New genus-specific primers for the PCR identification of novel isolates of the genera Nocardiopsis and Saccharothrix.

The taxonomic position of the genera Saccharothrix and Nocardiopsis has evolved in recent years to accommodate an increasing number of actinomycete strains that cannot be clearly distinguished by morphological characters. More recently, the taxonomic reorganization of the genus Saccharothrix has determined the creation of new, related genera, increasing the complexity of the identification of this taxon. Nevertheless, today these genera can still only be identified by applying chemotaxonomic and molecular criteria, and no other tools are available for the rapid distinction of members of the two genera. Phylogenetic analysis based on 16S rDNA nucleotide sequences of reference strains has shown that both genera represent complete distinct lineages within the order Actinomycetales. Differences in the nucleotide sequences of the 16S rDNAs of reference strains were used to design two pairs of genus-specific primers to identify novel members of the genera Nocardiopsis and Saccharothrix by PCR amplification. The genus specificity of these primers was validated with reference strains as well as with wild-type isolates that exhibited morphological characteristics common to both genera. The diversity and taxonomic position of the isolates identified with these tools is also discussed.