Genome Taxonomy Database Explained

Genome Taxonomy Database
Description:	Proposed prokaryotic nomenclature
Center:	Australian Centre for Ecogenomics, University of Queensland
Pmid:	30148503
Released:	2018
License:	CC BY-SA 4.0
Curation:	mixed
Version:	R07/RS207 (8 April 2022)

The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases.^[1] Information for archaea was added in 2020,^[2] along with a species classification based on average nucleotide identity.^[3] Each update incorporates new genomes as well as automated and manual curation of the taxonomy.^[4]

An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy.^[5] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources.^{[6] [7]}

The GTDB is incorporated into the Bergey's Manual of Systematics of Archaea and Bacteria in 2019 as its phylogenomic resource.^[8]

See also

• PhyloCode
• National Center for Biotechnology Information
• SILVA ribosomal RNA database
• List of Prokaryotic names with Standing in Nomenclature

Further reading

• Pallen . MJ . Rodriguez-R . LM . Alikhan . NF . Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database. . International Journal of Systematic and Evolutionary Microbiology . September 2022 . 72 . 9 . free. 10.1099/ijsem.0.005482 . 36125864.  - proposal to name unnamed GTDB taxa using meaningless random Latin syllables. Not affiliated with GTDB.
• 3 . Zhu . Q . Mai . U . Pfeiffer . W . Janssen . S . Asnicar . F . Sanders . JG . Belda-Ferre . P . Al-Ghalith . GA . Kopylova . E . McDonald . D . Kosciolek . T . Yin . JB . Huang . S . Salam . N . Jiao . JY . Wu . Z . Xu . ZZ . Cantrell . K . Yang . Y . Sayyari . E . Rabiee . M . Morton . JT . Podell . S . Knights . D . Li . WJ . Huttenhower . C . Segata . N . Smarr . L . Mirarab . S . Knight . R . Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. . Nature Communications . 2 December 2019 . 10 . 1 . 5477 . 10.1038/s41467-019-13443-4 . 31792218. 6889312 . 2019NatCo..10.5477Z . free .  - a similar independent effort that also evaluates GTDB taxonomic quality.

Notes and References

1. Parks . DH . Chuvochina . M . Waite . DW . Rinke . C . Skarshewski . A . Chaumeil . PA . Hugenholtz . P . A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. . Nature Biotechnology . November 2018 . 36 . 10 . 996–1004 . 10.1038/nbt.4229 . 30148503 . 10.1101/256800. 52093100 .
2. Rinke . Christian . Chuvochina . Maria . Mussig . Aaron J. . Chaumeil . Pierre-Alain . Davín . Adrián A. . Waite . David W. . Whitman . William B. . Parks . Donovan H. . Hugenholtz . Philip . 21 June 2021 . A standardized archaeal taxonomy for the Genome Taxonomy Database . Nature Microbiology . en . 6 . 7 . 946–959 . 10.1038/s41564-021-00918-8 . 34155373 . 235595884 . 2058-5276.
3. Parks . DH . Chuvochina . M . Chaumeil . PA . Rinke . C . Mussig . AJ . Hugenholtz . P . A complete domain-to-species taxonomy for Bacteria and Archaea. . Nature Biotechnology . September 2020 . 38 . 9 . 1079–1086 . 10.1038/s41587-020-0501-8 . 32341564 . 10.1101/771964. 216560589 .
4. For information on each update, see relevant change logs. For notable, paper-worthy changes, see "Cite GTDB" section on the About page.
5. Chaumeil . PA . Mussig . AJ . Hugenholtz . P . Parks . DH . GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. . Bioinformatics . 15 November 2019 . 36 . 6 . 1925–1927 . 10.1093/bioinformatics/btz848 . 31730192 . 7703759 . free.
6. Almeida . Alexandre . Nayfach . Stephen . Boland . Miguel . Strozzi . Francesco . Beracochea . Martin . Shi . Zhou Jason . Pollard . Katherine S. . Sakharova . Ekaterina . Parks . Donovan H. . Hugenholtz . Philip . Segata . Nicola . Kyrpides . Nikos C. . Finn . Robert D. . A unified catalog of 204,938 reference genomes from the human gut microbiome . Nature Biotechnology . 20 July 2020 . 39 . 1 . 105–114 . 10.1038/s41587-020-0603-3 . 7801254 . 32690973 . free .
7. Nayfach . Stephen . Roux . Simon . Seshadri . Rekha . Udwary . Daniel . Varghese . Neha . Schulz . Frederik . Wu . Dongying . Paez-Espino . David . Chen . I-Min . Huntemann . Marcel . Palaniappan . Krishna . Ladau . Joshua . Mukherjee . Supratim . Reddy . T. B. K. . Nielsen . Torben . Kirton . Edward . Faria . José P. . Edirisinghe . Janaka N. . Henry . Christopher S. . Jungbluth . Sean P. . Chivian . Dylan . Dehal . Paramvir . Wood-Charlson . Elisha M. . Arkin . Adam P. . Tringe . Susannah G. . Visel . Axel . Woyke . Tanja . Mouncey . Nigel J. . Ivanova . Natalia N. . Kyrpides . Nikos C. . Eloe-Fadrosh . Emiley A. . 1 . A genomic catalog of Earth's microbiomes . Nature Biotechnology . 9 November 2020 . 39 . 4 . 499–509 . 10.1038/s41587-020-0718-6 . 33169036 . 8041624. free .
8. Web site: Incorporation of Phylogenomics into BMSAB . Bergey's Manual Trust.