Two novel methods for using genome sequences to infer taxonomy

Next generation sequencing (NGS) is catalysing a host of new developments across microbiology. Two papers recently published in Microbiology (Jolley et al., 2012; Bennett et al., 2012) describe methods that exploit NGS genome data to classify bacterial genomes based on core gene sequences. In general, these methods agree with 16S rRNA phylogenetic trees, but the novel methods have the added advantage of providing strain resolution within a given species. Furthermore, these approaches are scalable for large numbers of genomes, do not depend on a reference genome and can use as input genomes from different formats: finished sequences or genome assemblies in multiple contigs. Both papers focus on a set of ‘core genes’ to use; 53 genes encoding ribosomal proteins in the case of ribosomal multilocus sequence typing (rMLST; Jolley et al., 2012) or a set of core genes defined through comparative genomics (Bennett et al., 2012).