have taken 80mg of omeprazole for years without any side effects. it controls my diarrhea and prevents me constantly running to the toilet. as soon as i stop it i get ibd, and after staying off it for a year ended up having half my bowel surgically removed. it is harmless to me. all this talk of bowel flora etc has to be weighed against the protective effect it has on the mucosa of the stomach and entire digestive tract. yes maybe there are more pathogens running round but the defenses are also much greater.