Someday soon, your medicine cabinet will have pills not just for you, but also for the microbes in your gut.

These pills will “treat and inhibit an enzyme in our microbes and elicit a health benefit in some chronic disease,” said cardiologist Stanley Hazen, MD, PhD, co-head of the Preventive Cardiology and Rehabilitation, Heart, Vascular and Thoracic Institute and director of the Center for Microbiome and Human Health at Cleveland Clinic.

Because evidence is mounting that the gut microbiome influences just about every major human disease. These trillions of microbes use our food to make substances called metabolites that can protect or harm our health, with consequences reaching far beyond our digestive tracts. Research has linked microbial metabolites to diabetes, cardiovascular disease, liver disease, obesity, high blood pressure, neurological disorders, depression, cancer, and more. Gastroenterologist Christopher Damman, MD, a clinical associate professor at the University of Washington Medical Center, Seattle, calls it a “growing theme” in microbiome science.

Now scientists are developing treatments targeting gut microbial pathways, designed to eliminate the bad metabolites and boost the good metabolites. One close to use in humans is an oral treatment from Hazen’s lab targeting the metabolite trimethylamine N-oxide (TMAO), a predictor of and contributor to both cardiovascular disease and chronic kidney disease. The drug, which blocks TMAO formation, is nearing clinical trials, Hazen said.

The advantage is safety. By targeting the microbe instead of, say, an enzyme, the host (you) must absorb little if any drug. Implications for the future of medicine are huge. “Gut microbial pathways contribute to diabetes, obesity, virtually everything,” Hazen said. “Therapies that target gut microbiome processes will probably even be used for psychiatric disorders within, I’ll say, 10 or 20 years.” About 100 trillion strains of bacteria live in our guts. As humans have evolved, so have they. Between 70% and 90% come from the phyla Firmicutes and Bacteroidetes, but the mix varies, depending on your genes, environment, and lifestyle. “Everyone’s microbiome is subtly different,” said Hazen. “So the combination of what they’re making is different. All these different biologically active compounds are influencing us in subtly different ways.”

How it works: When you eat, your microbes eat, breaking down food into metabolites that interact with the thin layer of epithelial cells lining your gut. Some can be absorbed through the lining and into your bloodstream, a phenomenon known as “leaky gut.” Once in your blood, they can trigger irritation and inflammation, potentially leading to a wide variety of health issues, from gas and bloating to autoimmune conditions and mood disorders. “On the other side of the epithelial lining, you have some of the largest concentrations of immune cells,” said Narendra Kumar, PhD, an associate professor of pharmaceutical sciences at Texas A&M University, College Station.