Rapamycin significantly affects the gut microbiome composition in dogs and mice, and this is expected in humans.

“one of the reasons why I think that there's reason to think that at least some of the changes in the microbiome could be causal for some of the effects of rapamycin is that one of the things we saw in our mouse study was a pretty profound increase in a bacterium called segmented filamentous bacteria or SFB and the rapamycin treated mice it turns out if you look in the literature there are links between SFB and diabetes and obesity and also between sfb and t-helper cell maturation so it could be the case that changes that rapamycin is having on this specific bacterium as well as other bacteria are then having effects both on potentially nutrient utilization and uptake but also direct effects on say immune function”