With the caveat that I’m not an evolutionary (or co-evolutionary) biologist, there have been a handful fo really interesting papers recently around these topics, although most methods are not implimented in QIIME.
However, its hard to know where to point you if you’re not sure what you want to know about host-bacterial interactions. So, you could approach from a standard perspective similar to a case-control study where you use characteristics about hte host grouping. For something like that, you may want to check out the dataset tutorials (the first like 5-6 in docs page) and ignore the time series pieces.
If you have additional information about the hosts, you could layer in things like host phylogeny or host interaction, but again, that depends on yoru design. For those, a quick google scholar search should help come up with the papers, which are alluding me right now.