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How Prebiotic Foods Keep Your Microbiome Healthy

May 14, 2026
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We co-evolved a symbiosis with our good gut bacteria, but we aren’t holding up our end of the bargain.

If you look at the classics—the most frequently cited articles in the scientific nutrition literature—the original glycemic index paper ranks tenth, cited more than a thousand times. Learning about fruits, vegetables, and cancer prevention comes in seventh. But hitting the top four, cited more than 2,000 times: “Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics.”

As I discuss in my video How to Keep Your Microbiome Healthy with Prebiotic Foods, prebiotics are the food components that nourish and feed the good bacteria in our gut, like fiber and resistant starch. Eating high-fiber plant foods is generally “a good foundation for a prebiotic-rich diet.”

Once upon a time, fiber was thought of as just the undigested part of food, known only for bulking up stools and keeping bowels regular. Then researchers discovered an array of receptors in the body that fiber-breakdown products fit into like a lock and key. We feed our good bacteria with fiber, and they feed us right back, munching the fiber and creating short-chain fatty acids. These fatty acids get absorbed into our bloodstream and fit into these receptors that are expressed on immune cells, generally having a direct anti-inflammatory effect.

So, the reason behind lower systemic inflammation in plant-based eaters may not just be due to the abundance of anti-inflammatory molecules in plant foods or the avoidance of proinflammatory molecules in animal foods, but from the production of anti-inflammatory molecules from scratch by our good gut bugs when we feed them fiber. Just to give you an idea of how protective fiber-rich foods can be, those randomized to get advice on eating fiber-rich plant foods during radiation therapy for cancer didn’t just experience reduced toxicity during the treatments—the benefit persisted even a full year later.

Indeed, the benefits of fiber are supported by more than a century of research. Prospective studies show “striking reductions” in death from all causes put together, including “total cancer deaths, total cardiovascular disease deaths and incidence, stroke incidence, and incidence of colorectal, breast, and oesophageal cancer.” And, in terms of protecting against heart attacks and stroke, type 2 diabetes, and cancer, dose-response relationships suggest that the more fiber, the better. So, at a minimum, fiber intake should be no less than 25 to 29 grams per day; higher intake may provide additional benefits. Yet, the average American only consumes about 16 grams of fiber each day.

We have coevolved with gut bacteria over millennia, becoming reliant on our good gut bugs in a kind of symbiosis for fiber digestion and the production of short-chain fatty acids and even certain vitamins. Yet we’re not holding up our end of the bargain. We’re supposed to be providing up to 100 or so grams of fiber a day, and we are barely passing along a measly 16 grams. The simplest solution to remedy this lack of dietary fiber is to encourage eating plant-based diets rich in fiber.

Doctor’s Note

A hundred grams of fiber a day?! Check out Paleopoo: What We Can Learn from Fossilized Feces.

And, for more on prebiotics, see Prebiotics: Tending Our Inner Garden.





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