Your gut is like a well-fortified Medieval castle. Credit: IStock

Think about the last time you ate an apple—from the apple’s perspective. Pulverized in your mouth and dunked in a cauldron of stomach acid, the fruit slowly passed through the intestine before its final, unceremonious exit. Digestion is a wild, wacky journey.

Scientists study how the body can both absorb life-sustaining nutrients and keep out harmful invaders. Understanding this balance—and how it can get thrown out of whack—could lead to better treatments for digestive diseases.

Most of the nutrients from food we eat get absorbed in the intestine, which is home to a vast population of bacteria known as the microbiome. These bacteria help break down complex particles that we can’t, such as the fiber in fruits and vegetables. But some gut bacteria, known as pathogens, cause disease. The immune system’s job is daunting: It must protect us from pathogens without targeting healthy gut bacteria or food particles.

The first line of defense is the barrier of cells that line the intestine. These immune cells allow only small particles to pass through, making the intestine a bit like a medieval castle: A small rat can slip through the walls, but people have to get past the guards. This castle has a moat, too: a slippery layer of mucus that keeps organisms from getting too close. And no castle is complete without archers staffing the walls. Immune cells fire off proteins called antibodies that stick to gut bacteria to prevent them from attacking the body.

The immune system also learns to tolerate common foods and gut bacteria so it can recognize them as harmless and unlikely to cause disease. Researchers are studying exactly how this works, but they think that the intestine is naturally wired to permit most foods and beneficial bacteria.

Sometimes, however, the immune system commits friendly fire and attacks the body when it shouldn’t. Two common examples are celiac disease, an immune response to gluten, and inflammatory bowel disease, a response to the microbiome in the gut. Scientists are not sure why people get these diseases, although some studies suggest that specific genes may be involved. But it’s clear that more research is needed to reveal the secret of how the immune system distinguishes food and friend from foe.

Jonathan Wosen is a PhD candidate in immunology at Stanford University, where he studies how the cells that line the intestines communicate with the surrounding immune system. Wosen was the 2017 American Physiological Society-sponsored AAAS Mass Media Science and Engineering Fellow at STAT News, a national science news publication based in Boston.