How badly can antibiotics mess up your digestive system?

Pretty badly: Antibiotics can have a profound effect on the normal bacterial flora of your bowels. In its most severe form it can cause pseudomembranous colitis due to toxin producing clostridium difficile overgrowth. It has been shown through meta-analysis that probiotics such as vsl#3 and florastor significantly decrease the incidence of antibiotic associated diarrhea and c. Difficile disease.