What’s the Best Diet for Your Gut Microbiome?

Written and medically reviewed by Nicole Grant, RD

The gut microbiome has gained significant attention in recent years for its profound impact on our health. Emerging research suggests that nurturing a healthy gut microbiome can play a crucial role in promoting overall well-being, from digestion to immune function and even mental health.

In this article, we’ll explore four key nutritional strategies that can support a flourishing gut microbiome, paving the way for digestive function and enhanced overall health.

What’s the Gut Microbiome and Why Is It Important?

The gut microbiome refers to the complex community of microorganisms that reside in our gastrointestinal tract, consisting of bacteria, viruses, fungi, and other microbes. The gut microbiome is incredibly diverse, with trillions (yes, trillions!) of microorganisms, and it is unique to each individual. The development of the gut microbiome begins at birth and typically reaches maturity within the first three years of life in healthy individuals. However, this development can be influenced and modified by various environmental factors, particularly the composition and quantity of one’s diet.

The gut microbiome performs a wide range of functions that are essential for our health. It helps in the digestion and absorption of nutrients, synthesizes certain vitamins, and metabolizes dietary compounds that our own body cannot break down. Moreover, the gut microbiome interacts with our immune system, playing a key role in regulating immune responses and defending against harmful pathogens. It also contributes to the development and maturation of the gut lining, influencing its barrier function and preventing the entry of harmful substances into the bloodstream. 

Additionally, as it’s connected to the gut-brain axis, emerging research suggests that the gut microbiome may have an impact on mental health by influencing neurotransmitter production and potentially affecting mood and cognitive function. Overall, the gut microbiome is a fascinating and vital component of our bodies, with implications for numerous aspects of our health.

What is Considered a Healthy Gut Microbiome?

A healthy microbiome refers to a balanced and diverse community of microorganisms. It’s characterized by the presence of a wide range of beneficial bacteria, viruses, fungi, and other microbes that interact harmoniously with the host (that’s you!). In addition to microbial diversity, some studies have associated that certain health and disease-associated patterns of the microbiome can be indicative of healthy aging. 

However, one distinct microbial pattern may not be necessarily better than the other. On average, any two individuals share about one third of their gut microbiota, with the other two thirds influenced by genetics, geographical location, history of antibiotic and medication use, mode of delivery at birth, diet, and other undetermined factors. Some research even indicates that two otherwise healthy individuals can have zero overlap in their microbiome composition in terms of variety and quantities of various species.

So, in addition to looking at microbial composition, it may be best to look at microbial function as well. For example, is your microbiome metabolically flexible — i.e., can it adapt to a shift in types, abundance, or absence of foods? Does it facilitate proper digestion? Does it support optimal immune function (70–80% of the body’s immune cells are present in the gut)? Does it promote an environment that is disease-free?

Ideally, a healthy microbiome contains a unique and diverse blend of microbes that supports proper digestion, metabolism, immune function, and overall health. 

4 Nutritional Strategies to Improve Your Gut Microbiome

Although nutrition for your microbiome can be individualized, these four nutritional strategies are likely to promote a flourishing gut microbiome in most people.

#1) Focus on Whole and Minimally Processed Foods

Whole, minimally processed foods such as vegetables, fruits, legumes, nuts, and seeds are rich in essential nutrients, dietary fibers, and other beneficial compounds that support the growth and diversity of the gut microbiota

Conversely, processed foods, which undergo refining, stripping, and ingredient additions, are typically low in fiber and high in unhealthy fats, added sugars, and artificial additives. They disrupt the gut-microbiome balance, reducing beneficial bacteria and promoting harmful ones. Furthermore, the lack of essential nutrients in processed foods can contribute to dysbiosis (an imbalance of beneficial versus harmful bacteria), inflammation, and an increased susceptibility to gastrointestinal disorders.

