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.