How to Eat for a Diverse Microbiome Diet

The community of microorganisms in the digestive tract, known as the gut microbiome, is composed of trillions of bacteria, fungi, and other microbes. This internal ecosystem is involved in digestion, immune function, and weight regulation. The composition of these microbial populations is unique to each individual and is significantly shaped by lifestyle factors, with dietary choices being a primary driver. A diet that promotes a varied microbial community is considered beneficial for overall health, as different microbes perform different functions.

The Impact of Dietary Choices on Microbiome Composition

The food consumed each day directly feeds both the body and the microbes within the gut. Dietary components that human enzymes cannot break down, such as certain fibers, pass into the large intestine where they become fuel for bacteria. This process of fermentation breaks down complex carbohydrates into beneficial compounds, most notably short-chain fatty acids (SCFAs). These SCFAs have numerous effects on health. Butyrate, for example, serves as a primary energy source for the cells lining the colon, helping to maintain the integrity of the gut barrier.

The production of SCFAs also lowers the pH of the colon, which influences the composition of the microbial community. A well-fed and diverse microbiome assists in producing nutrients like vitamins and amino acids. A diet rich in plant-based foods is associated with higher production of SCFAs. Conversely, a Western diet, high in red meat, saturated fat, and processed grains, is linked to lower SCFA production. The consumption of red meat can also lead to an increase in trimethylamine-N-oxide (TMAO), a metabolite generated by gut bacteria that is associated with inflammation.

Nourishing Gut Diversity Through Specific Food Categories

A diet rich in a variety of plant-based foods is fundamental to cultivating a diverse microbiome. Different microbes prefer different types of nutrients, and providing a wide array of plant sources helps them thrive.

Dietary Fiber and Resistant Starch

Dietary fiber, a category of carbohydrates the body cannot digest, is a main source of nourishment for gut bacteria. Resistant starch is a type of fiber that passes through the small intestine undigested and is fermented in the large intestine, acting as a prebiotic that feeds beneficial bacteria. Sources include green bananas, cashews, lentils, and whole grains. A process called retrogradation increases resistant starch in foods like potatoes, rice, or pasta when they are cooked and then cooled. Reheating the food does not significantly decrease this new resistant starch content.

Prebiotic Foods

Prebiotics are substrates that are selectively used by host microorganisms to confer a health benefit. Many high-fiber foods are naturally prebiotic, stimulating the growth of beneficial bacteria. Specific examples of prebiotic-rich foods include onions, garlic, leeks, asparagus, and Jerusalem artichokes. These foods contain compounds like fructo-oligosaccharides and inulin that nourish microbes such as Bifidobacteria.

Fermented Foods (Probiotics)

Fermented foods introduce live bacteria, or probiotics, directly into the system. A Stanford School of Medicine study found that a diet high in fermented foods increases microbiome diversity and may reduce markers of inflammation. Regular consumption of a variety of these foods appears to support gut health.

• Yogurt with live active cultures
• Kefir
• Sauerkraut
• Kimchi
• Miso
• Kombucha

Polyphenols

Polyphenols are natural compounds found in plant foods that also help shape the gut microbiome. These compounds are responsible for the vibrant colors in many fruits and vegetables and have antioxidant properties. Only a small fraction of polyphenols are absorbed in the small intestine; the rest travel to the colon where they are broken down by bacteria. Foods rich in polyphenols include berries, dark chocolate, almonds, onions, green tea, and extra-virgin olive oil.

Implementing a Diet for Enhanced Microbial Richness

Adopting a diet for microbial diversity focuses on inclusion rather than strict exclusion. Research from the American Gut Project revealed that individuals who ate 30 or more different types of plant foods weekly had a more diverse gut microbiome compared to those who ate 10 or fewer. This goal encourages moving beyond the standard five-a-day recommendation to actively seek out a wider array of nutrients.

Achieving this target can be incorporated into daily life through gradual changes. One approach is to “eat the rainbow,” consciously including fruits and vegetables of different colors in meals. Meal planning can help; strategies could include trying one new vegetable each week, choosing mixed salad greens instead of a single type, or adding a three-bean mix to a chili. Nuts, seeds, and herbs also count toward this weekly goal.

While the focus is on adding nutritious foods, it is also helpful to moderate the intake of items that can negatively affect microbial balance. Ultra-processed foods often contain additives like emulsifiers that may disrupt the gut’s microbial ecosystem. Artificial sweeteners, such as aspartame and sucralose, have been shown to alter the composition and function of gut bacteria.

Diets high in refined sugars can fuel the growth of less desirable bacteria and yeast. Similarly, a high intake of red and processed meats may encourage the growth of bacteria that produce harmful compounds. Limiting these foods helps create a better environment for beneficial microbes to flourish, supporting the positive changes made by increasing dietary variety.