There are lots of reasons to avoid processed foods. They’re often packed with sugar, fat and salt, and they tend to lack certain nutrients critical to health, like fiber. And now, new research suggests that some of the additives that extend the shelf life and improve the texture of these foods may have unintended side effects — not on our bodies directly, but on the human microbiome, the trillions of bacteria living in our guts.

These substances may selectively feed the more dangerous members of our microbial communities, causing illness and even death.

Consider the rise in deadly cases of clostridium difficile, or C. diff, a terrible infection of the gut. The bacterium tends to strike just after you’ve taken antibiotics to treat something else. Those antibiotics kill your native microbes, allowing C. diff to move in. Nearly half a million people develop the infection yearly, according to the Centers for Disease Control and Prevention, and around 29,000 die, sometimes after long bouts of painful, bloody diarrhea. By one estimate, deaths linked to C. diff increased fivefold between 1999 and 2007.

One reason the bug has become more virulent is that it has evolved antibiotic resistance and is not as easily treatable. But some years ago, Robert Britton, a microbiologist at Baylor College of Medicine, discovered something else about C. diff: More virulent strains were outcompeting less virulent strains in the gut.