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Top Nutrition Tips to Support Your Gut Microbiome

Mar 9, 2022 | Healthy Eating, Inflammation & Autoimmune Disease

Guest author: Jennifer Fong, graduate student at San Jose State University

Our gut microbiome is made of billions of microbes, including bacteria, viruses, and fungi. Most of the bacteria in our gut live in our large intestine. The bacteria there have many roles:

  • They digest the food that we eat when we are unable to digest it ourselves, and
  • The bacteria produce nutrients, among other things.

While we are still learning which bacteria is “good” or “bad”, we know that having a diverse microbiome is associated with a healthy gut. In contrast, a decrease in bacteria diversity is associated with cardiovascular disease, obesity, diabetes, gastrointestinal diseases, and cancer (1).

There are certain factors that can affect the growth, composition, and diversity of our bacteria. These factors include:

  • our age
  • genetics
  • medications
  • where we live, and
  • our diet (2).

Of the things on this list, the factor we have the most control over is our diet. Some studies show that diet can temporarily shift our microbiome composition within 24 hours (3), showing the strong influence our diet has on our gut. 

Are there any nutrients that can help diversify our gut microbiome? 


Knowing that diet can impact the composition of our microbiome, what nutrients should we be focusing on?  Dietary fiber is not considered an essential nutrient, but it is important in keeping our gut microbiome healthy and functioning. Dietary fiber is an indigestible fiber that acts as a fuel for the bacteria in our large intestine and is often referred to as a prebiotic. Bacteria in our digestive tracts feed on them. In return, the bacteria produce gases and short-chain fatty acids. These short-chain fatty acids include butyrate, propionate, and acetate (3).

These short-chain fatty acids become an energy source for the cells in our intestine lining. This is thought to strengthen the mucosal barrier in our small intestine, keeping foreign pathogens out, while still absorbing the nutrients that we need (4). Short-chain fatty acids lower the pH in our intestine, which prevents the growth of pathogens (5). These fatty acids also play a critical role in our immune system by

  • interacting with immune cells directly (3)
  • minimizing inflammation (6),
  • decreasing inflammation (7).

You can find high fiber from foods such as fruits, vegetables, legumes, nuts, and whole grains. Try to incorporate these foods into your diet every day.


Plant protein (such as pea protein) has been shown to increase short-chain fatty acids (3) compared to animal protein. Increased short-chain fatty acids decrease inflammation and improve gut barrier.  Animal protein is associated with a decrease in short-chain fatty acids and an increased risk of inflammatory bowel disease.


 A study showed that high consumption of dietary fat, in particular saturated fatty acids, can lead to a decrease in intestinal microbial diversity (1). This reduction in diversity leads to negative alterations of the mucosal barrier.

 Are there any specific foods that can help? 

In addition to feeding our gut bacteria with prebiotics, we can introduce good bacteria directly into our gut to either restore or expand our bacteria diversity. Consuming fermented foods with good bacteria is one way we can do this. They are known as probiotic-containing foods. Fermented foods include yogurt, kombucha, kimchi, and sauerkraut. A large percentage of the bacteria found in these fermented foods survive the digestive tract once eaten (8). When purchasing fermented foods, keep in mind that different brands contain different strains and amounts of bacteria. Not all fermented foods contain live bacteria. For example, beer, wine, and bread do not contain live microorganism cultures due to processing (9).

In addition to fermented foods, foods such as fruits, vegetables, tea, coffee, red wine, and dark chocolate are associated with increased bacteria diversity in the gut. These foods contain polyphenols, which are antioxidants. Antioxidants are involved in the prevention of cardiovascular disease, diabetes, and obesity (1).

Low-calorie sweeteners such as sucralose, aspartame, and saccharin have been shown to disrupt the diversity of gut microbiota in mice. Emulsifiers, a type of food additive found in processed foods, have been shown to decrease microbial diversity in mice (10). 

Are there any diets that can help?

Many popular diets have been studied for their effectiveness in the gut microbiome

  • The Western diet
  • Vegetarian diet
  • Vegan diet
  • Mediterranean diet,
  • The ketogenic diet
  • Gluten-free diets.

Most Americans consume a Western diet which is characterized by a diet high in animal fat and protein and low in fiber. Across several studies, the Western diet was shown to reduce the total number of bacteria, as well as certain “good” bacteria (3).  A gluten-free diet was associated with a decrease in healthy bacteria. The ketogenic diet was associated with a decrease in total bacteria and diversity (1). One study suggests that vegan and vegetarian diets could decrease diversity but do not decrease short-chain fatty acids. Another study suggests that the microbial composition of vegan and vegetarian diets is inconclusive. 

Fortunately, there is one diet that can be helpful. This is the Mediterranean diet. This diet emphasizes fruits, vegetables, olive oil, nuts, legumes, and moderate intake of fish, poultry, and wine. These items provide high monounsaturated and polyunsaturated fatty acids and high levels of polyphenols.  The Mediterranean diet is low in red meat, dairy, and sweets (3). Studies show that the Mediterranean diet increases total bacteria, microbiota diversity, and stability  (1,3). 

While we are learning more and more about how our diet interacts with the gut microbiome, there is still a lot we do not know. More research is needed to determine how our diets influence the microbiome and the mechanisms behind it. In the meantime, we can help keep our gut healthy by consuming enough fiber, probiotic-containing foods, and adopting a healthy diet that resembles the Mediterranean diet.

Please feel free to reach out and schedule a free discovery call with me.  You can also follow me on Instagram at @the.autoimmune.dietitian or Facebook at @annierubinnutrition or my website.

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