Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella.
Given the advances in molecular biology, many microbial taxonomists feel that a sequencing based method should be developed that can replace DNA-DNA hybridisation for species delineation. The potential of the gyrB gene to be used for phylogenetic studies has been investigated within a number of actinobacterial genera, including Gordonia, Micromonospora and the whorl-forming Streptomyces species. This study aimed to determine whether the gyrB gene can discriminate between type strains of the genus Kribbella. Previous studies, in the genus Micromonospora, have found that a gyrB-based genetic distance of 0.014 correlates to a DNA relatedness of 70% and that those strains with a genetic distance of greater than 0.014 are likely to be distinct species. In this study, the gyrB-based genetic distances between Kribbella type strains were found to range from 0.0164 to 0.1495, supporting the use of the 0.014 genetic-distance value as the threshold for species delineation within this genus. Phylogenetic analysis based on the gyrB gene had improved resolution (longer branch lengths) compared to that based on the 16S rRNA gene sequence. Based on this study, the gyrB gene can be used to distinguish between Kribbella type strains. Furthermore, it is proposed that a 390-nucleotide sequence of the gyrB gene of a Kribbella isolate is sufficient to assess whether it is likely to represent a new species, before time and effort is invested in polyphasic taxonomic characterisation of the isolate.
Kirby
Bronwyn M
BM
Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, 7701 Cape Town, South Africa. bkirby@uwc.ac.za
Everest
Gareth J
GJ
Meyers
Paul R
PR
D000192:Actinomycetales / Q000145:classification* / Q000235:genetics*; D001431:Bacteriological Techniques / Q000379:methods*; D002965:Classification / Q000379:methods*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D027081:DNA Gyrase / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D027081:DNA Gyrase