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Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences

¹Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
²Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Taejon, Korea

Author for correspondence: Yong-Ha Park. Tel: +82 42 860 4620. Fax: +82 42 860 4625. e-mail: yhpark{at}kribb4680.kribb.re.kr

ABSTRACT

The 16S rDNAs from 38 strains of the genus Nocardioides, two Aeromicrobium species and Terrabacter tumescens were directly sequenced and then analysed. The mean nucleotide similarity value between the type strains of validly described Nocardioides species was 96.1±3.0%. The mean nucleotide similarity value between the type strains of validly described Nocardioides species and the two Aeromicrobium species was 93.7±1.4%. T. tumescens was distantly related to the genera Nocardioides and Aeromicrobium. The mean intraspecific nucleotide similarity value of 16S rDNA sequences from Nocardioides albus was 99.5±0.5%. The mean intraspecific nucleotide similarity of 16S rDNA sequences from Nocardioides simplex was 100%, except for N. simplex strains ATCC 13260, ATCC 19565 and ATCC 19566, which were shown not to be members of the genus Nocardioides. ‘Nocardioides flavus’ strains IFO 14396^T and IFO 14397, and ‘Nocardioides fulvus’ JCM 3335^T showed a 16S rDNA similarity value of 100% with Nocardioides luteus KCTC 9575^T and Nocardioides albus JCM 5854. ‘N. fulvus’ IFO 14399 shared its highest 16S rDNA similarity with Nocardioides sp. ATCC 39419 at 99%. ‘N. fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 formed a phylogenetic lineage distinct from the genera Nocardioides and Aeromicrobium. ‘Nocardioides thermolilacinus’ strains IFO 14335^T and IFO 14336 displayed a close relationship to the genus Streptomyces. From 16S rDNA sequence analyses, it is considered that some strains that have been attributed to the genus Nocardioides should be taxonomically re-evaluated.

Key Words: Nocardioides • 16S rDNA sequence analysis • phylogeny

The GenBank accession numbers for the sequences reported in this paper are AF004988-AF005024, U61298, U81990, U82666 and U82667.

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				S.-J. Park, C.-H. Kang, Y.-D. Nam, J.-W. Bae, Y.-H. Park, Z.-X. Quan, D.-S. Moon, H.-J. Kim, D.-H. Roh, and S.-K. Rhee Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 895 - 898. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, H. W. Oh, J.-S. Lee, and T.-K. Oh Brevundimonas kwangchunensis sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol, March 1, 2006; 56(Pt 3): 613 - 617. [Abstract] [Full Text] [PDF]

				S.-G. Lee, S.-P. Hong, J. J. Song, S.-J. Kim, M.-S. Kwak, and M.-H. Sung Functional and Structural Characterization of Thermostable D-Amino Acid Aminotransferases from Geobacillus spp. Appl. Envir. Microbiol., February 1, 2006; 72(2): 1588 - 1594. [Abstract] [Full Text] [PDF]

				S.-Y. Jung, T.-K. Oh, and J.-H. Yoon Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea Int J Syst Evol Microbiol, January 1, 2006; 56(1): 33 - 37. [Abstract] [Full Text] [PDF]

				B.-C. Kim, J. R. Park, J.-W. Bae, S.-K. Rhee, K.-H. Kim, J.-W. Oh, and Y.-H. Park Stappia marina sp. nov., a marine bacterium isolated from the Yellow Sea Int J Syst Evol Microbiol, January 1, 2006; 56(1): 75 - 79. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, S.-Y. Jung, H. W. Oh, and T.-K. Oh Gaetbulimicrobium brevivitae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat of the Yellow Sea in Korea Int J Syst Evol Microbiol, January 1, 2006; 56(1): 115 - 119. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, and T.-K. Oh Dokdonella koreensis gen. nov., sp. nov., isolated from soil Int J Syst Evol Microbiol, January 1, 2006; 56(1): 145 - 150. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, C.-H. Lee, and T.-K. Oh Donghaeana dokdonensis gen. nov., sp. nov., isolated from sea water Int J Syst Evol Microbiol, January 1, 2006; 56(1): 187 - 191. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, and T.-K. Oh Marinomonas dokdonensis sp. nov., isolated from sea water Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2303 - 2307. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, C.-H. Lee, and T.-K. Oh Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2323 - 2328. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, S.-H. Yeo, and T.-K. Oh Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2339 - 2344. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, C.-H. Lee, H. W. Oh, and T.-K. Oh Halobacillus yeomjeoni sp. nov., isolated from a marine solar saltern in Korea Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2413 - 2417. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, S.-Y. Lee, M.-H. Lee, and T.-K. Oh Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1833 - 1837. [Abstract] [Full Text] [PDF]

				S.-Y. Jung, S.-J. Kang, M.-H. Lee, S.-Y. Lee, T.-K. Oh, and J.-H. Yoon Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1845 - 1849. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, C.-H. Lee, S.-J. Kang, and T.-K. Oh Psychrobacter celer sp. nov., isolated from sea water of the South Sea in Korea Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1885 - 1890. [Abstract] [Full Text] [PDF]

				J.-H. Yoon and T.-K. Oh Bacillus litoralis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1945 - 1948. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, S.-J. Kang, S.-Y. Lee, C.-H. Lee, and T.-K. Oh Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2051 - 2055. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, C.-H. Lee, and T.-K. Oh Aeromicrobium alkaliterrae sp. nov., isolated from an alkaline soil, and emended description of the genus Aeromicrobium Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2171 - 2175. [Abstract] [Full Text] [PDF]

				J.-H. Yoon, C.-H. Lee, and T.-K. Oh Nocardioides dubius sp. nov., isolated from an alkaline soil Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2209 - 2212. [Abstract] [Full Text] [PDF]

				J.-W. Bae, S.-K. Rhee, Y.-D. Nam, and Y.-H. Park Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes Nucleic Acids Res., July 19, 2005; 33(13): e113 - e113. [Abstract] [Full Text] [PDF]

				M. Lee, M. K. Kim, M. Vancanneyt, J. Swings, S.-H. Kim, M. S. Kang, and S.-T. Lee Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1409 - 1413. [Abstract] [Full Text] [PDF]

				J.-S. Zhao, D. Manno, C. Beaulieu, L. Paquet, and J. Hawari Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1511 - 1520. [Abstract] [Full Text] [PDF]