ORIGINAL PAPER Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis Gareth J. Everest • Andrew E. Cook • Bronwyn M. Kirby • Paul R. Meyers Received: 11 April 2011 / Accepted: 1 June 2011 / Published online: 14 June 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Partial recN gene sequences ( [ 1 kb) were obtained from 35 type strains of the genus Amyco- latopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA–DNA hybridization (DDH) for distinguishing closely related species was also assessed. The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN 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.A recN genetic distance of [ 0.04 between two Amycolatopsis strains 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 Á DNA–DNA hybridization Á Genetic distance Á recN Á gyrB Á Family Pseudonocardiaceae Introduction The genus Amycolatopsis (Lechevalier et al. 1986; family Pseudonocardiaceae, Zhi et al. 2009), con- tains actinobacteria that lack mycolic acids and contain meso-diaminopimelic acid, arabinose and galactose in their cell wall peptidoglycan. The genus currently contains 45 members (Euze ´by 2011), many of which are known to produce antibiotics, including the clinically important rifamycin (Sensi et al. 1959; Wink et al. 2003; Bala et al. 2004) and vancomycin (Wink et al. 2003). Due to the rise of antibiotic resistance (Thomson et al. 2004), there is a desperate need for the development of new antibiotics to combat these resistant strains. Given the fact that the genus Amycolatopsis contains many species that are known antibiotic producers, it has great potential for drug discovery programs. The GenBank accession numbers for the recN gene sequences obtained in this study are shown in Table 1. G. J. Everest Á A. E. Cook Á B. M. Kirby Á P. R. Meyers (&) Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa e-mail: paul.meyers@uct.ac.za Present Address: B. M. Kirby Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa 123 Antonie van Leeuwenhoek (2011) 100:483–496 DOI 10.1007/s10482-011-9604-z