Healthy gut diet: Foods you should eat for optimal gut health

We get a number of requests to post a “healthy gut diet”, which is impossible to do. The primary issue is that we’re all different. Thus, what’s best for your gut depends on several factors:

  • Are you trying to fix a problem or optimize an already healthy gut?
  • Genetics
  • Food allergies & intolerances
  • Activity levels
  • Sleep
  • Working day vs night shift?
  • Food preferences

Therefore, anytime you put forth a “healthy gut diet”, it’s important to provide context. What an individual eats to correct a microbiome imbalance is different than what someone with a balanced microbiome uses to optimize their gut health.

This gets back to personalized nutrition, which we covered in last week’s blog. You can check that out here. Thus, your healthy gut diet won’t be the same as Samantha’s.

The focus of today’s blog is on foods that build diversity and stability in the microbiome. These foods are of plant origin, and have components that are resistant to digestion by us.

Instead, they make it into our colon mostly intact, where the vast majority of our gut microbiome resides. There, they are available to attract microbes that metabolize them into products more bioavailable to us.

The 2 primary classes of these plant components are polyphenols and fiber. Today we discuss the characteristics of both, as well foods that contain them.

What are polyphenols?

Polyphenols are compounds in plants that normally function to protect against stress, pests, and pathogens. They affect the color and taste of plant foods, and many are resistant to digestion and absorption. As a result, many make it to the colon completely intact.

Despite their low bioavailability, diets high in polyphenols are associated with a decreased risk of many chronic disease including Cancer, cardiovascular disease, type 2 diabetes, GI problems, and neurodegenerative disease. Due to their poor bioavailability, their beneficial effects may go through the microbiome.

Polyphenols act on the microbiome in different ways. They increase abundance of microbes that metabolize them, and the byproducts of their metabolism bring other beneficial microbes. Additionally, they maintain their ability to act as natural pesticides against pathogens.

Polyphenols also tend to have a beneficial effect on maintenance of the intestinal barrier. They do this by increasing the presence of beneficial bacteria such as Lactobacilli and Bifidobacteria that help maintain a strong gut. Others, such as Faecalbacteria, block inflammation.

Polyphenols in a healthy gut diet

Foods high in polyphenols

Polyphenols come in different varieties, each with their individual benefits. However, as a general class of food compound, they tend to have similar effects, many of which center around the microbiome.

How polyphenols improve gut health


Anthocyanins are a colorful group of polyphenols that are found in darker-colored plants. Foods with anthocyanins tend to be purple, black, blue or red.

Anthocyanins increase the presence of Bifidobacteria species, which produce short chain fatty acids such as butyrate and protect against leaky gut. They also have inhibitory effects on pathogens.

Foods high in anthocyanins include blueberries, raspberries, blackberries, blackcurrant, black beans, blue corn, grapes, peaches, apples, wine, and red cabbage.


Catechins are a group of mostly colorless polyphenols found in a range of foods. They produce effects similar to anthocyanins on the microbiome.

Tea catechins have been shown to increase beneficial bacteria while inhibiting pathogens. They also increase short chain fatty acid production from the microbiome.

Foods high in catechins include tea, apples, pomegranate, plums, strawberries, cocoa, lentils, grains, and beans.

Other polyphenols

There are many other classes of polyphenols common in the human diet, each with different effects. This includes epicatechins, proanthocyanidins, chlorogenic acids, and isoflavones.

Eating a colorful diet is the best way to assure you get a diverse array of polyphenols. Typically, people are recommended to “eat the rainbow”, trying to consume plants of all different colors (Red, orange, green, purple/blue, and yellow/brown).

Polyphenols are an important component of a healthy gut diet due to their prebiotic effects on the microbiome.

What is fiber?

Dietary fiber is another part of edible plants that is resistant to human digestion. Like polyphenols, the resistance of fiber to digestion and absorption delivers it to the colon mostly intact.

As a result, microbes in the colon ferment certain types of fiber into nutrients that we can use. This includes short chain fatty acids such as butyrate, which is the preferred fuel source for colonocytes, the cells that line the colon.

Though generally classified as either soluble or insoluble, fiber is actually much more diverse than this. Fiber has different effects based on its physical characteristics, which includes solubility, viscosity, and fermentability.

This presents a range of variability in the effects that fiber has on health, as well as where these effects occur. Two fibers with similar fermentability but different viscosity may provide similar effects on bacterial populations, but in different parts of the GI tract.

Therefore, it’s important to not look at fiber as a single thing. Rather, it’s a class of nutrient resistant to digestion with varying effects on the host depending on the characteristics of the specific fiber.

Foods high in fiber

Like polyphenols, fiber is a nutritional component found exclusively in plants. Common sources of fiber in the human diet include cereal grains, beans and pulses, vegetables, fruit, nuts, and seeds.

Given the diverse physical properties of fiber, you can expect a wide range of effects depending on the source. Even within a food group such as beans, different beans will contain many different fibers with different properties.

