Updated 19th March 2024

How to improve your gut health and gut microbiome

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Having a diverse range of “good” bacteria is the cornerstone of a healthy gut. 

In fact, having a thriving, varied gut microbiome is important for overall health — not just gut health.

This article will outline some lifestyle tips and the best foods to eat to support your “good” gut bacteria and improve your gut health.

How to support your 'good' gut bugs

The trillions of bacteria, fungi, protozoa, and other microbes in your digestive tract make up your gut microbiome. The composition of that microbiome is unique to you. 

A healthy gut contains a wide variety of bacteria.

At ZOE, we run the largest nutritional study of its kind. Among other findings, we identified 15 “good” gut bugs linked to positive health outcomes and 15 “bad” bugs linked to poor health outcomes. 

We asked Dr. Will Bulsiewicz, a board-certified gastroenterologist and ZOE’s U.S. medical director, a simple question: What’s the best thing you can do to improve your gut health? He responded:

“If there's one thing, and one thing only, that you do to improve your gut health, it's eating a wider variety of plant foods.”

Here are 16 easy ways to improve your gut health. You can try them today.

1. Food variety is key

In agreement with Dr. B, ZOE’s scientific co-founder, Prof. Tim Spector, recommends aiming for 30 different plant foods each week. 

Try to “eat the rainbow” by mixing and matching plant foods with different colors. 

These foods are rich in fiber and polyphenols, which “good” gut microbes love. More on polyphenols in a moment.

The standard Western diet is low in variety. But the Mediterranean diet is more diverse, including a range of plants.

Studies have shown that people who follow a Mediterranean diet have more “good” gut bacteria and a more varied gut microbiome — a sign of a healthy gut.

Researchers have also found that a Mediterranean diet is linked to more positive health outcomes.

And some scientists believe that these health benefits might be due to changes in the gut microbiome.

If you’re interested in learning about your gut microbiome, ZOE’s poop test shows which of the 15 “good” and “bad” bugs live in your gut. This information can help you find the best foods to improve your gut health.

Take our free ZOE quiz to find out more. 

2. Eat more fruits and vegetables 

You don’t need to be vegetarian or vegan to have a healthy gut, but eating more plants can help. Fruits and vegetables are generally rich in fiber, which is the key fuel for your gut bugs. 

Many plant-based foods also contain polyphenols. These compounds are not easily absorbed through your intestines, so they move along your gut to the large intestine, where most of your gut bacteria live.

Here, microbes feed on polyphenols. In the process, they convert them into a variety of bioactive compounds.

Scientists have shown that polyphenols have a range of health benefits — likely due to their interaction with your gut bugs. 

Importantly, there's also evidence that polyphenols support “good” gut bacteria while inhibiting the growth of “bad” bacteria.

So, having more polyphenol-containing fruits and vegetables will help keep your gut microbiome happy.

Here’s a list of polyphenol-packed foods.

3. Choose nuts and seeds

Nuts and seeds are another excellent source of fiber and polyphenols. They also contain healthy fats, such as omega-3 fatty acids. 

Scientists have found that a diet rich in omega-3 fatty acids is linked to a more diverse gut microbiome. And a healthy gut microbiome is a diverse gut microbiome.

Along with benefiting your gut bacteria, healthy fats can improve your cardiovascular health and reduce the risk of blood sugar spikes after you eat carbs

Some good nuts and seeds to add to your diet include:

  • almonds

  • walnuts

  • cashews

  • hazelnuts

  • pine nuts

  • pistachios

  • chia seeds

  • pumpkin seeds

  • hemp seeds

  • sunflower seeds

  • sesame seeds

Important note: If you don't currently eat a lot of fruits, vegetables, and nuts, you might experience gas, bloating, and digestive issues when you add them to your diet.

So, if your body isn’t used to these foods, it’s a good idea to build them up slowly.

4. Add legumes to your diet

Legumes, like chickpeas and lentils, contain high levels of dietary fiber, plus a prebiotic fiber called galactooligosaccharide, which feeds “good” gut bacteria.

Studies have shown that galactooligosaccharide can help keep your gut microbiome “stable” and may support Bifidobacteria, a common type of “good” gut bacteria.

These legumes are a good place to start:

  • chickpeas

  • lentils

  • baked beans

  • soybeans

  • red kidney beans

  • peas

  • pinto beans

5. Choose whole grains

Whole grains are a great source of fiber for your gut microbiome. A review from 2019 looked at how whole grains influence gut bacteria. 

Of the 42 studies that the researchers looked at, 39 found that consuming whole grains was associated with a more diverse gut microbiome.

They concluded that “Increasing cereal fiber consumption should be encouraged for overall good health and for gut microbiota diversity.”

Whole grains also contain many other important nutrients and may lower your risk of chronic conditions like heart disease.

Common whole grains include:

  • oats

  • bulgur

  • quinoa

  • buckwheat

  • spelt

6. Eat prebiotic foods

Many fruits, vegetables, nuts, grains, and legumes contain prebiotics. Prebiotics are a type of fiber that feeds “good” gut bacteria.

They shouldn’t be confused with probiotics, which are live microorganisms.

