GtdB

The Genome Taxonomy Database (GTDB) is a free, publicly available resource that provides a genome-based taxonomy for Bacteria and Archaea. It aims to deliver a standardized framework for naming and classifying prokaryotic genomes based on whole-genome phylogeny rather than traditional cultivation-based or phenotype-driven schemes.

GTDB derives its taxonomy from a curated set of universal single-copy marker genes used to construct a concatenated alignment and a reference phylogenetic tree. The GTDB marker set includes 120 bacterial and 122 archaeal markers. Taxonomic ranks are assigned using relative evolutionary divergence, a rank-normalization approach designed to produce consistent naming across lineages. The database also stores genome metadata and assigns representative genomes to named taxa; genomes meeting quality thresholds may be placed within existing taxa or used to define new lineages.

GTDB releases are periodically updated to incorporate new genomes and revised placements. Each release updates taxonomic assignments and may redefine taxa to reflect phylogenomic relationships. The resource provides documentation and cross-references to other taxonomic systems to aid interpretation.

GTDB-Tk is the accompanying software toolkit for classifying bacterial and archaeal genomes and metagenome-assembled genomes against the GTDB taxonomy. It reports taxonomic labels, placement along with confidence scores, and can be integrated into genome-analysis pipelines to ensure standardized downstream analyses.

Access and use: GTDB is widely used in microbiology and metagenomics to support consistent, genome-based taxonomic assignments. Data are hosted on the GTDB website and related repositories, with downloadable genomes, trees, marker alignments, and documentation.