GTDB - R226 Statistics

Release 226 statistics

GTDB release date: 16th April, 2025

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Taxon overview

GTDB R226 spans 732,475 genomes organized into 143,614 species clusters.

	Bacteria	Archaea	Total
Phylum	169	20	189
Class	571	63	634
Order	1,976	171	2,147
Family	5,311	603	5,914
Genus	27,326	2,079	29,405
Species	136,646	6,968	143,614

Species overview

GTDB R226 is comprised of 715,230 bacterial and 17,245 archaeal genomes organized into 136,646 bacterial and 6,968 archaeal species clusters, respectively.

Release	Bacterial Genomes	Archaeal Genomes	Bacterial Species Clusters	Archaeal Species Clusters
R04-RS89	143,512	2,392	23,458	1,248
R05-RS95	191,527	3,073	30,238	1,672
R06-RS202	254,090	4,316	45,555	2,339
R07-RS207	311,480	6,062	62,291	3,412
R08-RS214	394,932	7,777	80,789	4,416
R9-RS220	584,382	12,477	107,235	5,869
R10-RS226	715,230	17,245	136,646	6,968
Growth from R09-RS220	22.39%	38.21%	27.43%	18.73%

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, unless a large portion of contamination could be attributed to strain heterogeneity. A few exceptions exist in order to retain well-known species with abnormal CheckM quality estimates, where contamination exceeds 10%.

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
Pseudomonadota 35,839	Gammaproteobacteria 19,731	Burkholderiales 7,245	Burkholderiaceae 4,466	Streptomyces 1,739
Bacillota 24,866	Bacteroidia 16,912	Bacteroidales 6,951	Lachnospiraceae 3,903	Collinsella 1,058
Actinomycetota 16,922	Alphaproteobacteria 15,970	Oscillospirales 5,467	Flavobacteriaceae 2,952	Pelagibacter 891
Bacteroidota 16,912	Clostridia 15,463	Flavobacteriales 4,528	Rhodobacteraceae 2,553	Prevotella 888
Patescibacteriota 6,435	Actinomycetes 10,924	Lachnospirales 4,263	Sphingomonadaceae 2,180	Pseudomonas_E 878
Chloroflexota 4,182	Bacilli 7,498	Rhizobiales 3,949	Streptomycetaceae 1,950	Flavobacterium 812
Acidobacteriota 3,758	Verrucomicrobiia 2,595	Pseudomonadales 3,843	Bacteroidaceae 1,845	Streptococcus 693
Verrucomicrobiota 3,351	Minisyncoccia 2,547	Actinomycetales 3,638	Chitinophagaceae 1,598	Mycobacterium 597
Planctomycetota 3,168	Acidimicrobiia 2,102	Mycobacteriales 2,983	Oscillospiraceae 1,587	Cryptobacteroides 555
Cyanobacteriota 2,718	Cyanobacteriia 1,943	Rhodobacterales 2,553	Microbacteriaceae 1,524	Microbacterium 451

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
Pseudomonadota 267,130	Gammaproteobacteria 226,629	Enterobacterales 133,925	Enterobacteriaceae 115,303	Escherichia 45,533	Escherichia coli 44,640
Bacillota 205,871	Bacilli 109,361	Bacteroidales 67,821	Lachnospiraceae 37,618	Klebsiella 28,408	Klebsiella pneumoniae 23,011
Bacteroidota 89,203	Clostridia 89,775	Lactobacillales 54,361	Staphylococcaceae 25,195	Staphylococcus 24,405	Staphylococcus aureus 17,542
Actinomycetota 59,430	Bacteroidia 89,203	Pseudomonadales 42,287	Muribaculaceae 24,600	Streptococcus 21,852	Salmonella enterica 17,159
Campylobacterota 12,704	Actinomycetes 45,222	Lachnospirales 38,784	Streptococcaceae 23,415	Salmonella 17,457	Pseudomonas aeruginosa 10,492
Patescibacteriota 10,847	Alphaproteobacteria 40,295	Burkholderiales 30,358	Pseudomonadaceae 21,139	Acinetobacter 14,084	Acinetobacter baumannii 10,048
Verrucomicrobiota 8,325	Campylobacteria 12,658	Staphylococcales 25,423	Bacteroidaceae 20,813	Mycobacterium 11,924	Streptococcus pneumoniae 9,446
Cyanobacteriota 7,057	Verrucomicrobiia 6,806	Oscillospirales 25,303	Burkholderiaceae 19,661	Pseudomonas 10,723	Mycobacterium tuberculosis 7,631
Chloroflexota 6,904	Coriobacteriia 6,002	Mycobacteriales 19,389	Mycobacteriaceae 16,757	Pseudomonas_E 8,551	Enterococcus faecalis 4,055
Acidobacteriota 5,462	Acidimicrobiia 5,487	Actinomycetales 13,693	Moraxellaceae 15,244	Vibrio 8,461	Enterococcus_B faecium 3,907

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.

Phylum names have been updated to follow the valid publication of 42 names in IJSEM. This has resulted in a large number of active phylum name changes relative to NCBI classifications at the time of this release. NCBI is also adopting these new phyla names.

Genomic statistics

Key genomic statistics for the GTDB species representative genomes and all genomes in the GTDB.

Genomes

Species

Nomenclatural types per rank

This plot shows the breakdown of placeholder versus latinized names for each taxonomic rank.

	Bacteria: Latin	Bacteria: Placeholder	Archaea: Latin	Archaea: Placeholder	Latin	Placeholder
Phylum	76 (44.97%)	93 (55.03%)	16 (80.00%)	4 (20.00%)	92 (48.68%)	97 (51.32%)
Class	170 (29.77%)	401 (70.23%)	41 (65.08%)	22 (34.92%)	211 (33.28%)	423 (66.72%)
Order	401 (20.29%)	1,575 (79.71%)	73 (42.69%)	98 (57.31%)	474 (22.08%)	1,673 (77.92%)
Family	856 (16.12%)	4,455 (83.88%)	111 (18.41%)	492 (81.59%)	967 (16.35%)	4,947 (83.65%)
Genus	4,230 (15.48%)	23,096 (84.52%)	294 (14.14%)	1,785 (85.86%)	4,524 (15.39%)	24,881 (84.61%)
Species	17,977 (13.16%)	118,669 (86.84%)	811 (11.64%)	6,157 (88.36%)	18,788 (13.08%)	124,826 (86.92%)