The Herxheimer Reaction is a short-term (from days to a few weeks) detoxification reaction in the body. As the body detoxifies, it is not uncommon to experience flu-like symptoms including headache, joint and muscle pain, body aches, sore throat, general malaise, sweating, chills, nausea or other symptoms.
This is a normal reaction that typically indicates that your body is actively dealing with issues in your gut, kind of like battle between good and bad bacteria. The biggest problem with the Herxheimer reaction is that people stop taking the supplement or medication that is causing the reaction, and thus discontinue the very treatment that is going to help to make them better. Although the experience may not make you feel particularly good, the Herxheimer Reaction is actually a sign that the products are working.
If you do feel discomfort be sure to ease back the amount of probiotics you're taking to where you feel comfortable again. Then, once you are steady at that amount for a while, you can slowly increase the amount over time. This can even be tapered back to a half or quarter capsule! Feel free to break open the capsule and add it to your food, a smoothie, or straight into your mouth to consume just half the contents of the capsule.