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Hey Life Warriors! Here we come with the last and most important chapter of our Microbiota series. In the first chapter, we explained what microbiota is and its main functions. In the second one, we went through the potentially severe consequences that dysbiosis (unbalanced microbiota) may have for your health. Today, we will give you good advice for maintaining a perfect balance of your microbes.
The good news is that we can take care of and improve our gut microbiota through healthy habits. Here are some science-backed practices to keep your gut “tenants” happy:
- Eat a fiber-rich, whole-grain diet: Fiber is a favorite food for our beneficial bacteria. Eating fruits, vegetables, legumes, nuts, and whole grains daily provides fiber and prebiotics that promote microbial diversity (1). Studies show that a high-fiber diet increases healthy fatty acid-producing bacteria and microbiome diversity (1). Conversely, a low-fiber diet starves the good microbiota. Include a variety of colors on your plate and think about feeding your microbes, too!
- Incorporate fermented foods (natural probiotics): Products such as yogurt, kefir, sauerkraut (fermented cabbage), kimchi (fermented Asian cabbage), kombucha (fermented tea), or miso are rich in live beneficial microorganisms (probiotics). Regularly consuming these fermented foods introduces friendly bacteria that can help strengthen the existing microbiota. For example, a study from Stanford University showed that a diet high in fermented foods increased bacterial diversity and reduced inflammatory markers (2). These foods will help you replenish healthy microbes in your gut.
- Choose natural prebiotics: Prebiotics are special types of fiber that selectively feed beneficial bacteria. They are found in foods such as garlic, onions, leeks, asparagus, bananas, artichokes, oats, and chicory root, among others. For example, the inulin found in garlic, onions, and asparagus promotes the growth of Bifidobacteria, a beneficial genus. Similarly, fructooligosaccharides (FOS) from bananas, leeks, and artichokes help increase microbial diversity and the production of healthy fatty acids (3). Including these vegetables in your daily diet is an effective way to ensure food for your good bacteria.
- ultra-processed foods, added sugars, and unhealthy fats whenever possible: While some foods nourish the microbiota, others harm it. Diets high in refined sugars and trans or saturated fats (processed pastries, fast food, sugary soft drinks) promote the proliferation of bacteria associated with inflammation and reduce beneficial populations (4). Try to limit these products and opt for more natural options. Your gut will thank you with improved digestion and energy.
- Use antibiotics only when necessary: Always follow medical advice and do not self-medicate with antibiotics for any discomfort. These drugs profoundly alter the intestinal microbiota (5). If you must take them, supplement with probiotics (as recommended by a doctor) and nourish your gut well during and after treatment to help it recover. Likewise, moderate the use of antacids or other medications that can disrupt the intestinal flora, in consultation with your doctor.
- Maintain an active lifestyle: You probably won’t be surprised to see that, in addition to all the benefits you already know exercise can offer, protecting your microbiota is another one. Moderate physical activity has been associated with a more diverse microbiota and a greater abundance of bacteria that produce anti-inflammatory compounds ( 6 ). For example, walking, cycling, or any other sport regularly can improve your microbial composition. However, extreme exercise without adequate rest can have negative effects, so find a balance. In general, moving your body helps move your bowels and cultivate healthy flora.
- Manage stress and take care of your rest: Since chronic stress can disrupt microbiota, it’s important to adopt stress management techniques. Practicing yoga, meditation, relaxation techniques, or simply taking time for hobbies and rest contributes to a favorable hormonal environment for your microbes. Likewise, sleeping well (7-8 hours per night) helps regulate body and gut rhythms. A good night’s sleep repairer is an ally of an intestine-balanced balanced. If you struggle with this, in this article, you can find some advice that might be useful for you.
- Maintain a healthy weight: Obesity has been linked to alterations in the microbiota (e.g., a higher Firmicutes / Bacteroidetes ratio ) (3). If you think you should lose a few pounds, check out this article, which tells you everything you need to know about fat loss. Try adding the foods we recommend here to your regular diet. It’s a virtuous circle: good habits -> healthy microbiota -> efficient metabolism -> balanced weight -> even healthier microbiota.
