Prolonged military-style training causes changes to intestinal bacteria, increases inflammation - A new study finds that long periods of physiological stress can change the composition of microorganisms residing in the intestines (Intestinal microbiota), which could increase health risks in endurance athletes and military personnel. Ref. Source 6u.
Military Training & Health (Hover)
I disagree with this study as it does not always take into play the diets of the people involved. I think being in very good shape and being able to do some of the things that is required for military personnel that you are looking at a whole different ball game than a athlete who is training for on certain event.
All my time in the military I never found anyone who has had a issue with their gut. I k ow some who have after they got out of the military but it can be attributed to other items and not the military diet or exercise. Like my pains in that area can be contributed by all the chemicals I was exposed to in desert shield/storm.