The Taxonomy of Bacteria in the Genomic Era

The taxonomy of bacteria has rapidly evolved since the capacity to obtain gene sequences was developed. The use of the single 16S rRNA gene sequence to generate evolutionary phylogenetic trees improved the analysis of the relationships among newly obtained strains and those already described, allowing a faster and more accurate classification than previously used methods. In addition, the use of multilocus sequences of housekeeping genes has shown an improved resolution for all the genera tested, these genera being frequently poorly discriminated by the 16S rRNA gene when intraspecies of the genus were analyzed. The next milestone in taxonomy is the use of whole-genome sequences. In the last few years, the development of new next-generation sequencing (NGS) technologies has made possible for most laboratories to obtain the genome sequence of their strains of study at affordable prices. These genomes can be used to avoid the classical and tedious wet DNA-DNA hybridization methods, directly generating in silico values using the overall genome relatedness index (OGRI). In most of the novel species description papers, the use of the genomes is reduced to the procurement of these values. Nevertheless, the genomes are full of taxonomic information that would greatly improve a new species description, including chemotaxonomic information, the existence of genes putatively encoding for the ability of the strain to use a carbon source, or its potential capacity of producing secondary metabolites and antibiotic resistance information.