Is this still the case with Metaphlan 4.0.5? And if not, what is the timeline for adding them back to the database? The removal of virus sequences was omitted from the changelog and the Metaphlan4 announcement. The manuscript implies that they are present but not extensively represented, rather than entirely absent:
The current methods also do not extensively incorporate viral or eukaryotic microbial sequences, due to their unique genomic architectures and quality control requirements relative to bacterial and archaeal genomes.
I now need to downgrade and reprocess several hundred samples.