GTDB - R202 Statistics

Taxon overview

GTDB R202 spans 258,406 genomes organized into 47,894 species clusters.

	Bacteria	Archaea	Total
Phylum	127	19	146
Class	360	47	407
Order	1,163	116	1,279
Family	2,886	336	3,222
Genus	12,037	851	12,888
Species	45,555	2,339	47,894

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-RS89	R05-RS95	R06-RS202	Growth from R05-RS95 (%)
Bacterial genomes	143,512	191,527	254,090	32.67
Archaeal genomes	2,392	3,073	4,316	40.45
Bacterial species clusters	23,458	30,238	45,555	50.65
Archaeal species clusters	1,248	1,672	2,339	39.89

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.

Phylum	Class	Order	Family	Genus
Proteobacteria 14,419	Gammaproteobacteria 7,998	Burkholderiales 2,491	Burkholderiaceae 1,668	Pelagibacter 841
Actinobacteriota 6,192	Alphaproteobacteria 6,379	Bacteroidales 2,083	Flavobacteriaceae 1,247	Streptomyces 762
Bacteroidota 5,818	Bacteroidia 5,402	Pseudomonadales 1,886	Lachnospiraceae 1,155	Pseudomonas_E 574
Firmicutes_A 4,062	Actinomycetia 4,864	Flavobacteriales 1,847	Pelagibacteraceae 1,114	Prevotella 383
Firmicutes 3,390	Clostridia 3,566	Enterobacterales 1,701	Rhodobacteraceae 1,015	Mycobacterium 339
Patescibacteria 1,601	Bacilli 3,352	Actinomycetales 1,678	Streptomycetaceae 846	Flavobacterium 319
Cyanobacteria 1,067	Cyanobacteriia 920	Mycobacteriales 1,426	Mycobacteriaceae 811	Collinsella 316
Chloroflexota 982	Verrucomicrobiae 699	Rhizobiales 1,395	Sphingomonadaceae 762	Streptococcus 301
Verrucomicrobiota 917	Paceibacteria 684	Lachnospirales 1,285	Pseudomonadaceae 731	Prochlorococcus_A 265
Planctomycetota 748	Coriobacteriia 594	Oscillospirales 1,249	Enterobacteriaceae 724	Microbacterium 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.

Phylum	Class	Order	Family	Genus	Species
Proteobacteria 120,757	Gammaproteobacteria 104,665	Enterobacterales 64,157	Enterobacteriaceae 55,347	Escherichia 23,687	Escherichia flexneri 14,743
Firmicutes 53,879	Bacilli 53,835	Lactobacillales 28,917	Streptococcaceae 16,112	Streptococcus 15,765	Staphylococcus aureus 12,022
Actinobacteriota 24,602	Actinomycetia 21,459	Pseudomonadales 19,449	Staphylococcaceae 15,139	Staphylococcus 14,962	Salmonella enterica 11,523
Bacteroidota 13,917	Alphaproteobacteria 16,016	Staphylococcales 15,215	Mycobacteriaceae 11,561	Salmonella 11,772	Klebsiella pneumoniae 9,621
Firmicutes_A 12,649	Bacteroidia 12,772	Burkholderiales 13,431	Pseudomonadaceae 10,859	Klebsiella 10,886	Streptococcus pneumoniae 8,405
Campylobacterota 5,968	Clostridia 11,762	Mycobacteriales 12,534	Burkholderiaceae 8,796	Mycobacterium 9,568	Mycobacterium tuberculosis 6,684
Patescibacteria 3,496	Campylobacteria 5,957	Bacteroidales 7,082	Moraxellaceae 6,881	Acinetobacter 6,462	Pseudomonas aeruginosa 5,211
Cyanobacteria 2,210	Cyanobacteriia 1,949	Campylobacterales 5,940	Vibrionaceae 4,865	Pseudomonas 5,311	Acinetobacter baumannii 4,766
Verrucomicrobiota 2,095	Verrucomicrobiae 1,742	Bacillales 4,944	Enterococcaceae 4,454	Pseudomonas_E 4,871	Escherichia coli 4,370
Spirochaetota 1,689	Paceibacteria 1,561	Rhizobiales 4,913	Lactobacillaceae 4,070	Vibrio 4,447	Streptococcus 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).

Interactive: false

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.