What to eat to improve the microbiome?

The microbiome diet is quickly becoming a popular approach for improving digestive health, boosting immunity, and enhancing overall wellness. This blog post explores which foods best support the gut microbiome and how dietary choices directly shape the composition and diversity of this vital internal ecosystem. You’ll discover how ancient grains, fermented foods, legumes, probiotics, high-fiber vegetables, and prebiotics positively impact your gut environment. We also explore how microbiome testing can highlight imbalances and guide new food strategies. If you’re wondering “What should I eat to improve my microbiome?”, this post provides nutrition-based insights and practical tips grounded in science to help you make confident, nourishing food choices every day.

Harnessing the Power of the Microbiome Diet: How Your Food Choices Influence Gut Microbiome Testing Results

Digestive health has taken center stage in recent years, thanks to increasing awareness of the gut microbiome—an intricate community of trillions of microorganisms living inside our digestive tracts. These microbes, primarily bacteria, influence everything from digestion and nutrient absorption to mood and immune function. With the rise of gut microbiome testing, individuals now have the ability to learn more about their unique microbiota composition and make changes based on scientific insights.

Gut microbiome testing involves analyzing your stool sample to assess microbial species and quantities present in the gut. These results allow individuals to understand imbalances—such as low diversity, overgrowth of harmful bacteria, or lack of beneficial strains—and offer dietary recommendations accordingly. One of the most effective interventions for improving test scores and gut health is adopting a microbiome diet, intentionally designed to nourish beneficial microbes and increase their diversity.

The microbiome diet is not a fad but a lifestyle that emphasizes whole, minimally processed foods, rich in fiber, plant-based compounds, probiotics, and prebiotics. It aims to create an environment where beneficial bacteria thrive while limiting foods that promote imbalance or inflammation. Scientific studies show that diversity in food intake leads to microbial diversity—more types of food mean more types of bacteria, which contributes to stronger gut resilience and immunity.

Your food choices directly influence not only the quantity of bacteria but also their behavior. Certain compounds such as prebiotics encourage bacterial growth, while fermented foods introduce new bacterial strains into the system. Fiber-rich foods act as substrate for these bacteria to ferment, releasing short-chain fatty acids like butyrate that protect gut lining and reduce inflammation.

In this guide, we will deep dive into food groups that support gut health. We’ll explore the effects of ancient grains, legumes, and fermented vegetables; the power of probiotic dairy like yogurt and kefir; the role of fiber-laden fruits and vegetables; and how polyphenol-rich foods and prebiotics enhance resilience. By aligning your eating habits with the microbiome diet and utilizing tools like gut microbiome testing, you can create a more symbiotic relationship with your gut.

Let’s explore this exciting frontier in wellness and discover how your next meal can be a step toward better health from the inside out.

Ancient Grains, Fermented Vegetables, and Legumes for Gut Microbiome Testing: Nourishing the Microbiome Naturally

When striving to improve your gut microbiome through diet, incorporating time-honored staples such as ancient grains, fermented vegetables, and legumes can provide foundational benefits. These foods have been nourishing diverse cultures for millennia, and modern science now confirms that they play a critical role in maintaining a healthy balance of gut flora.

Ancient grains like quinoa, millet, farro, amaranth, oats, and barley are more than just hearty additions to your plate—they’re jam-packed with dietary fiber, plant-based protein, and micronutrients. Unlike refined grains, these ancestral grains retain their bran and germ, providing resistant starches and fibers that serve as prebiotic fuel for colonic bacteria. These fermentable fibers not only support the growth of beneficial microbes but also encourage the production of short-chain fatty acids that improve gut lining integrity, regulate immune responses, and reduce inflammation.

Among these, oats and barley are particularly rich in beta-glucans—a type of soluble fiber that fortifies gut health and leads to measurable improvements in microbial diversity. Regular consumption of such grains has been associated with increased levels of Bifidobacteria and Lactobacilli, two dominant beneficial genera in the human microbiome. Adding ½ cup of cooked oats or barley to your breakfast or incorporating quinoa into salads can offer cumulative benefits over time.

Fermented vegetables bring live microbial cultures directly into the gut, acting as natural probiotics. Foods like sauerkraut (fermented cabbage), kimchi (a spicy Korean side dish made of radish, cabbage, garlic, and chili), and pickles (fermented in brine) contain lactic acid bacteria, a genus that includes Lactobacillus species. These bacteria have been shown to reduce gastrointestinal issues, support the immune system, and even mitigate symptoms of anxiety and depression, likely through the gut-brain axis. Kefir and kombucha are excellent beverages to include, but food-based options provide more substance and additional fiber.

Legumes—including lentils, chickpeas, black beans, pinto beans, and navy beans—are rich in soluble and insoluble fibers, which help bulk stool, feed microbes, and create a favorable gut pH. The fermentation of these fibers in the colon has been linked to increased abundance of butyrate-producing bacteria like Firmicutes and other beneficial SCFA-producing strains. Certain amino acids and phytonutrients in legumes further enhance anti-inflammatory gut functions.

Studies examining individuals following legume-rich diets showed enhanced microbiome profiles on gut tests, with clear increases in microbial richness and diversity. They also demonstrated enhanced metabolic markers like improved blood glucose and lower systemic inflammation—further benefits that highlight the gut’s influence beyond digestion.

