Can i take stool softeners with antibiotics?

Concurrent meds: Antibiotics are useful for targeting pathogenic bacteria (germs). They often have the additional side effect, however, of 'taking out' some of the 'good bacteria' in the colon. This means that a common side-effect of antibiotics is loose stool, since the digestion process is thrown off. For that reason, you may not need your stool softener while on antibiotics. You could restart those later.