Taxonomy involves naming, delimiting and organizing groups of organisms (taxa) on the basis of shared traits that, ultimately, reflect their evolutionary history. Taxonomy itself evolves and revising old taxonomic schemes is necessary. The GTDB aim to produce a more uniform and stable genome-based taxonomy is laudable and extremely useful. However, despite some improvements, there is still an important problem in the current GTDB nomenclature: several standing taxon names are being reused for a new phylogenetic delimitation (a different extent of organisms). This introduces confusion and prevents meaningful comparison with long-accumulated knowledge, especially for groups with a long history in microbiology science. I previously raised the problem (to Phil) and suggested to give new names to newly circumscribed taxa. This was fortunately done for some archaeal taxa. Thus, Euryarchaeota and Crenarchaeota, which encompassed clades of very different breadth in various GTDB releases as compared with classical taxonomic schemes since Woese’s formal definition in 1990, disappeared as GTDB phyla and were replaced by several phyla with different new names (Thermoproteota, Halobacterota, Methanobacteriota, etc.).
Unfortunately, the problem still affects some important classical taxa within Bacteria. I will mention two such cases. The first concerns the Proteobacteria, traditionally encompassing Alpha-, Beta-, Gamma-, Delta-, Epsilon- and Zetaproteobacteria. In the current GTDB release, Proteobacteria is reused to refer to only a subset of those clades excluding former Delta- and Epsilonproteobacteria clades (Desulfobacterota, Myxococcota, Bdellovibrionota, Campylobacterota, etc.). This is extremely confusing, since Proteobacteria is among the most diverse and studied taxa. A large body of knowledge about Proteobacteria integrate clades that are now excluded in the GTDB ‘Proteobacteria’. Could you consider changing the name of the GTDB ‘Proteobacteria’ phylum to a new name to prevent that confusion?
A similar situation affects the GTDB taxon Cyanobacteria, which classically corresponds to the clade including only ancestrally oxygenic photosynthetic bacteria (GTDB Cyanobacteriia) but that in the GTDB taxonomy includes also two taxa of related non-photosynthetic bacteria. Accumulated knowledge on cyanobacteria exclude those other taxa. In addition, this taxon also exists in the botanical code, such that it is likely that the same name, Cyanobacteria, persists in the future to refer to two different clades of organism, which complicates and obscures scientific progress. Again, would it be possible to simply give a different name to the clade formed by classical Cyanobacteria and its two related clades?
In general, renaming taxa differently rather than changing the semantics (the extent of organisms) of a given name would be extremely important for clarity in the (micro)biology community. Would you consider this element for future releases?
Thank you for the GTDB initiative, best wishes