by Emily Reich, RD
Your gut is home to trillions of microorganisms: bacteria, viruses, fungi, and other tiny life forms that together form what scientists call the gut microbiome. Think of it as a bustling ecosystem living inside you, and just like any ecosystem, diversity matters.
A diverse gut microbiome is associated with better immune function, improved mental health, lower inflammation, and reduced risk of chronic diseases like obesity and diabetes [1]. Conversely, low microbial diversity has been linked to various health problems, including metabolic disorders and digestive issues [2].
So what does all of this mean? What you eat has a profound impact on the health and diversity of your gut microbiome! Here’s how to make food choices that support gut health.
Eat a Variety of Plants Weekly
One of the most significant findings in gut health research comes from a study involving more than 10,000 participants from the U.S., UK, and Australia. In this study, researchers discovered that people who ate 30 or more different types of plants each week had significantly more diverse gut microbiomes, as well as reduced antibiotic resistant genes compared to those who ate 10 or fewer [3].
One thing to note is that it wasn’t about being vegetarian or vegan – it was the variety of plants that mattered most. Each type of plant provides different fibers, polyphenols, and nutrients that feed different species of gut bacteria [1].
What counts as a plant?
- Fruits and vegetables
- Whole grains (oats, quinoa, brown rice, barley)
- Legumes (beans, lentils, chickpeas)
- Nuts and seeds
- Herbs and spices
Practical tip: Start tracking your weekly plant intake. Add walnuts to your oatmeal, throw some chickpeas into your salad, add a fruit alongside each snack, or season dishes with different herbs and spices. Small additions throughout the day can make a big difference overall!
Prioritize Fiber-Rich Foods
Fiber is the primary fuel source for your gut bacteria. When beneficial bacteria ferment fiber, they produce short-chain fatty acids (SCFAs) like butyrate, which play important roles in gut health and lining, immune function, and even blood sugar regulation [4].
Studies show that higher fiber intake is associated with greater microbial diversity and a more resilient gut ecosystem [2,5]. Different types of fiber support different bacterial species, which is another reason variety matters.
Great fiber sources include:
- Beans and lentils
- Whole grains like oats, barley, and quinoa
- Vegetables, especially leafy greens and cruciferous vegetables
- Fruits with the skin
- Nuts and seeds
Add Fermented Foods
Fermented foods have been part of human diets for thousands of years, and research is now revealing their benefits for gut health. Fermented foods introduce live beneficial microorganisms into your gut and contain unique compounds produced during the fermentation process, and lead to positive impacts in the gut microbiome. In addition to this, diets high in fermented foods have been shown to increase gut microbiome diversity and decrease inflammatory markers, as well as positively impact the gut microbiome in both the short and long term [6].
Try incorporating:
- Fermented pickles
- Yogurt with live active cultures
- Kefir
- Sauerkraut and kimchi
- Kombucha
- Miso and tempeh
Embrace Polyphenol-Rich Foods
Polyphenols are plant compounds found in colorful fruits, vegetables, tea, coffee, and cocoa. While they’re known for their antioxidant properties, research shows they also act as prebiotics. Prebiotics feed beneficial gut bacteria and promote microbial diversity [7].
Studies show that polyphenols can increase the abundance of beneficial bacteria while reducing harmful species [8]. The gut bacteria also transform polyphenols into bioactive compounds that benefit your health.
Top polyphenol sources:
- Colorful vegetables like red onions, spinach, and artichokes
- Berries
- Dark chocolate (70% cocoa or higher)
- Green tea and coffee
- Extra virgin olive oil
Limit Ultra-Processed Foods
Ultra-processed foods appear to have negative effects on gut health. Research indicates that these foods are associated with decreased microbial diversity, lower levels of beneficial bacteria, and an increase in pro-inflammatory microorganisms [9]. Additionally, ultra-processed foods are typically low in fiber, which means they provide little fuel for beneficial bacteria.
Foods to minimize:
- Fast food
- Packaged snacks and chips
- Sugary cereals and beverages
- Processed meats
- Artificial sweeteners
- Frozen ready meals
Putting It All Together
Building a diverse gut microbiome doesn’t require a complete dietary overhaul. Start with small, sustainable changes:
- Add one new plant food per week. Try a vegetable you’ve never cooked before or experiment with a new grain.
- Include fermented foods throughout the week. Start with a serving of yogurt at breakfast or a side of sauerkraut with dinner.
- Eat the rainbow. Different colored foods contain different polyphenols, are typically high in fiber, and have nutrients that support diverse bacterial species.
- Cook more at home. This naturally reduces ultra-processed food intake and gives you control over ingredients.
- Use herbs and spices generously. They count toward your plant diversity and add beneficial compounds to every meal.
Your gut microbiome can respond quickly to dietary changes! While building long-term diversity takes time, you can start shifting your microbiome in a positive direction with your very next meal.
At Princeton Longevity Center, our registered dietitians work with you to develop personalized nutrition plans that support your gut health and overall well-being. If you have questions about optimizing your diet, we’re here to help.
References
1. Heiman ML, Greenway FL. A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol Metab. 2016.
2. Myhrstad MCW, et al. Dietary Fibre Modulates the Gut Microbiota. Nutrients. 2020.
3. McDonald D, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018.
4. Makki K, et al. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018.
5. Cronin P, et al. Dietary Fiber Intake and Gut Microbiota in Human Health. Nutrients. 2021.
6. Wastyk HC, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021.
7. Ma G, Chen Y. Polyphenol supplementation benefits human health. Nutrients. 2020.
8. Santhiravel S, et al. Dietary polyphenol impact on gut health and microbiota. Crit Rev Food Sci Nutr. 2022.
9. Rondinella D, et al. The Detrimental Impact of Ultra-Processed Foods on the Human Gut Microbiome. Nutrients. 2025.