Why? “When you eat, there is a natural increase in digestive enzymes and bile salt production as your digestive system prepares to, well, digest your food," explains Gregor Reid, Ph.D., the chief scientist at the probiotic company Seed . Those enzymes and bile salts can kill the bacteria in your probiotics long before they ever get to your small and large intestines, where their real work is done. Taking the supplements when you're not digesting food (and therefore there are lower levels of these substances in your stomach)increases the chances that the bugs will survive their transit intact so they can influence your healthFor these reasons, taking your supps after a meal might be a mistake, but before or as you start eating is an optimal window.