Fortunately, a whole-foods approach can be easy to incorporate no matter your dietary preference — paleo, vegetarian high carb, keto, etc. Plant products such as nuts, vegetables, legumes, and fruit can all contribute to a healthy microbiome, as well as minimally processed animal products such as fermented dairy, meat, and eggs.

#2) Up Your Prebiotic Intake

Prebiotics are non-digestible components of food that serve as fuel sources for beneficial bacteria in the gut. Common prebiotics include fibers such as inulin, fructo-oligosaccharides, and pectins as well as resistant starches such as those found in green bananas and potatoes that have been cooked and cooled.

Once prebiotics are consumed, they travel through the gastrointestinal tract undigested. When they reach the lower portion of the gut, the colon, the bacteria ferment the prebiotics and produce short-chain fatty acids (SFAs), particularly butyrate, acetate, and propionate. These byproducts then act as a major energy source for the cells within the colon and play an essential role in maintaining mucosal structure and overall gastrointestinal health

The USDA recommends getting at least 14 grams of fiber for every 1,000 calories. So, if you are consuming a 2,000-calorie diet, aim for 28 grams of daily fiber. For reference, one cup of cooked lentils has about 16 grams of fiber, one cup of raspberries has 8 grams, one avocado has 10 grams, one cup of cooked kale has 5 grams, and one ounce of almonds has 3.5 grams. 

Although there isn’t a standard recommendation on resistant starch from the USDA, research has suggested that a goal of 6 grams of resistant starch per meal is recommended for health benefits. Some commonly consumed foods with resistant starch include: uncooked rolled oats (7.7 g/100 g); ripe raw plantains (5.1 g/100 g); high-amylose potatoes that were cooked then chilled for 2 days (6.4 g/100 g); lima beans (6.4 g/100 g); and potato salad (5.2 g/100 g).

#3) Incorporate Fermented Foods

Fermented foods can have a positive effect on your microbiome by providing a source of both pre and probiotics. First, the consumption of fermented foods introduces live microorganisms, such as bacteria and yeasts, into the gastrointestinal tract. These live microorganisms can modulate the diversity and balance of the gut microbiome, promoting the growth of beneficial bacteria and inhibiting the proliferation of potentially harmful ones. This can lead to a more resilient and diverse microbial community, which is associated with improved gut health and overall well-being.

Many fermented foods also serve as prebiotics, providing substrate for flourishing microbes. For example, sauerkraut not only provides probiotics from the fermentation process, but the cabbage itself is also a rich source of oligosaccharides that serve as fuel for the microbes.

Common sources of fermented foods can be found around the world, and include yogurt, kefir, sauerkraut, tempeh, kombucha, kimchi, and pickles (fermented in well water, not vinegar). 

#4) Continue (or Consider) Starting a Fasting Protocol

Fasting is a powerful practice for restoring and promoting a healthy gut microbiome, in addition to numerous other benefits. By giving the digestive system a break from processing food, fasting provides an opportunity for the gut microbiome to reset and rejuvenate. Factors such as poor dietary choices, stress, sedentary lifestyles, and medication use can disrupt the balance of the gut microbiota, leading to digestive issues. So, by taking a break from food, fasting has been shown to positively influence the composition and diversity of the gut microbiome and reduce proinflammatory microbes.

The duration of a fast to reset the gut microbiome can vary depending on individual factors such as age, overall health, and dietary habits. For most, shorter fasting periods, such as 16–24 hours, are long enough to induce positive changes in the gut microbiome, promoting the growth of beneficial bacteria and reducing the populations of harmful microbes. However, more severe gut imbalances or conditions may require longer healing periods, ranging from a few weeks to several months. Consider working with a healthcare professional to determine the appropriate fasting approach for your individual needs.


Our gut health is vital for our overall health, and nutrition plays a key role in maintaining an optimally functioning microbiome. Focusing on a minimally processed diet, full of prebiotics and probiotics, while finding a fasting protocol that works for you are important strategies to maintain a healthy gut microbiome and, ultimately, a long and vibrant life.

Nicole Grant, RD
Posted in Health & Science

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