GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
By Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz. Nucleic Acids Res., 2021
1,988 citations recorded by the source corpus.
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.
Subfields: Ecology, Food Science, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/b1d0e09864bb91d4ed8332bed4358234a243e609
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Citations in the corpus
- iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, positive): “…database currently used in iPHoP, named “iPHoP_db_Sept21,” was built from 3 publicly available genome sets, namely the GTDB database (release 202; [34]), published genomes from the IMG database (as of July 7, 2021; [35]), and the Genomes from Earth’s Microbiomes (GEM) catalog [36], as follows.”
- Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool (2024, methodology): “In addition to the NCBI taxonomy database ( 16 ), iTOL now also supports GTDB (Genome Taxonomy Database) ( 17 ).”