Prebiotics pass through your gut without being digested and nourish your gut bacteria. A wide range of compounds act as prebiotics, including fructans and oligosaccharides. 

Foods rich in prebiotics include:


  • bananas

  • watermelon

  • blueberries

  • grapefruit

  • nectarines

  • pomegranate


  • bran

  • barley

  • oats

  • rye bread

  • rye crackers

  • couscous

  • wheat bran


  • cashews

  • pistachios


  • chicory

  • Jerusalem artichokes

  • garlic

  • onions

  • leeks

  • savoy cabbage 

  • green peas

7. Eat probiotic fermented foods

Probiotic foods contain live bacteria. They may help increase the diversity of your gut bacteria. 

Although research in humans is limited, there is some evidence that consuming these foods might encourage the growth of good bacteria and benefit overall health.

Probiotic fermented foods include:

  • natural yogurt

  • kefir

  • kombucha

  • sauerkraut

  • pickles

  • miso

  • tempeh

  • kimchi

  • cheeses that have been aged but not pasteurized

8. Drink coffee

ZOE’s research has shown that people who drink coffee may have more diverse microbiomes.

According to one of the study's authors, Dr. Nicola Segata:

“We saw a very strong correlation between drinking coffee and the composition of the gut microbiome. We noticed that people who drank coffee tended to have higher microbiome diversity.”

He also explained that this relationship was dose-dependent. In other words, those who drank at least four cups a day had more diverse gut microbiomes than those who drank less coffee.

9. Avoid ultra-processed foods

When possible, it’s best to limit ultra-processed foods — foods that undergo industrial processing.

These foods have high levels of refined sugars, salt, additives, and unhealthy fats. 

ZOE’s research shows that people who eat a lot of highly processed foods are more likely to have more “bad” bugs in their gut than those who typically avoid these foods.

Likewise, those who rarely eat ultra-processed foods have more “good” gut bacteria. 

10. Cut down on the sweet stuff

There’s nothing wrong with a sweet treat every once in a while. However, some evidence from animal studies suggests that a high-sugar diet might impact your gut microbiome.

By reducing numbers of “good” bacteria and increasing numbers of “bad” bacteria, a high-sugar diet may increase the risk of metabolic disorders, such as type 2 diabetes and obesity.

And artificial sweeteners might not be much better. Experts now believe that these compounds interact with the gut microbiome.

Some evidence suggests that artificial sweeteners might disrupt your gut microbiome.

Although much of the research so far has involved animals, there is evidence that certain artificial sweeteners can influence gut bacteria in humans.

Other ways to improve gut health

Changing your diet isn’t the only way to support your gut health. You can also tip the balance of your microbiome with lifestyle changes.  

11. Get more sleep

Scientists have shown that the gut microbiome can influence sleep and vice versa. And some studies have shown that better sleep is linked to increased gut bacteria diversity. 

One study — in mice — suggests that sleep disruptions can change which bugs are present in the gut.

These changes were associated with increased inflammation in fat tissue and poorer blood sugar control.

Although scientists haven’t fully explored the links between gut bacteria and sleep in humans, getting a good night’s rest will undoubtedly benefit your overall health.

12. Exercise regularly

Exercising is one of the best strategies for a healthier gut and may increase microbiome diversity.

Studies show that even low-intensity workouts can help maintain a healthy gut.

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13. Time your meals

Research into the effects of meal timing and intermittent fasting on the gut is still limited, but some evidence suggests that the microbiome may have its own circadian clock

Prof. Spector recommends limiting snacking and not eating late in the evening to allow your gut time to rest during the night. 

This keeps the lining of your gut healthy, which is important for the health of your gut, its microbiome, and your immune system. 

14. Take antibiotics only when necessary

Antibiotics save lives. But they can also impact your microbiome, and these changes can last. So, take antibiotics only when necessary and always as directed by your doctor.

15. Reduce stress

Whether its psychological, physical, or environmental, stress may disrupt the structure and function of your gut microbiome. However, scientists still don’t know exactly how these changes impact our health. 

Nevertheless, finding ways to reduce your stress levels may improve your gut health.

Here, find some useful tips for managing stress.

16. Avoid smoking

Smoking increases the risk of chronic intestinal disorders and digestive tract cancers. 

It’s also linked to a less diverse gut microbiome resembling that of individuals with inflammatory bowel disease and obesity. 

The takeaway

For a happier, healthier gut, try to eat a "rainbow" of plant-based foods, ideally around 30 types a week. A diverse diet supports a diverse microbiome. 

Overall, upping your plant intake is the best thing you can do. 

At ZOE, we follow the "everything in moderation" philosophy — no food should be off limits. You can still have a healthy, balanced gut with a diet that occasionally includes ultra-processed foods or a glass of wine. 

And changing your diet isn't the only way to improve your gut health.

Get a good night’s rest, keep your body moving, be mindful of stress levels, take antibiotics only when needed, limit the sweet stuff, and avoid smoking.

These habits are also important in supporting the complex needs of your microbiome. 

Discovering which foods and behaviors will create the best environment for your gut begins with understanding which microbes make up your unique microbiome.

With the ZOE program, our at-home test shows you which of the 15 “good” and 15 “bad” bugs you have in your gut and which foods can help you improve your gut health.


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