Phylophlan Nucleotide Database for marker genes


I wanted to use the nucleotide database of phlophlan in order to identify marker genes in some isolate genomes. After identifying markers, I will design PCR primers to target and sequence them.

I downloaded the databases from here:

Which was suggested in the wiki: Home · biobakery/phylophlan Wiki · GitHub

However, the database only contains protein sequences. Phlyophlan has the option to run on both protein and nucleotide, which implies that there should be a nucleotide database as well. Is it stored somewhere else, or do I misunderstand how PhloPhlAn works?

Thank you for your help,