The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed
nomenclature of
prokaryotes, following a
phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving
paraphyletic groups, this method also reassigns
taxonomic ranks algorithmically, updating names in both cases.[1] Information for
archaea was added in 2020,[2] along with a
species classification based on
average nucleotide identity.[3] Each update incorporates new genomes as well as automated and manual curation of the taxonomy.[4]
An
open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy.[5] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the
human gut microbiome and other
metagenomic sources.[6][7]
^Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004.
bioRxiv10.1101/256800.
doi:
10.1038/nbt.4229.
PMID30148503.
S2CID52093100.