Agreed. Additionally, one of the mechanisms keeping the gut bacteria from taking over the rest of the body is an oxygen gradient: anaerobic bacteria in the gut

Agreed. Additionally, one of the mechanisms keeping the gut bacteria from taking over the rest of the body is an oxygen gradient: anaerobic bacteria in the gut are unlikely to be interested in an exploration of the aerobic environment of the body. Oxygen diffuses freely across the blood brain barrier, so it would not serve as an analogous containment mechanism.