If you are tracking changes through a gut microbiome test, regularly incorporating these food groups can help create measurable improvements in beneficial bacteria and shifts in dysbiosis markers. Try a weekly rotation starting with quinoa bowls, legume soups, sauerkraut toppings, and fermented veggie slaws to keep your microbiome well-fed and resilient.

Yogurt, Kefir, and Other Beneficial Probiotics for Gut Microbiome Testing: Cultivating a Healthy Microbial Balance

When aiming to support your microbiome through diet, few interventions are as direct and beneficial as consuming probiotics. These are live microorganisms, often referred to as “good bacteria,” that, when ingested in adequate amounts, confer natural health benefits—mainly by restoring balance and variety in your gut ecosystem. Probiotic-rich foods offer one of the most straightforward and accessible ways to introduce beneficial bacteria into your digestive tract and are a recognized staple of the microbiome diet.

Yogurt is perhaps the most widely consumed and recognized probiotic food. It is made by fermenting milk with live bacterial cultures, most commonly Lactobacillus bulgaricus and Streptococcus thermophilus. High-quality yogurt often also includes additional strains like Lactobacillus acidophilus and Bifidobacterium lactis, which are known to colonize the intestines and improve gut barrier function. Consistent intake of yogurt is associated with improved digestion, reduced incidence of irritable bowel syndrome (IBS), and support for immune modulation. Choose plain, unsweetened yogurt with live active cultures to maximize health and minimize added sugar that could fuel harmful bacteria.

Kefir, a fermented milk drink originating in Eastern Europe, contains an even more diverse bacterial profile compared to yogurt. In addition to Lactobacillus and Bifidobacterium species, it includes several strains of yeast, such as Saccharomyces cerevisiae, which benefit gut flora by balancing bacterial overgrowth, such as Candida. Kefir contains up to 30 probiotic strains, making it a powerhouse for promoting microbial richness and is especially helpful following antibiotic treatments.

Other probiotic foods include tempeh (a fermented soy product), miso (a savory Japanese seasoning made from fermented soybeans), natto, traditional buttermilk, acidophilus milk, and probiotic pickles fermented in brine—not vinegar. Each introduces different microbes that collectively contribute to a dynamic internal environment. Consuming a mix of probiotic foods can more effectively diversify your gut microbiota than relying on a single source.

To make sure these probiotics contribute positively, it’s important to feed them adequately with prebiotics and fibers (discussed later). Also, consistency is key—fermented foods should be consumed frequently, if not daily, in small but regular servings (e.g., ¼ cup of sauerkraut or one serving of yogurt/kefir). If digestive issues persist, pairing dietary changes with gut microbiome testing can provide clearer indications of which strains are missing or dominant and inform personalized strategies.

For individuals unable to tolerate dairy, plant-based probiotics like coconut yogurt, almond kefir, and fermented drinks using live cultures can be suitable alternatives. Also, probiotic supplements are available and useful for targeted interventions, though whole-food forms tend to offer better nutrient support in conjunction with probiotics.

Fruits, Vegetables, and Whole Grains as Dietary Fiber Sources for Gut Microbiome Testing: Fueling Your Microbial Garden

One of the most reliable ways to cultivate a healthy gut microbiome is by feeding your existing microbial population with fermentable plant fibers—dietary components that human enzymes cannot digest, but gut microorganisms can. These fibers act as prebiotics when fermented in the large intestine and are converted into short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs nourish the colon lining, regulate the immune system, and even support brain health. Thus, fruits, vegetables, and whole grains form a pillar of the microbiome diet.

Fruits provide a rich variety of soluble and insoluble fibers, polyphenols (which we’ll cover later), vitamins, and minerals that together create an optimal environment for gut diversity. Berries stand out for their fiber and antioxidant levels. Blueberries, raspberries, blackberries, and strawberries provide not only about 8 grams of fiber per cup but also bioactive components shown to increase Lactobacillus and Bifidobacterium species. Bananas and apples contain inulin and pectin, respectively—fibers with strong prebiotic potential.

Vegetables, especially leafy greens and root varieties, offer a spectrum of fermentable fibers. Kale, spinach, Swiss chard, and collard greens provide insoluble fiber and are rich in magnesium, supporting motility and microbial balance. Sweet potatoes, beets, carrots, and Jerusalem artichokes are not only high in fiber but also contain resistant starch, which ferments slowly and benefits deeper regions of the colon.

Whole grains such as brown rice, steel-cut oats, bulgur, and barley are dense in fibers like beta-glucan and arabinoxylans, proven to support microbial richness. Oats deservedly have an iconic role in gut health, balancing blood sugar and cholesterol while enhancing populations of butyrate-producing bacteria. Pairing humble grains with fibrous veggies makes meals functional on multiple levels.

Improving fiber intake needs to be gradual, particularly if your baseline intake is low, to minimize bloating or discomfort. Aim for 25–35 grams of fiber daily, distributed across meals. Drink ample water, and ensure your fiber comes from diverse whole foods rather than supplement powders alone.

Microbiome testing from services such as InnerBuddies can help indicate which taxa are thriving or underrepresented in response to your current diet. For example, testing might reveal low butyrate levels, suggesting not enough fermentable fiber. In this case, increasing leafy greens or oats can prompt measurable benefits.

The practical takeaway: eating vibrantly colored, fiber-rich plant foods fuels your microbial allies and can produce testable improvements in as little as 2–4 weeks. Building meals around produce ensures you're targeting the most dynamic area of microbial nutrition directly from the source.