Issue using Silva classifier high number of only Bacteria assigned

@geryale29, I also just realized that you might be using an older version of the SILVA reference database, as suggested by the taxonomy rank:

Later versions of QIIME 2 now provide premade SILVA (v138) classifiers with a Greengenes-like taxonomy. These classifiers, and the files used to train them are available via the Data resource page. You can even curate SILVA, and other reference databases, with RESCRIPt.