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 proteins. In addition to breaking up paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, creating new names in both cases.[1] Information for archaea was added in 2020, along with a species classification based on average nucleotide identity.[2]
| 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 | https://gtdb.ecogenomic.org/ |
| Miscellaneous | |
| License | CC BY-SA 4.0 |
| Version | 95.0 (July 17th, 2020) |
| Curation policy | mixed |
An open source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy.[3] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources.[4][5]
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.
- 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.
- Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics (Oxford, England). 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. doi:10.1038/s41587-020-0603-3. PMID 32690973.
- 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. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. doi:10.1038/s41587-020-0718-6.
See also
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