Something you might already know intuitively but maybe need a written reminder of once in a while: Good gut health is the gateway to better overall health. “Our gut is a complex, complicated organ that controls almost every aspect of our biology,” explains functional medicine practitioner and cofounder of Function Health Mark Hyman, MD. “And our gut health inextricably influences nearly everything, including immune health, brain health, metabolic health, cardiovascular health, mental health, and more.”
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Because our gut microbiome is linked to so much, the warning signs that it is in jeopardy may not be so easy to spot. “Gut imbalances aren’t always gut-symptom specific,” explains nutritionist and founder of Grounded Nourishment Meg Gerber, RD, IFNCP, CGN. “For some it shows up as poor immune function or mental health conditions like anxiety or depression, while for others it can show up as eczema or acne.”
Contrary to popular belief, gut health isn’t just about what we eat. “Research shows gut function is deeply regulated by the autonomic nervous system, stress hormones, immune signaling, and blood sugar balance, often before microbes or food come into play,” Gerber says. “If your body doesn’t feel safe or lives in high-stress mode, digestion literally slows down. So you can have the ‘perfect’ diet and still struggle with constipation, bloating, reflux, acne, or hormonal symptoms if the nervous system, motility, or root imbalances aren’t addressed.”
Those imbalances, it turns out, require a bit more strategy than taking a probiotic to heal fully. Everyone has their own signature microbiome—like a fingerprint—that’s unique to them and made up of billions and billions of microorganisms. It starts from birth, and modern-day nutrition, stress, and lifestyle factors can influence it. “Gut health isn’t something you can fix quickly with a product, cleanse, or short-term protocol,” says registered dietician and wellness advisor for The Lanby Taylor Fazio, RD. “Those trendy gut detoxes or cleanse fads oversimplify a complex system.”
The good news is that healing and supporting your gut microbiome isn’t as complicated as it sounds. Many functional medicine practitioners, including Dr. Hyman, favor a holistic framework for gut restoration that follows five steps: remove, replace, reinoculate, repair, and rebalance. It’s a great starting point, and we asked top dieticians, nutritionists, and physicians to break down everything you need to know about restoring your gut flora for great gut health, below.
In This Article:
- Enlist a Professional
- Eliminate Harmful Triggers
- Replace Missing Digestive Factors
- Reinoculate With Beneficial Bacteria
- Repair the Gut Lining
- Rebalance Lifestyle Factors
- Stay Consistent
- What Are the Signs of an Unhealthy Gut?
- Meet the Experts
Enlist a Professional
Working with a professional can take the guesswork out of healing your gut. When you have a comprehensive look at what’s going on with your gut, it’s easier to craft a more targeted approach. “Effective gut protocols are highly individualized,” Gerber says. “What supports one person’s digestion may worsen symptoms for another, which is why personalization based on symptoms, history, and, when appropriate, targeted testing matters far more than a one-size-fits-all cleanse.”
There’s also value in microbiome or stool tests. “Getting a stool test should be like getting your blood pressure taken,” Dr. Hyman says. “There’s so much to be learned from the stool.” He notes that stool tests aren’t new and have long been used to test for fecal fat absorption, inflammatory markers, pancreatic enzymes, gut infections, and more. What is new is combining these into a more comprehensive test to help make more sense of what’s going on in your body. “With bacterial DNA analysis, we’re able to see the diversity and abundance of microbes in your gut, which populations are high or low,” Dr. Hyman says. “It’s important to have that data because it can indicate how that affects your health and what we can do about it.”
Eliminate Harmful Triggers (With Guidance)
“A poor diet with ultra-processed foods is often a huge contributing factor to an unbalanced microbiome,” Dr. Hyman says. While most of us likely know that the sugar-bomb chocolate chip cookie à la mode after dinner or a midafternoon bag of chips will leave us feeling less than stellar, many of us don’t know that certain foods (think eggs, tomatoes, or potatoes) could be an individual trigger that causes gastrointestinal upset. A short-term, targeted elimination diet can help. “Elimination diets can be especially helpful when it comes to food sensitivities and symptom relief,” Gerber says. “As a rule of thumb, the gold standard for food sensitivities is doing a dietitian-guided elimination diet with a plan to reintroduce the food in four to eight weeks.”