Additionally, listen to your body. Each person has a unique microbiota, so what works for most people might not work for you. Pay attention to how certain foods affect you; for example, if legumes make you gassy at first, introduce them gradually so your flora can adjust. Cultivating a healthy microbiota is an ongoing process, but the benefits—from better digestion to a better mood—are well worth the effort.
Recommended foods to take care of your microbiota
A practical way to support your gut microbiota is to stock your pantry with gut-friendly foods. Here’s a list of some of the most recommended by experts, along with their benefits:
- Fiber-rich fruits and vegetables: Apples, pears, bananas, avocados, artichokes, asparagus, carrots, broccoli, spinach… the more colorful, the better! Plant fiber acts as a prebiotic for good bacteria. Eating a variety of vegetables ensures a diversity of fiber and polyphenols that promote a robust microbiota.
- Legumes and whole grains: Lentils, chickpeas, beans, as well as oats, brown rice, quinoa, and whole wheat. They are excellent sources of soluble and insoluble fiber. Legumes contain resistant starch that reaches the colon intact, where bacteria ferment it, producing butyrate (an anti-inflammatory compound) ( 3). Including legumes several times a week and preferring whole grains over refined ones (whole wheat bread vs. white bread) will keep your microbes busy and happy.
- Fermented foods with probiotics: Natural yogurt (with live cultures), kefir (milk or water), sauerkraut, kimchi, miso, tempeh (fermented soy), and kombucha. All of these provide active cultures of beneficial bacteria that can help replenish and balance your gut. Yogurt, for example, contains Lactobacillus and Bifidobacteria that can survive gastrointestinal transit and temporarily colonize the colon, contributing to digestive health. Kefir is even more microbially diverse. Make sure these products are as artisanal or natural as possible (unpasteurized after fermentation, as pasteurization kills probiotics).
- Foods rich in natural prebiotics: Already briefly mentioned, certain vegetables and fruits are especially rich in prebiotic fibers. Some notable ones include garlic, onion, leek, spring onion, asparagus, artichoke, dandelion, chicory, beets, and legumes. Oats and barley also contain beta-glucans with a prebiotic effect. These foods selectively feed bacteria such as Bifidobacteria and Faecalibacteria (butyrate producers), strengthening the microbiota.
- Nuts and seeds: Almonds, walnuts, flax seeds, chia seeds, etc. In addition to fiber, they provide healthy fatty acids and polyphenols that benefit the flora. For example, consuming almonds has been associated with an increase in Bifidobacteria in small studies. Flax seeds, when hydrated, form mucilage that serves as a substrate for bacteria in the colon. Just remember to soak or grind the seeds to take advantage of their nutrients.
- Foods rich in polyphenols: Green tea, dark cocoa (dark chocolate ≥70% cocoa), coffee, berries (blueberries, raspberries), pomegranate, grapes, extra virgin olive oil. Polyphenols are antioxidant compounds that our bacteria can often metabolize into beneficial substances. For example, the polyphenols in blueberries may benefit Akkermansia. Muciniphila, a bacteria linked to less inflammation and improved metabolism. So, a small square of dark chocolate or a cup of tea a day can also be a treat for your microbiota (as well as your taste buds!).
- Water and healthy liquids: Staying well hydrated with water facilitates intestinal transit and the metabolic function of bacteria. You can also include herbal teas and natural broths. Avoid sugary soft drinks (due to sugar and additives) and excessive alcohol whenever possible, which can harm microbiota.
These foods, integrated into a balanced diet, act as quality fuel for your microbiota. Remember, it’s not about eating one or the other in isolation, but rather about achieving a varied dietary pattern, mostly based on plant-based, fermented, and minimally processed foods. With small, consistent changes to your diet, you’ll be cultivating an intestinal environment conducive to the flourishing of the bacteria that support your health.
