“The gut is the first to encounter the universe, and it is the first line of defense between you and the universe,” says Dr. Madiha Saeed, a holistic, functional and integrative doctor in Naperville, Illinois, and director of education for Documenting Hope and KnoWEwell. Home to trillions of bacteria, fungi and other microbes, the digestive tract forms a complex ecosystem known as the gut microbiome, which influences many aspects of health.

Microbes perform numerous functions. They help break down food, produce essential nutrients, support the immune system and influence mood, cognition and overall well-being. Diet, stress, sleep, medications and environmental exposures shape the makeup of our gut microbiota, which, in turn, impact the body’s propensity for health or disease. Efforts to restore and nurture gut health offer opportunities for us to enhance our well-being through simple lifestyle changes.

Gut Microbiome Basics

The intestinal environment is constantly changing, with new microbes entering and others disappearing daily, creating a dynamic community of tiny organisms that is unique to every individual. Different species have specialized roles. For instance, Faecalibacterium prausnitzii lowers inflammation by nourishing gut cells, while Akkermansia muciniphilamaintains the gut lining by breaking down mucus and supporting helpful bacteria. Each person hosts approximately 1,000 distinct microbial species, while humanity collectively harbors more than 10,000 species.

Like a garden, the gut microbiome contains a mix of helpful and harmful organisms. Beneficial microbes behave like healthy plants, supporting digestion, nutrient absorption and immune function. When cared for, these helpful organisms thrive, while also helping to keep harmful microbes (weeds) under control.

Our intestinal garden is shaped by how it is tended. Fiber-rich foods, fermented products and exposure to natural environments help nourish the good microbes, much like water, sunlight and compost nourish plants. By contrast, processed foods, excessive sugar and unnecessary antibiotics can disrupt the balance and allow harmful microbes to take over.

Many people experience gut imbalance, or dysbiosis, without realizing it. The gut is highly sensitive to its environment, and everyday choices like processed foods, medications and chronic stress can quietly disrupt the inner balance, making it harder for beneficial microbes to thrive.

Medications. “Though some medications can save your life, they do come with a side disadvantage, so you need to weigh your risks versus the benefits when it comes to taking any medications,” Saeed advises, noting that antibiotics, for example, reduce microbial diversity and richness, causing short-term changes in the microbiome. While most people recover within two months, their microbiota diversity and productivity may remain low, and some people may experience longer-lasting disruptions.

Common painkillers called nonsteroidal anti-inflammatory drugs (NSAIDs) such as aspirin and ibuprofen can also interact with the composition and function of the gut microbiome. They inhibit microbial growth, induce microbial cell death and increase gut permeability. NSAIDs can also interact with gut microbes, thereby impacting how well the drug is absorbed.

Foods. The food we eat significantly impacts the microbiome’s composition and metabolism. “Real foods nourish the good bugs, while processed foods fuel the bad,” says Saeed. Diets high in processed foods, sugars and additives create a toxic load that disrupts bacterial balance and triggers inflammation, leading to chronic disease. Eating these kinds of ingredients on a consistent basis can slowly damage the gut, as harmful microbes crowd out beneficial species, weakening the intestinal ecosystem over time without immediate signs of distress.

Stress. Chronic stress is another gut health disruptor. Stress hormones can reduce beneficial bacteria such as Akkermansia muciniphila, which has been identified as a potential protector against obesity and Type 1 diabetes. Stress also encourages yeast overgrowth, leading to inflammation and intensifying the stress response in a vicious cycle. Studies also show that stress, whether physical or perceived, can alter overall microbial composition.

A 2018 narrative review published in Frontiers in Microbiology analyzed existing preclinical studies and found that various psychological, environmental and physical stressors can alter gut microbiota composition and function. Furthermore, a 2023 systematic review published in Neuropsychobiology found that higher perceived stress was associated with lower microbial diversity and decreased abundance of beneficial genera such as Lachnospira, Veillonella and Phascolarctobacterium. Harmful bacteria like Methanobrevibacter rose in relative abundance in stressed individuals.

Signs of Imbalance

Indications of an unhealthy gut show up in various ways. Digestive issues such as bloating, gas and constipation often signal an imbalance. Fatigue, mood swings and skin conditions like acne or eczema may also be related to poor gut health. Unexplained weight changes, cognitive problems and food sensitivities may be caused by intestinal distress. A weakened immune system, trouble sleeping and bad breath can also indicate a need for gut support.

Repairing the Gut

Environmental factors influence the microbiome more than genetics, but when the gut has been harmed, Saeed explains, restoration takes more than just a probiotic.

Eat organic whole foods. “Food is medicine. Every bite can either help or hurt,” counsels Saeed, emphasizing the importance of daily food choices. Like humans, gut microbes need nourishment to thrive. When they eat well, human health flourishes. The typical Western diet is high in simple carbohydrates and fat, but low in fiber, offering little nourishment for beneficial microbes.

