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Taxon overview
Species overview
Genome categories
GTDB species representatives
Quality of GTDB representative genomes
Taxa with the largest number of species
Taxa with the largest number of sequenced genomes
Relative evolutionary divergence
Comparison of GTDB and NCBI taxa
Genomic statistics
Release 202 statistics
GTDB release date: April 27, 2021
Taxon overview
GTDB R202 spans 258,406 genomes organized into 47,894 species clusters.
BacteriaArchaeaTotal
Phylum12719146
Class36047407
Order1,1631161,279
Family2,8863363,222
Genus12,03785112,888
Species45,5552,33947,894
Species overview
GTDB R202 is comprised of 254,090 bacterial and 4,316 archaeal genomes organized into 45,555 bacterial and 2,339 archaeal species clusters. This is an increase of 63,806 (32.79%) genomes and 15,984 (50.09%) species clusters compared to GTDB R95.
R04-RS89R05-RS95R06-RS202Growth from R05-RS95 (%)
Bacterial genomes143,512191,527254,09032.67
Archaeal genomes2,3923,0734,31640.45
Bacterial species clusters23,45830,23845,55550.65
Archaeal species clusters1,2481,6722,33939.89
Genome categories
GTDB taxa are comprised of isolate genomes, metagenome-assembled genomes (MAGs), and single-amplified genomes (SAGs). The following plot indicates the proportion of taxa at each taxonomic rank comprised exclusively of isolate genomes, exclusively of environmental genomes (i.e. MAGs/SAGs), or both isolate and environmental genomes.
GTDB species representatives
Each GTDB species cluster is represented by a single genome. Genomes assembled from the type strain of the species were selected where possible, though the majority of species clusters are currently assigned only placeholder names. The proportion of representatives which are isolates, MAGs, or SAGs is given for each category.
Quality of GTDB representative genomes
The quality of the genomes selected as GTDB species representatives is given below. Genome completeness and contamination were estimated using CheckM and are colored based on the MIMAG genome standards. In general, representative genomes were restricted to having a quality satisfying completeness - 5*contamination >50. A few exceptions exist in order to retain well-known species with abnormal CheckM quality estimates.
Taxa with the largest number of species
Taxa encompassing the largest number of GTDB species clusters is given for each taxonomic rank.
PhylumClassOrderFamilyGenus
Proteobacteria 14,419Gammaproteobacteria 7,998Burkholderiales 2,491Burkholderiaceae 1,668Pelagibacter 841
Actinobacteriota 6,192Alphaproteobacteria 6,379Bacteroidales 2,083Flavobacteriaceae 1,247Streptomyces 762
Bacteroidota 5,818Bacteroidia 5,402Pseudomonadales 1,886Lachnospiraceae 1,155Pseudomonas_E 574
Firmicutes_A 4,062Actinomycetia 4,864Flavobacteriales 1,847Pelagibacteraceae 1,114Prevotella 383
Firmicutes 3,390Clostridia 3,566Enterobacterales 1,701Rhodobacteraceae 1,015Mycobacterium 339
Patescibacteria 1,601Bacilli 3,352Actinomycetales 1,678Streptomycetaceae 846Flavobacterium 319
Cyanobacteria 1,067Cyanobacteriia 920Mycobacteriales 1,426Mycobacteriaceae 811Collinsella 316
Chloroflexota 982Verrucomicrobiae 699Rhizobiales 1,395Sphingomonadaceae 762Streptococcus 301
Verrucomicrobiota 917Paceibacteria 684Lachnospirales 1,285Pseudomonadaceae 731Prochlorococcus_A 265
Planctomycetota 748Coriobacteriia 594Oscillospirales 1,249Enterobacteriaceae 724Microbacterium 206
Taxa with the largest number of sequenced genomes
Taxa encompassing the largest number of genomes in the GTDB is given for each taxonomic ranks.
PhylumClassOrderFamilyGenusSpecies
Proteobacteria 120,757Gammaproteobacteria 104,665Enterobacterales 64,157Enterobacteriaceae 55,347Escherichia 23,687Escherichia flexneri 14,743
Firmicutes 53,879Bacilli 53,835Lactobacillales 28,917Streptococcaceae 16,112Streptococcus 15,765Staphylococcus aureus 12,022
Actinobacteriota 24,602Actinomycetia 21,459Pseudomonadales 19,449Staphylococcaceae 15,139Staphylococcus 14,962Salmonella enterica 11,523
Bacteroidota 13,917Alphaproteobacteria 16,016Staphylococcales 15,215Mycobacteriaceae 11,561Salmonella 11,772Klebsiella pneumoniae 9,621
Firmicutes_A 12,649Bacteroidia 12,772Burkholderiales 13,431Pseudomonadaceae 10,859Klebsiella 10,886Streptococcus pneumoniae 8,405
Campylobacterota 5,968Clostridia 11,762Mycobacteriales 12,534Burkholderiaceae 8,796Mycobacterium 9,568Mycobacterium tuberculosis 6,684
Patescibacteria 3,496Campylobacteria 5,957Bacteroidales 7,082Moraxellaceae 6,881Acinetobacter 6,462Pseudomonas aeruginosa 5,211
Cyanobacteria 2,210Cyanobacteriia 1,949Campylobacterales 5,940Vibrionaceae 4,865Pseudomonas 5,311Acinetobacter baumannii 4,766
Verrucomicrobiota 2,095Verrucomicrobiae 1,742Bacillales 4,944Enterococcaceae 4,454Pseudomonas_E 4,871Escherichia coli 4,370
Spirochaetota 1,689Paceibacteria 1,561Rhizobiales 4,913Lactobacillaceae 4,070Vibrio 4,447Streptococcus pyogenes 2,136
Relative evolutionary divergence
The following graphs show the relative evolutionary divergence (RED) of taxa at each taxonomic rank from phylum to genus. RED values provide an operational approximation of relative time with extant taxa existing in the present (RED=1), the last common ancestor occurring at a fixed time in the past (RED=0), and internal nodes being linearly interpolated between these values according to lineage-specific rates of evolution. RED intervals for normalizing taxa at taxonomic ranks was operationally defined as the median RED value (indicated by a blue bar) at each rank ±0.1 (indicated by grey bars).

Bacteria

Archaea

Comparison of GTDB and NCBI taxa
Comparison of GTDB and NCBI taxonomic assignments across GTDB species representative genomes and all GTDB genomes which have an assigned NCBI taxonomy. For each taxonomic rank, a taxon was classified as being unchanged if its name was identical in both taxonomies, passively changed if the GTDB taxonomy provided name information absent in the NCBI taxonomy, or actively changed if the name was different between the two taxonomies.
Genomic statistics
Key genomic statistics for the GTDB species representative genomes and all genomes in the GTDB.