Fermented Foods vs. Fiber: What a Stanford Study Found About Gut Health and Inflammation

If you’ve spent any meaningful amount of time in the wellness world, you’ve probably been instructed to eat more fiber. Constipated? Fiber. Trying to improve your microbiome? Fiber. Want to support your heart, stabilize your blood sugar and maintain the bowel movements of a well-hydrated Labrador? Fiber.

And, to be clear, the advice isn’t wrong. Fiber is incredibly important. There is a substantial body of research connecting adequate fiber intake with better digestive, cardiovascular and metabolic health, and a decrease in chronic disease and all cause mortality. Though an interesting Stanford study offers a much better lesson than simply crowning another nutritional winner: The human body is an ecosystem, and ecosystems are a hell of a lot more complicated than “eat more of this.”

In 2021, researchers at Stanford School of Medicine published a randomized dietary intervention in the journal Cell comparing two increasingly popular approaches to supporting the gut microbiome: a diet high in fiber and one high in fermented foods. Thirty-six healthy adults completed the dietary intervention, with participants assigned to increase either fiber-rich foods such as legumes, whole grains, nuts, seeds, vegetables and fruit, or fermented foods including yogurt, kefir, fermented cottage cheese, kimchi, other fermented vegetables, vegetable brine drinks and kombucha. The diets were followed for 10 weeks, with researchers collecting blood and stool samples along the way to examine what was happening inside both the microbiome and immune system. 

The Fermented-Food Group Changed. A lot.

By the end of the intervention, the fermented-food group experienced an increase in gut microbial diversity. Researchers also found decreased activation among four types of immune cells and lower levels of 19 inflammatory proteins measured in participants’ blood. One of those proteins was interleukin 6, or IL-6, an inflammatory cytokine that has been associated with several chronic inflammatory conditions. The researchers also observed that greater fermented-food consumption was associated with stronger increases in microbiome diversity. 

The high-fiber group didn’t experience the same population-wide changes. Microbial diversity remained relatively stable, and researchers did not observe the broad reduction in inflammatory proteins seen in the fermented-food group. This makes for a very clickable headline: "Fermented foods beat fiber.' Though it isn’t really what the research tells us, and reducing the study to a nutritional cage match misses what might be its most interesting finding. Fiber didn’t suddenly stop being good for us.

Fiber Needs Something to Feed

We tend to talk about fiber as though it enters the body, flips the “gut health” switch and gets to work. Humans can't digest many types of dietary fiber on our own, so we rely on microorganisms living in the gut to help metabolize them. During that process, certain microbes produce short-chain fatty acids and other compounds that can influence intestinal, metabolic and immune health.

Researchers found that participants on the high-fiber diet increased their capacity to process fiber, but they also saw signs that the microbiome wasn’t fully adapting to the amount being consumed during the relatively short intervention. The researchers proposed several possible explanations, including that people living in industrialized societies may have microbiomes depleted of some fiber-degrading microbes and that a longer period of increased fiber intake could be necessary for meaningful changes in microbial diversity to emerge. In other words, simply supplying more food for beneficial microbes doesn’t necessarily mean the microbial community required to use that food is already thriving.

There was another clue hidden in participants’ starting microbiomes. According to Stanford’s description of the trial, participants in the high-fiber group who began with greater microbial diversity showed different immune responses than those who started with lower diversity. That raises a much bigger question than whether we should eat fiber or sauerkraut for lunch: How much does the condition of the ecosystem determine what happens to the food we put into it?

The Gut is an Ecosystem

This is the part of microbiome research I find far more compelling than another list of foods we’re supposed to buy. We have a tendency to think about health mechanistically. Protein builds muscle. Fiber fixes digestion. Probiotics add good bacteria. Vitamin C supports immunity. Put the correct thing into the machine, receive the desired biological output. But we aren’t machines.

The gastrointestinal tract contains a staggeringly complex community of microorganisms living alongside one another, competing for resources, producing metabolites, interacting with our food and communicating with our immune system. What happens when we introduce something into that environment depends, at least partly, on the environment that was there before it. Two people can eat the same meal and have different metabolic and microbial responses to it. That doesn’t make nutrition meaningless. It makes context important.

