Witt, D. ( 1990; ). Amycolatopsis methanolica sp. nov., a facultatively methylotrophic actinomycete. Int J Syst Bacteriol 40, 194–204.[CrossRef]
    [Google Scholar]
  7. Embley, M. T., Smida, J. & Stackebrandt, E. ( 1988; ). The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 11, 16–19.[CrossRef]
    [Google Scholar]
  8. Felsenstein, J. ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  10. Felsenstein, J. ( 1993; ). phylip (phylogenetic inference package) version 3.5c. Distributed by the author. University of Washington, Seattle, USA.
  11. Fitch, W. M. & Margoliash, E. ( 1967; ). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279–284.[CrossRef]
    [Google Scholar]
  12. Goodfellow, M., Brown, A. B., Cai, J., Chun, J. & Collins, M. D. ( 1997; ). Amycolatopsis japonicum sp. nov., an actinomycete producing (S,S)-N,N’-ethylenediaminedisuccinic acid. Syst Appl Microbiol 20, 78–84.[CrossRef]
    [Google Scholar]
  13. Goodfellow, M., Kim, S. B., Minnikin, D. E., Whitehead, D., Zhou, Z.-H. & Mattinson-Rose, A. D. ( 2001; ). Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int J Syst Evol Microbiol 51, 187–193.
    [Google Scholar]
  14. Gordon, R. E., Barnett, D. A., Handerhan, J. E. & Pang, C. H.-N. ( 1974; ). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24, 54–63.[CrossRef]
    [Google Scholar]
  15. Hasegawa, T., Takizawa, M. & Tanida, S. ( 1983; ). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319–322.[CrossRef]
    [Google Scholar]
  16. Henssen, A., Kothe, H. W. & Kroppenstedt, R. M. ( 1987; ). Transfer of Pseudonocardia azurea and “Pseudonocardia fastidiosa” to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 37, 292–295.[CrossRef]
    [Google Scholar]
  17. Huang, Y., Qi, W., Lu, Z., Liu, Z. & Goodfellow, M. ( 2001; ). Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil. Int J Syst Evol Microbiol 51, 1093–1097.[CrossRef]
    [Google Scholar]
  18. Huang, Y., Wang, L., Lu, Z., Hong, L., Liu, Z., Tan, G. Y. A. & Goodfellow, M. ( 2002; ). Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov. Int J Syst Evol Microbiol 52, 977–982.[CrossRef]
    [Google Scholar]
  19. Jones, K. L. ( 1949; ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57, 141–145.
    [Google Scholar]
  20. Kim, S. B. & Goodfellow, M. ( 1999; ). Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Bacteriol 49, 507–512.[CrossRef]
    [Google Scholar]
  21. Kim, B., Sahin, N., Tan, G. Y. A., Zakrzewska-Czerwinska, J. & Goodfellow, M. ( 2002; ). Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil. Int J Syst Evol Microbiol 52, 889–894.[CrossRef]
    [Google Scholar]
  22. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  23. Labeda, D. P. & Kroppenstedt, R. M. ( 2000; ). Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov. Int J Syst Evol Microbiol 50, 331–336.[CrossRef]
    [Google Scholar]
  24. Labeda, D. P., Donahue, J. M., Williams, N. M., Sells, S. F. & Henton, M. M. ( 2003; ). Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas. Int J Syst Evol Microbiol 53, 1601–1605.[CrossRef]
    [Google Scholar]
  25. Lechevalier, H. A. & Lechevalier, M. P. ( 1980; ). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, pp. 277–284. Society for Industrial Microbiology Special Publication no. 6. Edited by A. Dietz & D. W. Thayer. Arlington, VA: Society for Industrial Microbiology.
  26. Lechevalier, M. P., Prauser, H., Labeda, D. P. & Ruan, J.-S. ( 1986; ). Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36, 29–37.[CrossRef]
    [Google Scholar]
  27. Lee, S. D. & Hah, Y. C. ( 2001; ). Amycolatopsis albidoflavus sp. nov. Int J Syst Evol Microbiol 51, 645–650.
    [Google Scholar]
  28. Marmur, J. & Doty, P. ( 1962; ). Determination of base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[CrossRef]
    [Google Scholar]
  29. Minnikin, D. E., Hutchinson, I. G., Caldicott, A. B. & Goodfellow, M. ( 1980; ). Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188, 221–233.[CrossRef]
    [Google Scholar]
  30. Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. ( 1984; ). An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  31. Paściak, M., Ekiel, I., Grzegorzewicz, A., Mordarska, H. & Gamian, A. ( 2002; ). Structure of the major glycolipid from Rothia dentocariosa. Biochim Biophys Acta 1594, 199–205.[CrossRef]
    [Google Scholar]
  32. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  33. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  34. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  35. Warwick, S., Bowen, T., McVeigh, H. & Embley, T. M. ( 1994; ). A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44, 293–299.[CrossRef]
    [Google Scholar]
  36. Wu, C., Lu, X., Qin, M., Wang, Y. & Ruan, J. ( 1989; ). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology (English translation of Mikrobiologiya) 16, 176–178.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.02685-0
Loading
/content/journal/ijsem/10.1099/ijs.0.02685-0
Loading

Data & Media loading...

Most cited articles

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