Australian online 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. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as automated and manual curation of the taxonomy.
An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy. The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources.
The GTDB is incorporated into the "Bergey's Manual of Systematics of Archaea and Bacteria" in 2019 as its phylogenomic resource.
Methodology.
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.
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. The "relative evolutionary divergence" (RED) metric, which determines the taxonomic ranks used, is derived from the two main trees by the PhyloRank program.
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.
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.
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".
Contents of the database.
Each release contains:
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.
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.
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, 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. Many of the names published under the under the "Prokaryotic Code" have already been validated. (The "SeqCode" requires registration of the names for valid publication, which has also been done.)
References.
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