GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Donovan H. Parks, Pierre-Alain Chaumeil, Aaron J. Mussig, Christian Rinke, Maria Chuvochina, Philip Hugenholtz
Abstract
The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB release 10 (R10-RS226) spans 715 230 bacterial and 17 245 archaeal genomes organized into 136 646 bacterial and 6968 archaeal species clusters. Fewer new major branches of prokaryotic life are being discovered with each release of GTDB, suggesting that we are beginning to saturate readily discoverable microbial diversity through culture-independent analyses. However, species discovery continues unabated as >95% of bacterial and archaeal species remain to be genomically elucidated based on conservative projections. We present additions to the GTDB website, methodological improvements, policy changes, notable nomenclatural updates, and user applications. We conclude with a summary of future plans for the resource including a fungal taxonomy and a nomenclatural extension to classify pathogens.