On the other hand, microbiota-accessible carbohydrates (MACs) such as legumes, root vegetables, fruits, nuts and seeds are essential for a diverse and resilient microbial community. Because MACs are not broken down by digestive enzymes, they are fermented by gut microbes, feeding and promoting the growth and activity of beneficial bacteria.

Choosing organic produce helps avoid synthetic pesticides and herbicides sprayed on produce to eliminate pests and weeds. These chemicals have been shown to negatively affect the gut microbiome and human health. “It’s best to eat local food that is not sprayed,” advises Dr. Patrick Hanaway, a board-certified functional medicine family physician, educator and chief medical officer of KnoWEwell.

Supplement wisely. Probiotics and prebiotics are vital for healing the gut. Probiotics, whether found in foods like yogurt and other fermented products or taken as supplements, introduce live bacteria into the body. Prebiotics act like fertilizer, feeding good bacteria and helping restore overall balance. Fiber-rich foods such as asparagus, bananas, garlic, onions, oats, apples and legumes naturally support a thriving gut ecosystem.

As Hanaway explains, “A probiotic is a live bacteria that can be ingested and move into the stomach and populate the body. A prebiotic is a component that helps feed the commensal [beneficial] bacteria in the gut. Probiotics are highly specific. They have great benefits for specific strains for specific diseases in specific doses. Yet, the probiotic is a tourist; it doesn’t stay in the body. It’s great to have tourists in the economy, but if an economy becomes entirely dependent on tourism, it becomes a problem.”

When choosing supplements, quality matters. Due to limited regulations, it is best to purchase from reputable brands. Supplements in fillable capsules tend to have fewer fillers and more active ingredients. Vitamins and minerals are best absorbed from whole foods, so supplements should complement, not replace, a balanced diet.

Start a garden. Gardening increases the availability of fresh, fiber-rich, seasonal fruits and vegetables in the diet, but the very act of putting our hands in the dirt may also help increase the diversity of our gut microbiome. A 2022 cohort study of 19 families over one growing season by scientists at the University of Illinois and published in the journal Nature found that when compared to non-gardeners, families that grew plants and produce in their backyards had more gut bacteria linked to fiber fermentation, greater microbial diversity and even some microbes in their guts that appeared to come from the soil. Families that gardened also ate more fiber-rich foods.

Commit to small actions. Healthy microbiomes grow with consistent care—not perfection—and even small lifestyle changes can build a more resilient ecosystem for better overall health. There is no magic bullet for healing the gut. The key is to commit one hour a week to health education and to small actions focused on rebuilding the inner ecosystem one change at a time.

“A strictly-diet approach isn’t the answer; a lifestyle approach is,” says Dr. Tom O’Bryan, an expert on food sensitivities, environmental toxins and the development of autoimmune diseases, as well as the host of the Regenerative Whole Health Show at KnoWEwell.com. “Dietary regimens can go only so far if something else persists, like mold in the house, high glyphosate levels or accumulated mercury in the body.” Addressing the macrocosm around us helps fix the microcosm inside us.

Indoor air filtration and water purification measures might be necessary to counteract an unhealthy indoor environment. Small changes like storing leftover food in glass rather than plastic can help keep harmful compounds out of the gut. Herbs such as chamomile and holy basil in diffusers and teas may aid the chronically stressed. Even simply chewing our food slowly, with mindfulness and gratitude, can help aid the digestion process.

The gut microbiome is a complex ecosystem that plays an essential role in overall health. Understanding what it is, what harms it and how to recognize signs of imbalance empowers us to take practical steps to restore and maintain gut health. By nourishing the microbiome with whole foods, managing stress, using supplements wisely and embracing small lifestyle changes, individuals can cultivate a resilient inner garden that supports well-being for life.

Hannah Tytus is a researcher and content creator for KnoWEwell, P.B.C. and former technical writer for the National Institutes of Health’s National Center for Complementary and Integrative Health.

Repairing the Gut Lining

Dr. Madiha Saeed, a holistic, functional and integrative doctor in Naperville, Illinois, and director of education for Documenting Hope and KnoWEwell, stresses that repairing the gut lining is key for nutrient absorption. She recommends foods rich in zinc; vitamins A, C, and D; vitamin E; and selenium to reduce inflammation. Additionally, omega-3 fatty acids, often found in fish, help reduce inflammation and support the gut lining. Digestive enzymes found in fruits and vegetables such as avocados, pineapples, papayas, mangoes and bananas break down food, reducing intestinal inflammation. L-glutamine, found in bone broth, animal proteins, spinach, red cabbage and parsley, helps preserve the gut lining.