The “variety” of bacteria living in your gut has a deep connection to your health.

While this has been suggested for some time, a rigorous scientific study examining how fermented foods influence this was published in 2021 by a Stanford University team in the journal Cell.

Fermented Foods vs. Dietary Fiber: A 17-Week Comparison

The study was a randomized controlled trial conducted over 17 weeks with 36 adults.

Participants were divided into two groups. One group followed a “high fermented food diet” (consuming 6-8 servings daily of yogurt, kefir, fermented vegetables, kombucha, and similar foods), while the other group followed a “high fiber diet” (rich in vegetables, legumes, and whole grains).

Which would bring about greater changes in gut bacteria? The results were striking: fermented foods proved far more effective than dietary fiber.

Gut Microbiota Diversity Increased Steadily

In the high fermented food group, the “diversity” (measured by Shannon diversity index) of gut bacteria increased significantly throughout the experimental period.

A dose-response relationship was also confirmed, with multiple fermented foods—yogurt, vegetable brines (the liquid from fermented vegetables), and others—contributing to improved diversity.

Gut microbiota diversity is known to correlate with immune regulation capacity and metabolic stability. The high fiber group showed no comparable changes.

19 Types of Inflammatory Proteins Decreased

Even more noteworthy was the effect on immunity.

The high fermented food group showed a reduction in 19 types of inflammatory proteins (cytokines). Chronic low-level inflammation has been linked in numerous studies to lifestyle-related diseases and disrupted immune function. The study also found decreased activation in three types of immune cells.

A trend was observed where greater increases in microbiota diversity correlated with larger decreases in inflammatory proteins. A potential correlation may exist between diversity and inflammation suppression.

Why Fermented Foods Increase Gut Microbiota Diversity

The research team also explored this mechanism.

Fermented foods contain living microorganisms—lactic acid bacteria, yeast, and others—that interact with the gut environment and alter the composition of the bacterial community. Additionally, short-chain fatty acids (SCFAs) and bacteriocins produced during fermentation appear to contribute to intestinal health and stability.

A review article published in the journal Foods in June 2025 also summarized, based on multiple clinical studies, how fermented foods are involved in immune regulation, metabolic homeostasis, cognitive function, and inflammation suppression (PubMed ID: 40647044).

What You Can Start with Fermented Foods in Daily Life

What this trial suggests is that everyday fermented foods—not specialized functional products—when consumed consistently, may bring tangible changes to your gut environment.

Traditional Japanese fermented foods like miso, natto (fermented soybeans), and nukadoko pickles (vegetables fermented in rice bran) belong to the same category as the yogurt and fermented vegetables used in this trial. The fact that change emerged over a 17-week period through consistent daily consumption carries real significance for how we approach eating.

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The diversity of your gut bacteria is built through the accumulation of what you eat each day.

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A Note from Toshi

The Stanford University research I’m sharing today left a lasting impression on me.

I’ve heard many times that fermented foods are good for you. But honestly, I think part of me had always viewed it as something “empirically known to be beneficial”—without deeper understanding.

Yet this research showed that change clearly, in the form of gut microbiota “diversity.” And the finding that fermented foods produced even greater change than dietary fiber was truly fascinating.

The image most people have is strong: gut health means fiber. Of course that matters, but this research made me reconsider the significance of introducing microorganisms from outside—as fermented foods do—rather than relying on fiber alone.

What struck me most was the decrease in inflammatory proteins. Perhaps the daily fatigue and fluctuations in how we feel aren’t unrelated to these subtle inflammations. When you think about it that way, you quietly sense how much impact the daily accumulation of meals has on your body.

The foods used in this study weren’t special or exotic—just everyday yogurt and fermented vegetables. That maps directly onto Japanese tables: miso, natto, nukadoko pickles.

There’s something reassuring about seeing a food culture that has continued for generations validated by science.

Your gut environment doesn’t change overnight. That’s precisely why it’s important to do things that you can sustain without strain.

Incorporating fermented foods isn’t so much about “fixing” your body as it is about quietly cultivating an inner landscape.

When you’re running every day and paying attention to how your body feels, the changes are incredibly gradual. Yet there’s a definite sense that something is coming into balance.

Nothing dramatic. And that’s exactly what makes it trustworthy.

Moving forward, I want to keep meeting fermented foods at my daily table, slowly nurturing my body through this practice.

※ This article is based on personal experience and publicly available information. It is not intended to diagnose, treat, or prevent any disease. If you have health concerns, please consult a doctor or registered dietitian. See our Disclaimer.