GTDB

GTDB provides a phylogenetically consistent, rank-normalized genome-based taxonomy for bacteria and archaea.

Key Features:

• Genome coverage: Contains 254,090 bacterial genomes and 4,316 archaeal genomes organized into 45,555 bacterial species clusters and 2,339 archaeal species clusters.
• Species delimitation (ANI): Uses average nucleotide identity (ANI) to delineate prokaryotic species and selects a single representative genome per species cluster.
• Proposed species clusters: Proposes 24,706 species clusters, with 8,792 based on published names and 15,914 assigned placeholder names for uncultivated genomes.
• Phylogenetic markers — bacteria: Derives bacterial taxonomy from concatenated protein sequences.
• Phylogenetic markers — archaea: Derives archaeal taxonomy from a 122-protein phylogeny.
• Rank normalization and polyphyly resolution: Normalizes taxonomic ranks based on relative evolutionary divergence and resolves polyphyletic groups.
• Bias and rate heterogeneity handling: Accounts for rate heterogeneity and compositional bias in genomic data to improve taxonomic stability.
• Inclusion of MAGs: Incorporates metagenome-assembled genomes (MAGs) to expand representation of uncultivated microorganisms.
• Genome-level tracking and quality assessment: Tracks taxonomic changes, assesses genome assembly quality, and identifies genomes assembled from type material or used as species representatives.
• Nomenclatural alignment: Aligns classifications with the International Code of Nomenclature of Prokaryotes and incorporates proposals for new ranks and using genome sequences as type material.

Scientific Applications:

• Prokaryotic systematics: Enables systematic studies of prokaryotic evolution and taxonomy using genome-based phylogenies.
• Genome classification and naming: Provides a structured framework for naming and classifying bacterial and archaeal genomes.
• Study of uncultivated diversity: Expands genomic representation and taxonomic placement of uncultivated microorganisms via MAGs.
• Species boundary definition: Supports species delineation and representative selection using ANI-based clustering.

Methodology:

Taxonomy derived from concatenated protein sequences for bacteria and a 122-protein phylogeny for archaea; ranks normalized by relative evolutionary divergence; polyphyletic groups resolved; ANI used for species delimitation and selection of single representative genomes; inclusion of MAGs and procedures for tracking taxonomic changes and assessing genome assembly quality.