GTDB Forum

Major differences between the r95 GTDB and NCBI taxonomy

Normalizing phylogenetic depth based on the relative evolutionary divergence (RED) resulted in both, division and amalgamation, of archaeal NCBI phyla in GTDB r95 taxonomy. The most extensive changes were required for the NCBI phylum Euryarchaeota and the NCBI superphylum TACK and are outlined below. Further details are provided in Rinke et al. 2020.

NCBI phylum Euryarchaeota
Divided into five separate phyla in the GTDB taxonomy due to its anomalous depth:
p__Halobacteriota
p__Thermoplasmatota
p__Methanobacteriota
p__Hadarchaeota
p__Hydrothermarchaeota

Note: when possible phylum names were derived from the oldest validly published class name in each group using the recently proposed standardised phylum suffix -ota (Whitman et al., 2018); e.g. the Thermoplasmatota phyl. nov. from the class Thermoplasmata (Anna-Louise Reysenbach, 2001)

TACK superphylum (Guy and Ettema, 2011)
Reclassified as a single phylum:
p__Thermoproteota

Subsequently, several NCBI-defined TACK phyla required demotion to lower-level lineages, including:
c__Nitrososphaeria (NCBI phylum Thaumarchaeota)
c__Thermoprotei (NCBI phylum Crenarchaeota)
c__Korarchaeia (NCBI phylum Korarchaeota)
c__Bathyarchaeia (NCBI phylum Bathyarchaeota)
c__Methanomethylicia (NCBI phylum Verstraetearchaeota)
o__Caldarchaeales (NCBI phylum Aigarchaeota)

Note: GTDB endeavours to follow the Prokaryotic Code which requires all ranks up to class to be built from a genus stem, hence demoted phyla such as Thaumarchaeota and Verstraetearchaeota needed to be renamed according to the designated type genus or the oldest validly named genus in their respective classes.

Note, the name Hadarchaeota has been proposed in Chuvochina et al. 2019

“Here we propose Candidatus Hadarchaeum yellowstonense based on the highest quality MAG available, YNP_45 (GCA_001515205.2) as the first named species within the lineage that can serve as the type for naming higher taxa containing this species: Hadarchaeaceae (family), Hadarchaeales (order), Hadarchaeia (class), and Hadarchaeota (phylum)”