Divorcing Strain Classification from Species Names

Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of, and speed at which, new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database-fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification can be independent of nomenclature. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets. Traditional classification schemes for bacteria were not designed to deal with an influx of large amounts of genomic data or with an eye toward metadata curation by nontaxonomists.Taxonomy for environmentally ubiquitous bacteria, such as Pseudomonas syringae, is particularly prone to confusion given their lifestyle as facultative pathogens.Implementation of classification schemes based upon whole-genome comparisons could provide much needed continuity across databases and publications.