Genome Taxonomy Database (original) (raw)

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Australian online database

Genome Taxonomy Database

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]

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

1. ^ 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.
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" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.
3. ^ 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.
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 (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.
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. (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.
7. ^ 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.
8. ^ "Incorporation of Phylogenomics into BMSAB". Bergey's Manual Trust.

• Pallen, MJ; Rodriguez-R, LM; Alikhan, NF (September 2022). "Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database" (PDF). International Journal of Systematic and Evolutionary Microbiology. 72 (9). doi:10.1099/ijsem.0.005482. PMID 36125864. – proposal to name unnamed GTDB taxa using meaningless random Latin syllables. Not affiliated with GTDB.
• Zhu, Q; Mai, U; Pfeiffer, W; et al. (2 December 2019). "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea". Nature Communications. 10 (1): 5477. Bibcode:2019NatCo..10.5477Z. doi:10.1038/s41467-019-13443-4. PMC 6889312. PMID 31792218. – a similar independent effort that also evaluates GTDB taxonomic quality.