Note that this is hard to do, not just in KBase, but in general. To do this 1) annotate the 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 - as currently there are no KBase Apps to complete this task.