Do You Really Need Probiotics After Taking Antibiotics? Antibiotics are a common remedy to fight off bacterial infections. But they have an unfortunate side effect. They destroy the beneficial bacteria in the microbiome. Antibiotics also commonly cause diarrhea, which can cause dehydration. So, is it beneficial to take probiotics alongside your antibiotics? The answer is a bit complicated. In a recent Israeli study, researchers found that probiotic strains were able to colonize the gut despite antibiotic damage. However, the colonization delayed the recovery of the microbiota, which remained disturbed for the six month study. Subjects who took placebos recovered within three weeks. It seems we have a lot to learn about the microbiome.