GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
2021/09/08 by Donovan H. Parks, Donovan H Parks, Maria Chuvochina +5 · 164 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology #Probiotics and Fermented Foods
paper · pdf · doi:10.1093/nar/gkab776
openalex publication_date 2021/09/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
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 R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.
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