Prokaryotic taxonomy and nomenclature in the age of big sequence data

Abstract

The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.

Fig. 1. Key events in prokaryotic taxonomy and nomenclature over the past 100 years.

Taxonomic events are shown in the left panel and nomenclatural events in the right panel. Time is shown on the vertical axis from 1920 (top) to present (bottom).

Fig. 2. Proportion of Latin, Candidatus and placeholder prokaryote names by taxonomic rank based on GTDB Release 05-RS95 [44].

Total number of taxa per rank are shown below each rank name. Most recognised prokaryotic taxa only have placeholder names, and the majority of these fall outside the Prokaryotic Code because they lack cultured representatives (Box 3). Only 7.2% of this excluded fraction have adopted the nomenclatural provisional status of Candidatus. The proportion of validly named taxa (Latin names) is likely to fall as MAG sequencing overtakes isolate sequencing. Note that there are no validly published names of phyla as the rank of phylum is not (yet) covered by the rules of the Prokaryotic Code [122].