Using Core Genome Alignments to Assign Bacterial Species

With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method is needed to assign bacterial species designations using genomic data that is consistent with the classically-obtained taxonomy. This is particularly acute for unculturable obligate intracellular bacteria like those in the Rickettsiales, where classical methods like DNA-DNA hybridization cannot be used to define species. Within the Rickettsiales, species designations have been applied inconsistently, often obfuscating the relationship between organisms and the context for experimental results. In this study, we generated core genome alignments for a wide range of genera with classically defined species, including Arcobacter, Caulobacter, Erwinia, Neisseria, Polaribacter, Ralstonia, Thermus, as well as genera within the Rickettsiales including Rickettsia, Orientia, Ehrlichia, Neoehrlichia, Anaplasma, eorickettsia, and Wolbachia. A core genome alignment sequence identity (CGASI) threshold of 96.8% was found to maximize the prediction of classically-defined species. Using the CGASI cutoff, the Wolbachia genus can be delineated into species that differ from the currently used supergroup designations, while the Rickettsia genus is delineated into nine species, as opposed to the current 27 species. Additionally, we find that core genome alignments cannot be constructed between genomes belonging to different genera, establishing a bacterial genus cutoff that suggests the need to create new genera from the Anaplasma and Neorickettsia. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method for bacterial nomenclature that is aligned with classically-obtained results.