I am using metaphlan3 for creating relative abundance profile of bacteria and viruses in faecal metagenomics samples. Looking at the abundance profiles of 3 donors, none of them contain crassphage which is against the literature (crassphage comprises up to 90% of the gut virome). However, kraken2 results were consistent with what I expected. I am wondering what the issue is with metaphlan3 and whether it is a reliable pipeline for viral metagenomics as well as for bacteria.