Work with a dietician or trusted practitioner to eliminate known inflammatory foods. (Think gluten, dairy, soy, and eggs, as well as foods that contain sugar, caffeine, and alcohol.) As you slowly reintroduce them, one by one, see how your body responds. The goal is to determine which foods may trigger you specifically so you can limit them to improve and smooth digestion.
Replace Missing Digestive Factors
It’s not just about what you eat; it’s also about how your comprehensive digestive system breaks down and absorbs the nutrients from what you eat. Our bodies naturally produce digestive enzymes—typically in the salivary glands, pancreas, and small intestines—to help break down food efficiently to allow for maximum nutrient absorption. If your body is struggling to produce enough digestive enzymes, it can cause uncomfortable side effects around mealtime, such as cramping, bloating, constipation, diarrhea, and more. “Digestive support, like digestive bitters or enzymes, is generally supportive and well tolerated by most people,” says Gerber, who notes that those with active gallstones or kidney stones should avoid bitters. Electrolytes with foundational minerals like sodium, potassium, and magnesium can be beneficial as a baseline too. “We need minerals to help make digestive juices like stomach acid and digestive enzymes,” Gerber adds. “Digestive bitters and enzymes naturally help upregulate your own digestive-juice secretions. It gives a natural nudge to your stomach acid, digestive enzymes, and bile to help you digest your food better.”
How you eat your food is also crucial. “Start with chewing well,” says Gerber, who suggests 10 to 12 chews per bite, ideally until the food is liquefied, before you swallow. “And slow down, take deep breaths, and sit down for all meals.”
Reinoculate With Beneficial Bacteria
You’ve probably heard about good bacteria versus bad bacteria. Bad bacteria can cause illness, inflammation, and digestive issues when they overgrow, invade, and crowd out the beneficial bacteria. Stress, diets high in ultra-processed foods and refined sugars, and certain medications, such as antibiotics, are associated with harmful gut microbes. “There are as many bacteria as there are cells in our body and 100 times as much bacterial DNA regulating everything about our health,” Dr. Hyman says. When you’re in gut-repair mode, it’s crucial to bring back the good bacteria. “Your good gut bugs love diversity when it comes to allowing them to flourish and survive,” Gerber says.
Probiotic-rich foods like sauerkraut, kimchi, pickles, unsweetened yogurt or kefir, miso, and more introduce live good bacteria directly into your gut. Prebiotic fiber—the soluble fibers found in Jerusalem artichokes, garlic, onions, leeks, dandelion greens, jicama, chicory root, asparagus, and more—is essential too. It serves as fuel for probiotics, providing energy to nourish and grow beneficial bacteria.
Polyphenols act as prebiotics and can help inhibit harmful bacteria too. “Eat an abundance of polyphenol-rich vegetables daily,” Dr. Hyman says. Some great examples are spinach, broccoli, carrots, artichokes, red onions, and asparagus.
If your diet is lacking these essential nutrients, a high-quality comprehensive probiotic supplement can help restore microbiome balance, as can a multivitamin and prebiotic fiber to support intestinal health and gut barrier function. However, while probiotics can be wonderful tools for supporting gut health for many people, there is some nuance, and your symptoms, history, and tolerance should be taken into consideration. “Not all probiotics are created equally,” Fazio says. “Different strains and profiles can deliver different targeted results, so it’s best to find the specific one that will work for you with a trusted practitioner.”