The fermented-food findings become particularly interesting through that lens. The increase in microbial diversity couldn’t simply be explained by bacteria from fermented foods moving into the gut and setting up permanent residence. The researchers reported that many of the microbes that increased in participants weren’t detectable in the fermented foods themselves, suggesting the foods may have altered the intestinal environment in ways that allowed other microbial populations to flourish.

That’s a fundamentally different way of thinking about food.

Instead of asking only, “What bacteria am I adding?” we can begin asking, “What environment am I creating?”

Probiotics Have Entered the Chat

Once we learned that bacteria living inside us could influence health, we figured out how to put bacteria into capsules and sell them by the billions. Walk into almost any health store and you’ll find shelves of probiotic supplements promising various strains and increasingly impressive colony-forming-unit counts.

Probiotic supplements can absolutely have legitimate uses, and certain strains have been studied for specific conditions. But “probiotic” is an enormous category, not a single intervention. Different organisms can behave differently, and swallowing an isolated bacterial strain isn’t biologically identical to eating a fermented food containing microbes alongside proteins, carbohydrates, organic acids and metabolites created during fermentation.

The distinction is worth making because wellness has become remarkably good at productizing biology. We want the capsule, powder, wearable or protocol that allows us to identify a variable, optimize it and consider the problem handled. Food is messier. Ecosystems are messier. Human beings are considerably messier. We're missing the point.

Please Don't Stop Eating Fiber

Before you replace every vegetable in your refrigerator with kimchi, there are important limitations to understand. This was a relatively small study involving healthy adults. It does not establish that fermented foods treat inflammatory diseases, nor does it prove that eating fermented foods will lower inflammation in every person. It certainly doesn’t demonstrate that fiber is ineffective.

Ten weeks is also a relatively short amount of time when we’re talking about changing an ecosystem that has been shaped by years of diet, environment, medication exposure and other factors. The researchers themselves noted that a longer high-fiber intervention could potentially produce different results, and the evidence supporting fiber extends far beyond this single experiment.

The more useful interpretation is that the fermented-food group demonstrated a particularly interesting biological response under the conditions studied, while the fiber findings showed us how much individual microbiomes may matter when interpreting nutritional interventions.

Both things can be true at once. Fermented foods can be critical while fiber still being essential. 

This is usually the point where wellness content transforms an interesting piece of research into a rigid morning routine involving 14 ingredients and something you have to order online. I’d rather not.

You don’t need to go from zero fermented foods to six servings a day because participants in one study consumed high amounts of them. If fermented foods agree with you, introducing more variety into your diet might mean adding plain yogurt with live cultures, kefir, kimchi, sauerkraut, tempeh or other traditionally fermented foods you genuinely enjoy. And yes, continue eating fiber-rich plants, whole grains, legumes, nuts and seeds if you tolerate them.

More importantly, consider the pattern rather than obsessing over a single food. A diverse microbial ecosystem probably isn’t going to be built by eating the same “perfect” breakfast 365 mornings a year. It is shaped over time, and researchers are still working to understand how diet, lifestyle, medications, environment and countless other factors interact to influence it.

Which is admittedly less satisfying than being told to take one capsule before breakfast.

Modern wellness loves reductionism. Find the molecule. Isolate the ingredient. Package the mechanism. Optimize the metric. Then move on to the next thing we’ve decided is responsible for our health. But the deeper we look at human biology, the harder it becomes to separate one system from everything surrounding it. The gut microbiome is perhaps one of the clearest examples. We aren’t carrying around a static collection of “good” and “bad” bacteria waiting for us to add the correct probiotic. We’re hosting a dynamic ecosystem that is constantly responding to what we eat and how we live.

Maybe the lesson from this Stanford study isn’t that fermented foods are superior to fiber. Maybe it’s that our obsession with finding a single superior input is the problem in the first place.

Eat plants. Eat fiber. Experiment with fermented foods you tolerate. Eat a diverse diet instead of the same five foods every day because someone on the internet assigned them a health halo. Remain appropriately skeptical whenever one study, including this one, is used to declare that we’ve finally discovered the food everyone should be eating.

Peace, love, plants. Thanks for reading.