Antibiotics are considered a miracle of modern medicine our “magic bullets” that kill harmful microorganisms and spare our bodies in the war against infection. Conan MacDougall explains that the story is much more complex. Most of the bugs that would do us harm usually co-exist with us on our skin, in our gut and in our cells themselves. The indiscriminate killing of bacteria by antibiotics and disinfectants may deprive us of nutrients and deny our immune system the “training” it needs to distinguish self from non-self leading to an increase in autoimmune diseases. And the rise of antibiotic resistance requires us to examine how we deal with uncertainty and risk and our responsibilities to current and future patients.