Top Foods for a Healthy Gut Microbiome

Written by: Kari Raman, PharmD, RPh
Published June 7, 2023

Your gut microbiota is a complex community of bacteria, yeasts and other (hopefully) beneficial organisms that live in your digestive tract. These bacteria play a vital role in your health, helping to digest food, absorb nutrients, and fight off infection. At my pharmacy, some patients are sometimes surprised to learn that they have bacteria and other single cell organisms living in their gut – but this is totally normal! 

It’s easy to disrupt your microbiome’s health

A lot of our modern lifestyle isn’t helpful to your gut’s microbiome. The obvious thing that can mess up your gut’s microbiome are antibiotics – these are drugs that are designed to kill bacteria. (And as a pharmacist, I can tell you lots of people have to take courses of antibiotics for very important reasons – and if your doctor prescribes them, take them!) But antibiotics aren’t the only thing in our lifestyle that can change the balance in your gut. 

A diet that is high in processed foods, sugar, and unhealthy fats can disrupt the balance of bacteria in the gut. Too little fiber and other healthy starches and natural prebiotics can also contribute to an imbalance in the gut microbiome; the bacteria in your gut need the right foods to thrive!

Stress is another factor. Stress hormones can have all kinds of negative effects on your body, including influencing your gut’s balance. (If you want to learn more about some of the links between stress and the microbiome, check out this article “The microbiome: stress, health and disease” Mamm Genome.

Alcohol, smoking, lack of exercise – there are a whole host of other modern lifestyle factors that can cause gut issues that impact the health of your digestive system and its micro organisms. 

But let’s dive into how you can use your diet to improve your microbiome’s health.

Top foods for a health gut microbiome

There are many habits you can do to promote a healthy gut microbiota, including eating a healthy diet. A healthy diet for the digestive system is rich in plant-based foods, fiber, and probiotics is one of the best factors for helping make your gut a healthier place for the best micro organisms to live and thrive. Another added benefit to a gut friendly diet is that if you are taking probiotic supplements, the right foods are also the best foods for those probiotics to thrive in and successfully colonize your digestive system.

One important note – if you are having serious digestive issues, you should see your doctor! Gut problems can be signs of serious health problems, and you may need medical advice. 

Plant-based foods

Plant-based foods are a great source of fiber, which is essential for a healthy gut microbiota. Fiber helps to feed the beneficial bacteria in your gut, which helps to keep them healthy and growing. Basically, you can not actually digest fiber – it’s a type of carbohydrate that the body cannot digest. It travels through the digestive tract undigested and is fermented by bacteria in the gut. This fermentation process produces short-chain fatty acids (SCFAs), which are beneficial for health.

There are a couple of types of fiber – soluble and insoluble fiber. This type of fiber dissolves in water during digestion. It increases stool bulk and may decrease blood cholesterol levels. Soluble fiber can be found in fruits (such as apples, oranges, and grapefruit), vegetables, legumes (such as dry beans, lentils, and peas), barley, oats, and oat bran. Insoluble fiber is a type of fiber that remains unchanged during digestion. It promotes normal movement of intestinal contents. Get it from whole grains, brown rice, etc. I have an entire article on how you can take fiber with probiotics here.

From what I have read, many experts recommend a total dietary fiber intake of 25 to 30 grams per day with about a quarter of that — 6 to 8 grams per day — coming from soluble fiber.

Some good sources of fiber include fruits, vegetables, whole grains, and legumes.

Fermented foods

Fermented foods are another great way to boost your digestive system’s microbiota. Fermented foods are made by adding bacteria to food, which allows the bacteria to grow and multiply. Fermentation often gives food a sour taste, like you’d expect from an unsweetened yogurt. It produces lactic acid, which not only helps preserve food (think about how much longer yogurt lasts vs. milk!) but also gives it the distinctive taste and texture that yogurt lovers, well, love. I’ve written about how many probiotics yogurt contains, and also reviewed the strains in Chobani, which has some great bacteria and yeast! Of course, it usually comes with lactose, which can be an issue for some people.

Some good sources of fermented foods include yogurt, kefir, sauerkraut, kimchi, and tempeh.

Other foods that are good for the gut microbiota

In addition to plant-based foods and fermented foods, there are other foods that are good for the gut microbiota. These include:

  • Prebiotics: Prebiotics are non-digestible food ingredients that feed the beneficial bacteria in your intestines. Some good sources of prebiotics include onions, garlic, asparagus, and bananas.
  • Probiotics: Probiotics are live bacteria that are similar to the beneficial bacteria that live in your gut. Probiotics can be found in fermented foods, as well as in probiotic supplements.

What to avoid

There are also some foods that you should avoid if you want to promote a healthy gut microbiota. These include:

  • Processed foods: Processed foods are high in unhealthy fats, sugar, and salt. These ingredients can disrupt the balance of bacteria in your digestive system.
  • Sugary drinks: Sugary drinks are high in sugar, which can feed harmful bacteria in your intestines.
  • Red meat: Red meat is high in saturated fat, which can increase inflammation in your gut. A little is probably fine, but too much can cause a whole host of problems for your health and gut microbiome. 

Conclusion – the best foods for a health gut microbiome

By eating a healthy diet, you can promote a healthy gut microbiota. A healthy gut microbiota is important for overall health and well-being.

If you are not sure what foods are good for your gut microbiota, talk to your doctor or a registered dietitian.

Here are some additional tips for promoting a healthy gut microbiota:

  • Eat a variety of foods
  • Drink plenty of water
  • Get regular exercise
  • Get enough sleep
  • Manage stress

By following these tips, you can help to keep your digestive system microbiota healthy and thriving.

Pharmacist Kari Raman

I’m Kari Raman PharmD, RPh, and I am a licensed, practicing pharmacist. I hold a Doctorate in Pharmacy from The University of the Pacific, and I’ve served patients in retail, compounding and hospital pharmacies.

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