A vaccine, like any medicine, could cause a serious reaction. But the risk of a vaccine causing serious harm, or death, is extremely small.
Long-term use often leads the body to compensate by producing more of the hormone "gastrin". This hormone signals the stomach to increase acid production acid. Excessive levels of gastrin have been linked to the growth of esophageal, pancreatic, and gastric cancer cells.
One possible way to reduce the side effects is to reduce the dosage. If you were taking two probiotic pills daily, try taking only one probiotic pill per day. As your body becomes accustomed to the lower dosage, then you can increase the dosage to higher levels. But taking too many probiotic CFUs too quickly may result in probiotic overdose.