For decades, we have fought a war against bacteria, with antibiotics as our primary weapons. These drugs have been very successful because they effectively kill the bacteria while apparently sparing us. Unless, of course, we have been wrong about what is “us.” We now know that humans are home to an ecosystem of trillions of beneficial microbes – the human microbiome – that affect our susceptibility to infections and autoimmune disease. Our health is intimately linked to theirs. We have recently come to understand that antibiotics indiscriminately kill both pathogens as well as these beneficial microbes. War is unpredictable, and waging war against our microbes has unpredictable consequences. Bernat Olle argues that we must develop new medicines that nurture this ecosystem of beneficial microbes instead of carpet-bombing it.