Magnifying Glass Uncovering The Best Diet For Gut Health

What is the Best Diet for Gut Health?

[Hint: It’s Not What We Thought]

In the last decade alone, we’ve learned so much about the gut, the microbiome, and how to eat in ways that support the health of both. That said, the world of gut health science is fast-paced and constantly changing, with new things uncovered almost every day. Inevitably, some of those findings contradict what we’ve previously known to be true, and we often change our beliefs and recommendations to align with the latest research. 

I’ve seen this happen many times throughout my years practicing medicine. And just recently, I read a new piece of evidence — in the form of a clinical study done by researchers at the Stanford School of Medicine — that revealed something surprising about the best diet for gut health!

You can imagine my excitement… I couldn’t wait to share this with you!!

For years we thought that eating a high fiber diet was the best way to increase microbial diversity in the gut. That’s the whole premise behind Fiber Fueled , a new book by my GI colleague, Dr. Will Bulsiewicz. But this study contradicts what we thought we knew, which is why this week, I wanted to dive into the effect nutrition has on gut microbiome health and inflammatory markers in the body— and how we can all make sure we’re eating to optimize our gut for total wellness. Because as you know (as a reader of my blog), the gut is the cornerstone of your health

A surprising shift in the gut-friendly diet paradigm

When it comes to gut health, there are two measurements that are particularly important. The first is gut microbial diversity, which is the diversity (i.e. range of species) of bacteria living in the intestinal ecosystem. This is important because certain bacteria perform specific functions and low diversity is linked to health issues like obesity and IBS . The second measurement is the levels of inflammatory markers in the gut and blood, which when high can mean a leaky gut and chronic inflammation. In the Stanford study, the scientists found that while a high fiber diet may help gut health in the long-term, the most dramatic improvements in microbial diversity and  inflammatory markers is best achieved through a fermented foods diet (at least in the short-term). We’re talking sauerkraut, kimchi, fermented cottage cheese, yogurt, and kefir—the works. 

Now, if you’re up-to-date on my latest gut health recommendations, you’ll know that it’s not a new discovery that fermented foods are gut-friendly. We’ve long known that fermented foods contain valuable probiotics that promote better digestion and overall better gut health. (In fact, last year around this time I did a three-part blog series on this exact topic !) That said, this discovery points to a potentially major change in the paradigm! Let me explain… 

Previously, we thought fermented foods were a complement to a gut-friendly diet—not the foundation for it—and that a high fiber diet was the most important way to create diversity in the gut microbiome (the Holy Grail of gut health!). This Stanford study, though, suggests that it’s the reverse. Fermented foods should actually be the foundation of a gut-friendly diet. Unfortunately for the proponents of high fiber diets, this study presents evidence that challenges anyone (well, we know some of them) pushing fiber as a cure-all for gut health. I once thought so myself.

My thoughts on fiber vs. fermented foods

As “ America’s Gut Doctor ,” this study caught my eye and left me thinking about the difference between high fiber foods and fermented foods. The researchers compared the influence of two different diets (both healthy): a fiber-rich diet versus a diet high in fermented foods. 

Let me cut to the chase! 


The study findings...

Fermented foods improved microbial diversity and reduced inflammatory markers—challenge the beliefs myself and others previously held around the benefits of fiber for the gut microbiome. I’m not saying that fiber isn’t necessary for optimal gut health, because it absolutely is . Fiber provides a prebiotic food source for our gut flora, which ferments the fiber into short-chain fatty acids like butyrate. These fatty acids are critical for the health of the colon, blood sugar regulation, as well as learning and memory among other things.

Not Enough Fiber

Also, it’s worth noting that the average American isn’t getting nearly as much fiber as is recommended for overall good health. The recommended amount of fiber per day for men and women up to 50 years old is 38 grams and 25 grams, respectively. Meanwhile, the average American only eats 10 to 15 grams of fiber total per day—less than half of the suggested intake.

So even though fiber may not be the end-all, be-all for improving your microbial diversity, this is NOT a sign or suggestion that you should stop eating it.

Let me summarize it for you in simple terms. I want you to keep the following takeaways from the Stanford study in mind, and remember that more research needs to be done on this topic. Studies like these are great, because they are potentially groundbreaking and they make us ask questions about commonly-held beliefs. But studies are imperfect, and this one has a couple of issues that would be irresponsible of me not to point out. 

Here they are:

  • The study only included a small number of participants. A bigger group of participants would give the study more power and help verify if this is true for the general population.
  • The study subjects were mostly white women, so I would love to see it repeated with a more diverse study population.
  • The diet interventions only lasted for 10 weeks, and the study authors suggested that a longer duration for the high-fiber diet group may be needed to see greater changes in the gut microbiome.

What You Need To Know About The Best Diet For Gut Health

My most important takeaways from the study: 



Fiber-rich diets improve the functioning of your little gut helpers — your microbiome — namely the production of short-chain fatty acids, which are important for overall health.



The fiber rich diets also lead to an increase in your gut’s ability to process complex carbohydrates, like sweet potato and butternut squash, due to an increase in the quantity of the types of bacteria capable of digesting fiber.



What a fiber-rich diet didn’t do, that a diet high in fermented foods did… The fermented foods diet increased microbiome diversity and reduced 19 inflammatory markers (which as we learned earlier, are two of the key factors for a healthy gut AND body). Woohoo! That’s pretty amazing. 



In the participants eating a fiber-rich diet, their inflammatory response varied depending on each individual’s baseline microbial diversity. This is important for understanding why different individuals have very different immune responses to infections — some getting much worse, and others just having a light cold with a bit of sniffles.



Above all, this study suggests that in western societies, where increased inflammation and loss of microbial diversity are common, a fermented foods diet may be valuable in countering these effects. In other words, we need to redefine what is the BEST DIET not just for gut health, but also for total wellness. 