Infographic: Factors that influence the intestinal microbiota
Infographic – The gut microbiota throughout life: richness, diversity, and factors that shape it. The following infographic (published by Gut Microbiota for Health, an initiative of the European Society of Neurogastroenterology) visually illustrates how the microbiota evolves throughout the different stages of life and what factors influence its balance. The top section shows the progression of microbial diversity: it increases during the first 1000 days (from conception to age 2, a critical stage where factors such as the type of delivery (vaginal or cesarean), breastfeeding vs. formula and infant diet leave their mark), remains stable in adulthood (with diet and lifestyle being the main modulators at this stage), and can decrease in old age (accompanying the decline of physiological functions and often the increased use of medications).
At the bottom, the infographic lists the main factors that shape gut microbiota: maternal nutrition and health (before and during pregnancy), mode of birth, host genetics, lifelong nutrition (diet), lifestyle (including exercise), environment, use of antibiotics and other medications, and changes associated with aging. Each icon represents a factor: for example, the mother transmits her microbes to the baby, especially if she delivers vaginally and through breastfeeding; antibiotics unbalance the gut flora; a varied diet enriches it, while a sedentary or stressful lifestyle can negatively affect it. Taken together, this infographic reinforces the concept that our life choices and circumstances have a direct impact on the health of our gut microbes, from birth to old age.
Conclusion: Empower your gut health
Knowing and caring for your gut microbiota is an investment in your present and future health. Think of these microorganisms as tiny warriors and caregivers working day and night for your well-being: helping you digest, protecting you from germs, educating your immune system, and even influencing your mood. An imbalance in this community can manifest itself in discomfort and illness, but you have a lot of control over keeping it in harmony.
Eat a varied, whole-food diet, move frequently, manage stress, and avoid harmful things like unnecessary antibiotics and ultra-processed diets. Scientific studies support that these habits promote a diverse and resilient microbiota, which translates into a stronger digestive system, better digestive balance, stronger immunity, and greater overall well-being (6).
Every little decision counts: that extra portion of vegetables, that glass of kefir, or that walk in the fresh air not only benefits you, it also nourishes the trillions of microscopic allies you carry within. Take care of your gut microbiota and it will take care of you! On the path to a healthy and fulfilling life, you are not alone, you are accompanied by an army of friendly microbes, pushing you to achieve true well-being from within.
References
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- Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 5;184(16):4137-4153.e14. doi : 10.1016/j.cell.2021.06.019. Epub 2021 Jul 12. PMID: 34256014; PMCID: PMC9020749.
- Kumar Suresh, Mukherjee Riya, Gaur Pratibha, Leal Élcio , Lyu Xiaoming, Ahmad Saheem, Puri Paridhi, Chang Chung-Ming, Raj V. Samuel, Pandey Ramendra Pati. “Unveiling roles of beneficial gut bacteria and optimal diets for health.” Frontiers in Microbiology. Volume 16 – 2025. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1527755 . DOI=10.3389/fmicb.2025.1527755. ISSN=1664-302X
- Hrncir T. Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options. Microorganisms. 2022 Mar 7;10(3):578. doi :10.3390/microorganisms10030578. PMID: 35336153; PMCID: PMC8954387.
- Madison A, Kiecolt -Glaser JK. Stress, depression, diet, and the gut microbiota: human-bacteria interactions at the core of psychoneuroimmunology and nutrition. Curr Opinion Behav Sci. 2019 Aug;28:105 -110. doi : 10.1016/j.cobeha.2019.01.011. Epub 2019 Mar 25. PMID: 32395568; PMCID: PMC7213601.
- Clauss Matthieu, Gérard Philippe, Mosca Alexis, Leclerc Marion. Interplay Between Exercise and Gut Microbiome in the Context of Human Health and Performance. Frontiers in Nutrition. Volume 8 – 2021. https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2021.637010 DOI: 10.3389/fnut.2021.637010. ISSN: 2296-861X