Content area
Full Text
Antonie van Leeuwenhoek (2009) 95:111 DOI 10.1007/s10482-008-9280-9
ORIGINAL PAPER
The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis
Gareth J. Everest Paul R. Meyers
Received: 27 June 2008 / Accepted: 1 September 2008 / Published online: 21 September 2008 Springer Science+Business Media B.V. 2008
Abstract Partial gyrB sequences ([1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of gyrB sequence analysis as an alternative to DNADNA hybridization was also assessed for distinguishing closely related species. The gyrB based phylogeny mostly conrmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. In particular a genetic distance of [0.02 between two
Amycolatopsis strains (based on a 315 bp variable
region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).
Keywords Amycolatopsis DNADNA
hybridization Genetic distance gyrB
Phylogeny
Introduction
The genus Amycolatopsis belongs to the family Pseudonocardiaceae and was proposed by Lechevalier et al. in 1986 to accommodate nocardioform actinomycetes that lack mycolic acids and contain meso-diaminopimelic acid, arabinose and galactose in their cell wall peptidoglycan. The genus currently contains 38 members (http://www.bacterio.cict.fr/a/amycolatopsis.html
Web End =http://www.bacterio.cict.fr/a/ http://www.bacterio.cict.fr/a/amycolatopsis.html
Web End =amycolatopsis.html ), many of which are known to produce antibiotics. Some of these include balhimycin [glycopeptide] (Amycolatopsis balhimycina) (Wink et al. 2003), decaplanin [glycopeptide] (Amycolatopsis decaplanina) (Wink et al. 2004), as well as the clinically important rifamycin [ansamycin] (Amycolatopsis mediterranei and Amycolatopsis rifamycinica) (Bala et al. 2004; Sensi et al. 1959; Wink et al. 2003) and vancomycin [glycopeptide] (Amycolatopsis orientalis) (Wink et al. 2003).
With the current need for the development of new antibiotics, due to the rise of antibiotic resistance
The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in...