The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed

nomenclature Nomenclature (, ) is a system of names or terms, or the rules for forming these terms in a particular field of arts or sciences. The principles of naming vary from the relatively informal conventions of everyday speech to the internationally ag ...

of prokaryotes, following a

phylogenomic Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields ...

approach based on a set of conserved single-copy proteins. In addition to breaking up paraphyletic groups, this method also reassigns

taxonomic rank In biological classification, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system consists of species, genus, family, order, class, phylum, kingdom, domain. While ...

s algorithmically, creating new names in both cases. Information for archaea was added in 2020, along with a

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

classification based on

average nucleotide identity Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp to over 14 Mbp. A study that included, but was not limited to ...

. Each update incorporates new genomes as well as human adjustments to 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 Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut mi ...

and other

metagenomic Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

sources. The GTDB is incorporated into the ''

Bergey's Manual of Systematics of Archaea and Bacteria ''Bergey's Manual of Systematic Bacteriology'' is the main resource for determining the identity of prokaryotic organisms, emphasizing bacterial species, using every characterizing aspect. The manual was published subsequent to the ''Bergey's Man ...

'' in 2019 as its phylogenomic resource.

References

{{reflist Genome databases

See also

References