Note that this is hard to do, not just in KBase, but in general. If I were to attempt this, I would 1) annotate my entire metagenome assembly, 2) identify contigs that fall into the different categories of interest (bacteria/archaea/viruses/eukaryotes), 3) filter out contigs belonging to eukaryotes/viruses, 4) summarize remaining results. A major challenge here will be the unambiguous identification of the different domains of life, which is sometimes tricky (e.g. prophages). Another note: file manipulation outside of KBase would be required to perform this task - we currently do not have KBase apps to complete this task.