Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella
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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.
KeywordsKribbella Nocardioidaceae gyrB Actinobacteria Phylogeny Genetic distance Horizontal gene transfer
The authors wish to thank Di James, University of Cape Town (UCT), for DNA sequencing, and Iulia Sfarlea and Ndatiyaroo Agapitus for isolating K. solani strain YB2, Dr Martha Trujillo for providing the type strain of K. lupini and Drs Ingrid Groth and Karin Martin for providing the two non-type strains of K. aluminosa. Bronwyn Kirby held a Scarce Skills Scholarship from the National Research Foundation (NRF) and a UCT Postgraduate Research Associateship. Gareth Everest held a Scarce Skills Scholarship from the NRF, a KW Johnstone Scholarship and a Benfara Scholarship, UCT. This work was supported by research grants to Paul Meyers from the NRF (Grant number 2073133) and the University Research Committee (UCT).
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