IBS, gluten or lactose intolerance, parasites in gut too can be the cause. A stool
test should be done
for worms, giardiasis etc. Also if nothing is found then food challenge test to detect food intolerance should be done.If you have missed periods, it could be pregnancy. PCOD too should be looked into.
Since I cannot examine you and know other related conditions you may be having, nor is a detailed history possible on net, I have listed the various possibilities that should be looked into.