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    You are at:Home»Health»How to Fix Gut Microbiome: Stop Making These Mistakes
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    How to Fix Gut Microbiome: Stop Making These Mistakes

    Earth & BeyondBy Earth & BeyondDecember 13, 2025008 Mins Read
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    How to Fix Gut Microbiome: Stop Making These Mistakes
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    Your gut microbiome has an almost unlimited significance in your body. Simply put, it’s the massive community of bacteria, fungi, viruses, and other microbes that dwell in your digestive tract and regulate a ton of physiological processes. The sheer size is hard to wrap your head around: up to 100 trillion individual microbes collectively weighing more than two pounds, according to some estimates.

    Based on the term “gut microbiome,” you’d probably assume that this teeming internal environ primarily affects your GI system, but evidence is mounting that its impact extends far beyond that—to everything from your metabolism, to your immunity, to your mental state. In essence, “someone’s microbiome composition affects their overall health,” Amy Burkhart, MD, RD, a physician and registered dietitian, tells SELF.

    That composition includes both beneficial bacteria that can exert a positive influence and harmful bacteria (or pathogens) that can do the opposite. If the balance is off (say, harmful bacteria outnumber beneficial bacteria), you might experience fatigue or poor sleep; feel stressed, depressed, or anxious; notice digestive issues like bloating, gas, heartburn, constipation, and diarrhea; or find yourself coming down with illnesses on a regular basis, to name a few possible signs and symptoms. This imbalance—clinically known as “dysbiosis”—has been linked to a wide range of serious health issues, including obesity, diabetes, heart disease, inflammatory bowel disease, irritable bowel syndrome, autoimmune disorders, and cancer.

    While your gut microbiome is largely determined in early childhood—the first two to three years of your life, to be precise—lifestyle factors such as diet also play a role. In fact, changing what we eat is actually the main step we can take “to make sure that we foster a healthy microbiome,” Desiree Nielsen, RD, a recipe developer with a focus on plant-based nutrition, tells SELF. Here are eight common nutrition habits that you might not know could be hurting rather than helping.

    1. Eating the same foods day in and day out.

    “Different bugs in the microbiome respond to different foods,” Dr. Burkhart says, so varying what you eat rather than sticking to the same thing is key to building a healthy ecosystem down there. Diversity within your diet will translate to diversity within the microbiome—and you want diversity above all else. “That means you see better digestion, better nutrient absorption, a better immune system,” Dr. Burkhart says. “It also helps resiliency, which is the ability of the gut microbiome to bounce back when somebody takes antibiotics”—which disrupt the microbiome by killing beneficial bacteria along with bad ones—“or recover when someone gets sick”—which can also alter microbiome composition and function. By the same token, she says, limited diversity is associated with a range of health conditions, including many of those we called out in the intro. (And before you ask, the diversity rule also applies to quote-unquote “healthy” foods! While it’s not harmful, per se, to eat roast chicken for dinner three nights a week, Dr. Burkhart says, it’s more optimal to change things up.)

    2. Chowing down on processed foods.

    This “is the most common problem I see,” Dr. Burkhart says. While the term “processed foods” is fairly broad, it often refers to foods that are modified to contain additives like emulsifiers, stabilizers, thickeners, and preservatives—“things that when you read the labels, you don’t know what they are.” Dr. Burkhart singles out two additives in particular: carboxymethyl cellulose (often found in candy, chewing gum, snacks, baked goods, and ketchup) and polysorbate-80 (often found in ice cream, canned foods, prepared foods, and salad dressings). While “there are other food additives that are lesser players,” she says, those are the “big ones that we know significantly alter the gut microbiome and increase inflammation”—a state that can induce harmful changes in the resident microorganisms and increase the risk of disease. Specifically, Dr. Burkhart explains, they “make the gut more permeable and harm the mucosal lining,” the protective layer of cells that coats the inside of the intestine, allowing pathogens in and potentially setting the stage for infection. To prevent these harmful changes, try to minimize your processed food intake. “Eat more whole grains, eat more real food, plants, fruits, vegetables, legumes, those types of things,” Dr. Burkhart says. (Which is not to say that you can or should never enjoy processed products, of course—just that they should be enjoyed sparingly rather than regularly.)

