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Genome Taxonomy Database

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Genome Taxonomy Database
Content
Data types
captured		Proposed prokaryotic nomenclature, phylogenomic data
Contact
Research centerAustralian Centre for Ecogenomics, University of Queensland
Authors
  • Phil Hugenholtz
  • Maria Chuvochina
  • Christian Rinke
Primary citationPMID 30148503
Release date2018
Access
Websitegtdb.ecogenomic.org
Download URLgtdb.ecogenomic.org/downloads
Web service URLgtdb.ecogenomic.org/tree
Miscellaneous
LicenseCC BY-SA 4.0
Version09-RS220 (24th April 2024)
Curation policymixed

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]

Methodology

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The genomes used to construct the phylogeny are obtained from NCBI (RefSeq and Genbank), and GTDB releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB.[9]

Genomes first undergo gene calling to extract genes. The taxonomy is based on trees inferred with FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria under a WAG model, and with IQ-TREE from a concatenated set of 53 (since RS207; 122 before) marker proteins for Archaea under the PMSF model. Additional marker sets are also used to cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes.[9] The relative evolutionary divergence (RED) metric, which determines the taxonomic ranks used, is derived from the two main trees by the PhyloRank program.[1]

Species are deliminated using average nucleotide identity and alignment fraction, both calculated by skani. For species existing in a previous release, GTDB compares the quality and position of two genomes and may decide to switch to a new species representative genome.[9]

Taxomony comes from the following sources:

GTDB personnel curates the taxonomy from the aforementioned sources by checking them against the results of PhyloRank and the tree.

  • The tree node corresponding to a taxon name may have a RED inappropriate for its rank. The name may either be moved onto another node or (by changing the Latin suffix) into a different rank.[1]
    • Splitting may happen on the level of species or genera if the divergence turns out too high. Doing so creates new taxa.[3]
  • The taxon may turn out to be polyphyletic. The curator first restricts the taxon to the clade containing its type material. A new taxon is created for each of the other clades.[1]

For the each new taxon, the curators try to find a proposed name in literature for it. If there is no name proposed, the taxon is given a placeholder name by adding a suffix to the original name, e.g. Lactobacillus gasseri_A. After "Z" comes "AA".[1]

Contents of the database

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Each release contains:[10]

  • Taxonomy tables containing the assignment of all included genome assemblies to the phylum-to-species taxonomy. (One per domain.)
  • Files containing the metadata given to each genome assembly, including original taxonomy from NCBI, original strain identifier, GTDB taxonomy, quality estimates, and presence of important genes (tRNA and rRNA). (One per domain.)
  • Species tree Newick files containing the species-representative genomes (1 per species), built as described in the previous section. (One per domain.)
  • For species-representative genomes:
    • alignments of marker genes identified from these genomes
    • file containing one 16S rRNA sequence from each species
    • tarballs containing amino acid and nucleotide versions of all predicted genes in these genomes
    • tarball containing the full contents of all these genomes
  • For all genomes that pass quality check:
    • alignments of marker genes identified from these genomes
    • file containing all 16S rRNA sequences identified from these genomes
  • Auxiliary files; see the full FILE_DESCRIPTIONS.txt。

The web interface displays a tree based on the taxonomy (not the entire Newick file), down to the genome assembly level. Each genome assembly has a page detailing its metadata and a history of how it's classified in each GTDB release. There is a search functionality.

Effects on the accepted taxonomy

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GTDB "has now become an important resource for prokaryotic taxonomy". Both its species tree and elements of its methodology are used by taxonomists to improve the current, accepted taxonomy under the Prokaryotic Code. For example, a taxonomist may make references to the GTDB tree on top of their own phylogenetic tree to further support a taxonomic proposal.[11]

There has been even more ambitious proposals to import large parts of the database into the accepted taxonomy. A 2022 article in the IJSEM, written by third-party authors, proposes to assign names based on meaningless Latin syllable to over 65 thousand GTDB taxa,[12] though none of these names have made their way into the LPSN. A 2023 article by the GTDB team proposes to import 223 higher-order taxa into the Prokaryotic Code system and 49 under the SeqCode system.[13] Many of the names published under the under the Prokaryotic Code have already been validated.[14] (The SeqCode requires registration of the names for valid publication, which has also been done.)

See also

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References

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  1. ^ a b c d e f g h 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" (PDF). 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. ^ a b 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.
  9. ^ a b c "METHODS.txt (GTDB release 220)". data.gtdb.ecogenomic.org. 2024.
  10. ^ "220.0/FILE_DESCRIPTIONS.txt".
  11. ^ Gupta, Radhey S.; Patel, Sudip; Saini, Navneet; Chen, Shu (1 November 2020). "Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5753–5798. doi:10.1099/ijsem.0.004475.
  12. ^ 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.
  13. ^ Chuvochina, M; Mussig, AJ; Chaumeil, PA; Skarshewski, A; Rinke, C; Parks, DH; Hugenholtz, P (17 January 2023). "Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes". FEMS microbiology letters. 370. doi:10.1093/femsle/fnad071. PMC 10408702. PMID 37480240.
  14. ^ Oren, Aharon; Göker, Markus (1 February 2024). "Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi:10.1099/ijsem.0.006173.

Further reading

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  • AnnoTree - third-party tool for visualization of genome annotations using the GTDB (R95 or R214) species tree.
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