Divorcing Strain Classification From Species Names

Abstract

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 and nomenclature need not be the one in the same. 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.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

“…Previous efforts to expand the bacterial and archaeal reference genomes by targeted sequencing of phylogenetically underrepresented lineages have enabled vast improvements in taxonomic assignment in metagenomic data sets 5 . Furthermore, access to completed genomes enables more accurate whole-genome-based taxonomic assignments 6,7 and improved phylogenies 8,9 .…”

Residential Bacteria on Surfaces in the Food Industry and Their Implications for Food Safety and Quality

“…are commonly isolated from plant surfaces, soil, water, and raw materials and may be frequently introduced into the processing environment through many routes. Because Pseudomonas is a very heterogeneous genus, the nomenclature has changed considerably over time, and different methodologies provide different species identities (Baltrus 2016), it is difficult to determine the most frequent species across different studies. However, it appears from single studies that the diversity among isolated Pseudomonas is high and that the human pathogen P. aeruginosa is uncommon (Guδbjornsdottir and others 2005;Liu and others 2013;Møretrø and others 2016).…”

Genome analysis of Pseudomonas syringae pv. lachrymans strain 814/98 indicates diversity within the pathovar

“…We previously attempted to describe the collected cucumber strains (OlczakWoltman et al 2007;Słomnicka et al 2015); however, a more precise methodology and new data are beginning to challenge old conclusions. Baltrus (2016) proposed a sequence-based classification system that is unambiguous and would enable microbial classification without abandoning previous taxonomic systems. Establishing such a system is imperative because the existence of distinct clusters of strains within pathovars is reported often after genome sequencing, which forces nomenclature revision.…”