    3. Guzzling sugary beverages.

    “Consuming a lot of sugary foods or drinks decreases diversity, increases inflammation, and increases [gut barrier] permeability,” Dr. Burkhart says—none of which you want, as we’ve covered. Reduced diversity, for example, can manifest as a decline in one type of bacteria, Bacteroidetes, and an uptick in another, Proteobacteria—a pattern often associated with dysbiosis and resulting health conditions. Because of this, Dr. Burkhart recommends limiting stuff like sodas and sweet fruit juices and replacing them with water or another unsweetened beverage if you’re thirsty.

    4. Not eating enough fiber…

    By far the most substantial dietary change that you can make for your gut microbiome is eating more fiber, according to Nielsen. Consider it “almost like a medicine,” Dr. Burkhart says. Why? Well, a high fiber intake supports beneficial bacteria—the ones that help to “improve gut barrier function, communicate with the immune system, and keep chronic inflammation at bay”—since fiber is their primary food source, Nielsen explains. By contrast, she says, cutting out fiber boosts harmful bacteria that tend to cause inflammation—hence why adopting an animal product-based carnivore diet à la influencers like Steak and Butter Gal or the Liver King is “the worst thing you can do for your microbiome.” In fact, fiber is so critical that even though whole foods are always a better option, Dr. Burkhart often recommends fiber supplements to people struggling to reach their daily fiber goal. Getting 30 to 50 grams per day is “really, really important for gut health,” she says.

    5. …or drinking tons of prebiotic soda in lieu of eating high-fiber foods.

    Prebiotic soda refers to a class of sodas that contain the namesake fibers, which, like their brethren, feed the microbes in your gut and stimulate the growth of beneficial bacteria. Don’t get us wrong: “They’re amazing, and they offer a great boost, but they don’t function the same way as whole foods,” Nielsen says. Compared to prebiotic sodas, which often contain a specific prebiotic known as inulin but not much else, whole foods offer a much broader array of beneficial nutrients—including polyphenols. Found in plant foods like fruits and vegetables, these antioxidant and anti-inflammatory compounds may not be as well-known as fiber, but they play a big role in “driving the growth of a healthy microbiome, too,” Nielsen says. Fundamentally, this is a prime example of the importance of diversity: Sweet and tangy as those Poppis and Olipops may be, they’re pretty one-note. When it comes to your fiber fix, fruits and veggies are a way better bet.

    6. Steering clear of foods that cause digestive side effects.

    “There’s a lot of really bad advice out there that if certain foods—say, legumes, for example—cause a symptom, that means you’re intolerant to them and shouldn’t eat them for your gut health, when literally the opposite is true,” Nielsen says. It all comes down to the fiber content. Most Americans are severely deficient in fiber and would thus benefit from eating fiber-rich foods like legumes more often, but increasing your fiber intake all at once can initially cause the exact digestive issues it’s supposed to prevent—gas, bloating, diarrhea—since your body isn’t prepared for the higher load. So rather than signaling that you have an intolerance toward a specific food, these symptoms are actually “a sign that you need to double down and actually consume more of those things,” Nielsen says. But GI issues aren’t an inevitability: Starting slow with “consistent, small amounts” can help minimize your chances of tummy trouble.

    7. Going too hard on probiotic supplements…

    On the surface, taking a probiotic supplement—a pill, capsule, powder, or gummy packed with beneficial microbes, including bacteria and yeasts—might seem like a no-brainer strategy for boosting your gut microbiome. Per Nielsen, however, not all probiotics are equal in efficacy, and not all even target the same site (or health issue), so they won’t necessarily have the effects you think they will. In some cases, probiotics can even backfire, throwing off the delicate balance of microbes and causing digestive symptoms. If you still feel a probiotic supplement would be helpful regardless, Nielsen recommends first making sure the specific one you’re considering has evidence to back it up by checking out usprobioticguide.com, a free website that compiles probiotic research. “That’s like the number-one thing,” she says. Then, based on the information in the guide, make sure it’s right for your health concerns. If you want to treat gas and bloating, for example, don’t choose an option that addresses constipation.

    8. …and if so, treating probiotic supplements as a permanent solution.

    Okay: You’ve checked out the probiotic guide, decided that this path is right for you, and started a course. While you might feel like your work to improve your gut microbiome is done, however, “it’s really important that people don’t make a probiotic [supplement] their front line,” Nielsen says. In other words, don’t let it become a substitute for larger, more substantial modifications to your diet. Instead, Nielsen says, think of probiotic supplements as a “temporary stand-in.” Enticing as the concept of a magic bullet for your microbiome is, eating well is the best strategy for long-term healthy change—and nothing else can really compare.

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