You are right, studies can mean whatever you want them to mean, but that doesn't mean this idea isn't on the right path at least.
The basis is 2 main ideas that don't have anything to do with studies, and that really aren't in any dispute:
1. The human mind is drastically affected by the mix of chemicals inside the body
2. Permanently changing the balance of the majority of the bacteria in the body (and thus the balance of waste byproducts), will change the mix of chemicals inside the body.
It doesn't really matter WHAT causes the bacteria mix to change, but we now know that messing with it can have some serious long-term side effects, and some of those side effects could explain very common "epidemics" such as obesity, autism, food allergies, and the impending zombie apocalypse.