Integration of metagenomics data from different studies


I have 16S metagenomics data from 3 different organisms, all of which have gone through a certain dietary intervention and their control groups. I have analyzed the data of each organism separately because the reads have different depths and have been sequenced in separate facilities. We are especially interested in differentially abundant features, which turns out to be different in each studied organism. Now, we want to bring everything together, somehow to contextualize our data or maybe dig deeper in an integrative way. For example, is there anything in common between the studied organisms’ changes in their gut microbial composition? How one can detect such features?
Any commonly used tools, similar papers, or ideas would be of great help! :slight_smile: