High hopes rest on manipulating the gut microbiome in order to treat a multitude of disorders. Clinical validation for the idea has come from the success of fecal microbiome transplants to treat chronic Clostridium difficile infections. Such transplants are in clinical trials to treat other gastrointestinal disorders, and more targeted methods to manipulate the microbiome are being developed as well, not just for infections, but in a multitude of other indications. Targeting the gut microbiome may turn into a way to alleviate inflammatory bowel disease, food allergies, and even psychiatric conditions.