This is important when identifying sources of fiber to include in your personal healthy gut diet. Some people may experience unpleasant effects from certain types of fiber such as gas or bloating. But having a bad response to one type of fiber shouldn’t dissuade you from trying others.

Try many types of fiber, find what works for you, and try to include as many types as you tolerate. The recommended daily intake for fiber is 38g/day for men and 25g/day for women. Most Americans consume less than half the recommended intake.

Since our focus is on the microbiome, we’ll discuss some different types of fermentable fiber that act as prebiotics for members of the gut microbiome.


FOS is commonly incorporated into processed foods due to its sweet taste and low caloric value. Increased FOS intake stimulates the presence of beneficial Bifidobacteria species, though some pathogens also ferment FOS. For some, this can lead to excessive gas and bloating.

Foods that contain FOS include onions, bananas, garlic, asparagus, blue agave, leeks, wheat and barley.


GOS, like FOS, increase the presence of Bifidobacteria in the gut. Furthermore, they inhibit the growth of pathogens, improve immune function, promote microbial synthesis of vitamins, and enhance the absorption of nutrients.

Foods that contain GOS include beans/legumes(red kidney beans, lentils, split peas, lima beans, chickpeas, baked beans), artichokes, seaweed, and dairy products.


Inulin is much like FOS and GOS in that it promotes the growth of beneficial bacteria in the gut while inhibiting pathogens. It is found in thousands of different foods and normally makes up a large part of our dietary fiber intake.

Foods high in inulin include leeks, onions, dandelion, bananas, asparagus, artichoke, chicory, garlic, wheat, and rye.

Some people may be sensitive to inulin. It’s high content in the diet may be problematic for people with an overgrowth of bacteria that ferment it, causing gas, bloating, and diarrhea.

Therefore, some people may benefit by restricting inulin and replacing it with other sources of fiber.

Resistant starch

As the name suggests, resistant starch is resistant to digestion, and has similar effects as the other types of dietary fiber. There are 4 types of resistant starch, which consist of starches that are naturally resistant to digestion due to their shape, as well as starches that have been modified by cooking and cooling, or by chemical means.

Foods that contain resistant starch include green bananas, raw potatoes, oats, green peas, various beans, rice, corn, and lentils. Cooking potatoes and rice and then cooling them for 24 hours increases their resistant starch content dramatically, provided you consume them cold.

Incorporating fiber and polyphenols into your healthy gut diet

As you can imagine, based on this information, plant foods are important for building a strong, healthy gut. But that doesn’t mean you should just go out and start hammering down high fiber plant foods.

If you’ve been consuming a low fiber diet, it’s important to slowly increase fiber to prevent GI discomfort. Particularly if you’re coming off a restriction diet such as the Carnivore diet, Ketogenic diet, or low FODMAP diet.

It may be a good idea to start with things like tea or fruit that have a high polyphenol content but low fiber content to decrease the likelihood of gas and bloating. Another useful strategy is to diversify your fiber sources rather than focusing on a single source.

It’s very common to focus on just a couple of foods to increase fiber intake, and this has significant drawbacks. This is a sure-fire way to increase the risk of gas and bloating.

Rather than adding a huge amount of cooked and cooled potatoes to your diet, start with something small like a little bit of garlic or onion. Then try some normally cooked potatoes or lentils, followed by a small amount of peas.

If something causes gas or bloating even in small amounts, pullback and try something else. If you’re already eating something in the list of fiber types without issue, try something else that falls under the same classification with different polyphenols. Color is an excellent guide.

Keep in mind that your individual tolerance to these foods may be different than someone else. So don’t completely change your diet to emulate someone else’s diet. Keep your current diet, try new foods, and keep the ones you respond well to.

Focus on foods that make you feel good, and try to remove highly processed foods as you go along.


Our gut microbiome plays an important role in the health of our gut. Since most of our microbiome is found in our colon, it’s important to eat foods that have components that make it there intact.

Both polyphenols and fiber are resistant to human digestion. As such, they make it to the colon where our microbes ferment them into beneficial metabolites that improve our gut and overall health.

Fortunately, a wide range of plant foods contain both polyphenols and fiber. Since they’re contained in a large number of foods, most people can find a combination of plant foods that they enjoy and tolerate to get these benefits.

Thus, the incorporation of well-tolerated and preferred plant-based foods is an essential part of developing a healthy gut diet.

One thought on “Healthy gut diet: Foods you should eat for optimal gut health

  1. Cate says:

    Seemingly overnight, I am having trouble with FODMAPS, (particularly garlic and onion), which never bothered me before. I have just gone through a very stressful long distance move and have a number of other stressors. I’ve signed up for your program and I’m hoping that lifestyle changes will help me be able to eat the foods I love again. Are sensitivities to things like FODMAPS typically permanent, or can they be reversed if things like SIBO are addressed through lifestyle changes?

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