Repair the Gut Lining
Your gut flora will thrive when it’s consistently fueled with a wide variety of plant fibers from vegetables, fruits, legumes, whole grains, nuts, and seeds. However, there’s only a thin cell layer between your intestines and body—and that determines what should be absorbed into your body. Think of it as a coffee filter: The filter prevents the grounds from getting into your coffee, leaving you with only the clear, rich liquid. But if there’s a hole in your filter, the grounds can leak into your coffee. The same is true for your intestines; if you have increased intestinal permeability (a.k.a. leaky gut), what could leak into your body is fungus, not-so-good bacteria, or undigested food.
You can support the gut-lining healing process with targeted nutrients such as L-glutamine, zinc, antioxidants, and omega-3s. “Different fibers feed different microbes, which is how we support diversity and resilience over time,” Fazio says. “From there, adequate protein is essential for gut-tissue repair, and healthy fats, particularly omega-3s, help regulate inflammation.” Fazio also pays close attention to micronutrients like zinc, magnesium, and vitamin D. “Deficiencies of these can quietly impair gut integrity and immune function even when the diet looks healthy on the surface,” she says. Supplements can help fill in the gaps. “Targeted probiotics, specific herbal supports, soluble fiber, magnesium, digestive enzymes, or nutrients such as zinc or glutamine may be helpful,” Fazio says. Again, supplements are highly individual and best used under a practitioner’s guidance.
Rebalance Lifestyle Factors
Good gut health is influenced by how your body is being supported day to day—not just food choices. “Your microbiome is essentially listening to your thoughts,” Dr. Hyman says. “Stress, sleep, environmental toxins we’re exposed to, medications like antibiotics, and more can change the composition of your microbiome.” By managing lifestyle factors like stress and sleep, you can help heal your gut. “Chronic stress directly changes gut motility, increases permeability, and disrupts the microbiome,” Fazio says. “Sleep is just as important. Inadequate or irregular sleep interferes with the circadian rhythms that regulate digestion and microbial balance.”
Stay Consistent
If you’ve done the work, the benefits of a healthy gut are many. But gut health isn’t a one-and-done fix. What good is nourishing and healing your microbiome only to fall back into the same rhythm that damaged it in the first place? “While the microbiome can shift within days in response to dietary changes, those changes are often temporary unless they are supported by consistent habits,” Fazio says. “The gut is a very dynamic ecosystem that responds to patterns over time.” To heal your gut, lasting improvements come from sustained, individualized nutrition and lifestyle support rather than quick fixes or detoxes. Otherwise, you can end up right back where you started.
Everything You Need to Know
What Are the Signs of an Unhealthy Gut?
Microbiome imbalances are rarely caused by one single factor, and the signs can be all over the place. “Common contributors include chronic stress, poor sleep, restrictive dieting, low fiber intake, excess alcohol, frequent antibiotic use, and certain medications,” Fazio says. Pay attention to patterns, rather than isolated symptoms. “Chronic bloating, irregular bowel movements, persistent reflux, unexplained fatigue, frequent infections, skin issues, or new food intolerances can all signal that the gut may need support,” Fazio adds. “It is also important to notice resilience. With a healthier gut, disruptions like travel, stress, or dietary changes may cause a temporary issue but do not tend to spiral into longer-term symptoms.”
That being said, there are a few initial signals you should consider. “Early signs often include bloating after most meals, constipation or diarrhea, increased food sensitivities, frequent illness, or changes in mood and energy,” Gerber says. “While it is common to hear about gut issues, it is not normal to have symptoms of gut dysregulation all the time.”
Meet the Experts
- Mark Hyman, MD, is a family physician and functional medicine practitioner. He is also the cofounder and chief medical officer of Function Health, the founder and director of The UltraWellness Center, the founder of the Cleveland Clinic Center for Functional Medicine, and a board member of The Institute of Functional Medicine.
- Meg Gerber, LDN, IFNCP, CGN, is a registered dietician, nutritionist, cofounder of digestive-bitters brand Jüj, and founder of Grounded Nourishment, a private functional nutrition practice in Austin.
- Taylor Fazio, RD, is a New York–based registered dietician and wellness advisor for The Lanby.