How do Antibiotics work? Antibiotics are used to treat bacterial infections and work by weakening the bacteria so your immune system can easily overpower it. Unfortunately, antibiotics don't always just target the bad bacteria. Broad spectrum and prophylactic antibiotics have been shown to kill off beneficial bacteria and reduce microbiota diversity, overall weakening your gastrointestinal (GIT) structure, function and immunity. And this can happen after just one round of An