Hi Anthony
We transform the output of MetaPhlAn4 (SGBs) to the corresponding GTDB taxonomy. It’s my understanding the Huttenhower group ran all their SGBs through the GTDB-tk to obtain the GTDB taxonomy. In my opinion, GTDB is a gold standard taxonomy assignment, but of course, there is debate.
See Total Bacteria species relative abundance no longer sums to 1 after converting the SGB profile to GTDB for some discussion, though.
Cheers,
Scott