Maria Chuvochina: Navigating the space of prokaryotic taxonomy and nomenclature in the age of big sequence data

Navigating the space of prokaryotic taxonomy and nomenclature in the age of big sequence data

Expansion of metagenomic data over the last decade called for creationof genome-based taxonomy that would incorporate genomic sequences fromboth cultured and uncultured prokaryotes into a single framework. Thisidea was translated into the public resource called the Genome TaxonomyDatabase (GTDB) at the Australian Centre for Ecogenomics. The uniquefeatures of the GTDB include normalisation of taxonomic ranks based on relative evolutionary divergence and incorporation of genomes fromisolates, metagenomic-assembled genomes and single-cell assembledgenomes. GTDB provides both an objective classification for publicgenomes as well as the tool to assess the user genomes classification.GTDB is not a nomenclature resource per se, and it relies on namesinformation from primarily resources such as LPSN. However, there isstill a great ambiguity around application of names for uncultured taxaand this has been recently tackled by the initiative called SeqCode.SeqCode aims to provide a framework for naming uncultured taxa based on genomes as nomenclature types and supports name registration through adedicated online registry, with the final goal being a standardized nomenclature for all prokaryotes. GTDB is going to adopt names validly published under the SeqCode in its next taxonomic release which presentsboth opportunities and challenges.