I feel that there is a push/pull immune relationship in the gut. The two most important elements are the active immune system (macrophages, neutrophils, etc.) and also the gut flora.
When immunity is suppressed such as in heavy metal toxicity, the gut flora can often hold off overt illness. However, Antibiotics or another trigger serves as the catalyst and then all hell breaks lose and the immune system cannot overcome it.
Look at the people who get infections during surgery etc. and go on IV Antibiotics but suffer no long-lasting effects. Obviously something else is at play.