My observations on gut health abroad

As a Functional Medicine Doctor specializing in gut health, I strive to stay at the forefront of gut health research as well as immerse myself in different countries and cultures in an effort to observe their gut health habits. In light of the recently released book Fiber Fueled , for example, a pre-pandemic trip I took to Africa in early 2020 feels pertinent here. Fiber Fueled emphasizes the importance of eating the rainbow for microbiome diversity, but when I went to Africa to spend time with the Hadza people—whose microbiomes have been studied and praised—that concept didn’t hold true. They don’t eat the rainbow of fruits and vegetables, because that rainbow is simply not available to them in their hunting and gathering lifestyle.

There are a number of studies on the Hadza population and their microbiomes, so I wanted to see for myself the kind of lifestyle they lead. I went hunting and gathering with them, foraging for root vegetables, and ate them raw, freshly dug out of the earth. We went into the bush, tracking down a beehive hidden inside a tree’s bark, and I got to sample fresh, raw honey, with the honeycomb and even ate live bees that got mixed in with the honey. Gross?! Well, these were not like the bees you think of when I mention a bee. They looked more like tiny flies. Hey, when in Tanzania… do as the Hadza do and eat raw honey and tubers.  

The Hadza people represent one of the last hunter-gatherer societies on the planet—there are only about 1000 of them in existence—and their diet is primarily made up of root vegetables (aka tubers), berries, wild honey, baobab fruit, and small to medium-sized game animals. Their diet is not the rainbow, and yet when compared to an age-matched Italian control group, they had a more diverse gut microbiome than people in the West. In fact, that study showed that their gut flora are even more diverse than those following an Italian/Mediterranean diet. And all this while eating a non-rainbow diet, still rich in fiber, but devoid of the color diversity found in westernized societies.

The Hadza have no diabetes, no heart disease, no cancer, and no obesity. Of course, the Hadza are not eating fermented foods (to my knowledge), but they are getting exposed to the diverse microbiome from the soil (they eat straight from the soil, no thorough hand-washing). This experience brought up a lot of questions for me about what the best diet for gut health is and if fiber is really enough. Based on this study, fermented foods are really what’s important, because we need to be exposed to other microbiomes outside of us in order to be healthy. It’s part of the ongoing education of our immune system, and what helps keep inflammation at bay.

Should we forget the fiber?

The key takeaways here from this study is that the fiber-rich diet did not increase microbial diversity or reduce inflammatory markers. We won’t say “hey, forget the fiber,” because it’s still good for the gut, especially for blood sugar balance, memory, inflammation, and colon cancer prevention. And fiber did have some immunomodulatory effect, depending on the baseline microbial diversity of the person. Perhaps having stayed on a high-fiber diet for longer than the 10 weeks done in the study would have had more of a noticeable effect on microbial diversity. Fermented foods, on the other hand, played a significant role in improving the diversity of the gut microbiome AND reducing 19 inflammatory markers. I think that data speaks for itself.

The Best Fermented Foods You Can Eat

If you’ve read the last few paragraphs and you want to add fermented foods to your diet ASAP, here are the fermented foods that had the greatest impact on microbiome diversity, according to the study.  I recommend buying your fermented foods at the farmer’s market (where they will be homemade and preferably not packaged in plastic containers) or making them yourself (check out my guide to getting started with fermentation at home).


1. Greek Yogurt

Plain is best, no added sugar is second best


2. Kefir

A drinkable probiotic yogurt, plain or low sugar is best. You can also find kefir made from non-dairy sources like coconut water (see recipe below).


3. Fermented Cottage Cheese

My favorite brand is Nancy’s


4. Sauerkraut

And its juice, aka “kraut juice” — these are abundant at your local farmer’s market !


5. Kimchi

Any variety will do! You can choose from non-spicy to very spicy, but beware, the spicier it is the harsher on your gut it will feel.


6. Pickles

Not all pickles are fermented, make sure to look for ones that are. I personally love buying them at my local farmer’s market.


7. Fermented Vegetables

These are different from pickled veggies, so read the labels or try making your own .


8. Kombucha

Look for lower sugar varieties, like Wild Tonic and Revive. Or my favorite flavor — Ginger-Lemon by Health-Ade .

However great it is to buy fermented foods, especially from trusted sources, nothing beats making your own. Here’s an easy do-it-yourself fermented recipe from my bestselling book, Happy Gut .

Coconut Kefir Water

Coconut Water Kefir

A healthy prebiotic- and probiotic-rich carbonated beverage great for helping balance your gut ecosystem.

Makes 1 quart.


  • 3 tablespoons water kefir grains
  • 1 quart pasteurized coconut water
  • 1 cup fresh strawberries or blueberries (optional)
  • ½ cup fresh lemon juice (optional)


  1. Place the water kefir grains and the coconut water in a jar. Cover the jar loosely or with a cheesecloth and allow the kefir grains to culture the coconut water ideally for 24 to 36 (and no longer than 48) hours at room temperature.
  2. Once the culturing is complete (the mixture will have thickened), remove the kefir grains with a slotted spoon and store in a separate glass container with a teaspoon of sugar to keep the kefir grains alive and active.
  3. You may drink the Coconut Water Kefir by itself, but for an added twist (and some prebiotic love), puree the cultured coconut water with the berries and lemon juice to your desired consistency. The Coconut Water Kefir will last 1 to 3 weeks in the fridge; when blended with the berries and lemon juice, it will last for 2 to 3 days in the fridge. Serve cold.

For more on how to ferment your own foods, check out my blog post “ Getting Started With Fermentation: A How-To Guide! ” In it, I interview my friend and fermentationist Summer Bock about how to get started with fermentation, how to shop for fermented foods, and so much more!

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