Large-scale, community-based description of prokaryotes

A large fraction of prokaryotes remain poorly described, although genomes from isolates or metagenomes exist for many of them. This genomic information can be used to describe existing taxa and name new ones. The latter can now be done according to the rules of the SeqCode. Descriptions of taxa are essential to provide concise information to others unfamiliar with them, which is classically done in the form of protologues. As any single method of analysis provides only one piece of information at a time, accurate bacterial descriptions require multi-layered analysis to capture comprehensive information on the taxonomy, ecology and functions of the taxon under study. This requires sophisticated bioinformatic tools, which, combined with the large number of unknown taxa, makes the process of describing prokaryotes tedious and slow. Our bioinformatic tool Protologger (www.protologger.de) provides all the elements needed to describe novel prokaryote isolates or metagenomic-assembled genomes from their 16S rRNA gene and genome sequences within a few hours. It is hosted at de.NBI for stable deployment and accessible via a Galaxy interface for ease of use. Protologger has also been updated to use POCPu to determine genus delineation, analyse additional functional pathways, and include archaea. To speed up the process of prokaryote description by orders of magnitude, we propose a community-based approach. Protologger is being used to process all genomes available in the Genome Taxonomy Database (GTDB) (1,650 processed so far). All results are available via a Wikibase instance, allowing the community to contribute comprehensive descriptions. An API will be implemented to interface with the SeqCode registry, allowing the association of high-quality descriptions generated in this project with proposed name. Training videos have been produced to help users navigate the system and workshops will be organised by NFDI4Microbiota (https://nfdi4microbiota.de) to facilitate community participation.