GTDB - R89 Statistics

Release 89 statistics

GTDB release date: June 17, 2019

Taxon overview

GTDB r89 spans 145,904 genomes organized into 24,706 species clusters.

	Bacteria	Archaea	Total
Phylum	112	16	128
Class	296	36	332
Order	816	96	912
Family	1,969	238	2,207
Genus	7,372	534	7,906
Species	23,458	1,248	24,706

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 species clusters comprised of isolates or environmental genomes is given for each species 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.

Domain	Phylum	Class	Order	Family	Genus
Bacteria 23,458	Proteobacteria 7,630	Gammaproteobacteria 4,645	Burkholderiales 1,273	Burkholderiaceae 856	Streptomyces 470
Archaea 1,248	Actinobacteriota 3,118	Alphaproteobacteria 2,955	Pseudomonadales 1,270	Flavobacteriaceae 675	Pseudomonas_E 404
	Bacteroidota 2,843	Actinobacteria 2,735	Enterobacterales 1,186	Lachnospiraceae 615	Prevotella 229
	Firmicutes_A 1,886	Bacteroidia 2,677	Flavobacteriales 1,045	Mycobacteriaceae 611	Streptococcus 224
	Firmicutes 1,878	Bacilli 1,878	Bacteroidales 1,029	Rhodobacteraceae 578	Prochlorococcus_A 178
	Patescibacteria 1,031	Clostridia 1,836	Rhizobiales 961	Streptomycetaceae 528	Flavobacterium 176
	Cyanobacteria 654	Cyanobacteriia 597	Mycobacteriales 948	Pseudomonadaceae 514	Vibrio 140
	Halobacterota 411	Paceibacteria 392	Actinomycetales 944	Enterobacteriaceae 509	Corynebacterium 133
	Verrucomicrobiota 358	Verrucomicrobiae 292	Lactobacillales 674	Rhizobiaceae 476	Mycolicibacterium 122
	Chloroflexota 350	Bacilli_A 283	Lachnospirales 662	Sphingomonadaceae 398	Microbacterium 119

Taxa with the largest number of sequenced genomes

Taxa encompassing the largest number of genomes in the GTDB is given for each taxonomic ranks.

Domain	Phylum	Class	Order	Family	Genus	Species
Bacteria 143,512	Proteobacteria 65,677	Gammaproteobacteria 58,746	Enterobacterales 37,723	Enterobacteriaceae 32,509	Escherichia 13,879	Staphylococcus aureus 9,444
Archaea 2,392	Firmicutes 36,312	Bacilli 36,312	Lactobacillales 19,567	Streptococcaceae 12,474	Streptococcus 12,273	Escherichia flexneri 9,084
	Actinobacteriota 14,912	Actinobacteria 14,045	Staphylococcales 11,372	Staphylococcaceae 11,330	Staphylococcus 11,225	Salmonella enterica 8,698
	Bacteroidota 5,620	Alphaproteobacteria 6,870	Pseudomonadales 10,071	Mycobacteriaceae 9,384	Salmonella 8,878	Streptococcus pneumoniae 8,201
	Firmicutes_A 5,049	Bacteroidia 5,288	Mycobacteriales 9,911	Pseudomonadaceae 5,171	Mycobacterium 6,112	Mycobacterium tuberculosis 5,596
	Campylobacterota 3,912	Clostridia 4,929	Burkholderiales 7,087	Burkholderiaceae 4,378	Klebsiella 4,527	Klebsiella pneumoniae 4,086
	Patescibacteria 2,469	Campylobacteria 3,903	Bacillales 4,037	Moraxellaceae 3,831	Acinetobacter 3,623	Acinetobacter baumannii 2,796
	Cyanobacteria 1,158	Cyanobacteriia 1,048	Campylobacterales 3,894	Vibrionaceae 2,937	Pseudomonas 2,808	Pseudomonas aeruginosa 2,744
	Spirochaetota 1,096	Paceibacteria 942	Rhizobiales 3,317	Listeriaceae 2,579	Vibrio 2,643	Escherichia coli 2,432
	Halobacterota 758	Verrucomicrobiae 607	Bacteroidales 2,614	Campylobacteraceae 2,490	Listeria 2,568	Mycobacteroides abscessus 1,589

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.