Frequently asked questions

How can I classify my own genomes with the GTDB?
We have developed a stand-alone application called GTDB-Tk.

Why has the suffix of phyla names been changed to -ota?
We have adopted the proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes as originally proposed by Oren et al. (2015) and updated by Whitman et al. (2018) to use the suffix -ota to denote phyla.

Why are some genus names formed from a strain identifier?
A strain identifier is used as a placeholder for the genus name when there is no existing genus name and no binomially named representative genome. For example, the genome GCF_000318095.2 has the NCBI organism name Prevotella sp. oral taxon 473 str. F0040. However, this genome is more closely related to Prevotellamassilia and Alloprevotella. Consequently, we assign it to the placeholder genus g__F0040. If the organism had been assigned a binomial species name such as Prevotella oralitaxus str. F0040 we would assign it to the placeholder genus g__Prevotella_A to indicate it is not a true Prevotella species, but that there are representative genomes that have been assigned to a species.

Why do some genera and species names end with an alphabetic suffix?
Genera and species names with an alphabetic suffix indicate genera and species that are polyphyletic or needed to be subdivided according to taxonomic rank normalisation according to the GTDB reference tree. The lineage containing the type strain retains the unsuffixed (valid) name and all other lineages are given alphabetic suffixes, indicating that they are placeholder names that need to be replaced in due course.

Why do some family and higher rank names end with an alphabetic suffix?
Taxon names above the rank of genus appended with an alphabetic suffix indicate groups that are not monophyletic in the GTDB reference tree, but for which there exists alternative evidence that they are monophyletic groups.


References

Oren A, et al. (2015). Proposal to include the rank of phylum in the international code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 65, 4284-4287.

Whitman WB, et al. (2018). Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'. Int J Syst Evol Microbiol 68, 967-969.