Indigestion, diarrhea, and other stomach issues are common side-effects of strong/broad-spectrum antibiotics because they kill nearly all of the healthy gut bacteria. Some bacteria though can escape due to a combination of factors, some are replenished from the appendix (turns out it is now thought to be a reservoir), and food. Probiotics have been found to be entirely useless in these cases.
In some extreme cases, doctors might recommend stool transplants, where a stool sample is brought in from a “stool bank” which is then transplanted into the patient via enema or an oral capsule.