Genome Taxonomy Database

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Genome Taxonomy Database - Wikipedia

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Genome Taxonomy Database
Content
Description	Proposed prokaryotic nomenclature
Contact
Research center	Australian Centre for Ecogenomics, University of Queensland
Authors	Phil Hugenholtz Maria Chuvochina Christian Rinke
Primary citation	PMID 30148503
Release date	2018
Access
Website	gtdb.ecogenomic.org
Miscellaneous
License	CC BY-SA 4.0
Version	R07/RS207 (8 April 2022)
Curation policy	mixed

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]

References

^ Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
^ 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" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.
^ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
^ For information on each update, see relevant change logs. For notable, paper-worthy changes, see "Cite GTDB" section on the About page.
^ Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
^ 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. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
^ Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
^ "Incorporation of Phylogenomics into BMSAB". Bergey's Manual Trust.

See also

References

Further reading