Everyone seems to be trying to improve their gut health and nourish their gut microbiota, and for good reason. The intestinal microbiota, a community of bacteria and other microbes of the digestive system, influences everything from digestion to immune function and even brain health. A happy gut is characterized by a diverse microbiota, regular digestion, minimal bloating, and stable energy levels.
However, some foods marketed as “healthy” actively disrupt gut health. Hidden sugars, artificial additives and other harmful ingredients can damage the microbiota and impair digestion. In this article, we’ll explore ten seemingly healthy foods that may be sabotaging your gut health and share smarter alternatives to keep your microbiome happy and thriving. Read on, and to find out what to eat instead, check out the 10 Best Probiotic Supplements for Gut Health, According to a Registered Dietitian.
Yogurts high in sugar

Yogurt is often touted as a protein- and probiotic-rich food that supports gut health and immunity. Actually, some research shows that yogurt modulates the intestinal microbiota, the intestinal barrier and the immune cells of the intestine. However, many flavored yogurts contain added sugars. Research shows that eating too much sugar can reduce diversity of your intestinal microbiota and promote inflammation.
Instead of flavored yogurt, choose plain Greek yogurt and add fresh fruit for natural sweetness. If that’s not an option, consider mixing 50% flavored yogurt with 50% plain yogurt. This way, you’ll still get the benefits of yogurt but without as much sugar.
Artificially sweetened diet drinks


Diet sodas and other sugar-free drinks often contain artificial sweeteners like aspartame and sucralose. Some research has shown that these sweeteners can negatively affect your gut microbiota, reduce microbial diversity and potentially lead to problems with your metabolism.
If you like carbonated drinks, consider replacing diet soda with sparkling water with a little fruit juice for a gut-friendly fizz without artificial sweeteners.
High Sugar Kombucha


Kombucha is often praised for its probiotic content, but some brands load their drinks with sugar, which diminishes its gut benefits. Too much added sugar can nourish the bad bacteria into your gut, negating the potential benefits of this fermented tea. For reference, the Dietary Guidelines for Americans recommends limiting added sugars to less than 10% of their daily calorie intake. This equates to about 12 teaspoons of sugar per day. When possible, choose kombucha brands with less than five grams of sugar per serving, or consider making your own!
Pasteurized fermented foods


Fermented foods like sauerkraut, pickles, and kimchi are great for gut health, but pasteurization kills the live bacteria that makes them beneficial. Without live bacteria, these foods may not have the same positive effects on the balance of the intestinal microbiota. However, some studies show that even pasteurized fermented foods can contain microbial byproducts beneficial to human health, so choosing pasteurized fermented foods has some advantages.
Look for raw, unpasteurized versions of your favorite fermented foods in the refrigerated section of the grocery store. Bubbie’s Fine Foods And Flanagan Farm are two brands whose naturally fermented pickles and sauerkraut make a delicious and tangy addition to any meal.
Gluten-Free Packaged Foods


Although gluten-free diets can be helpful for sensitive people (and life-saving for people with celiac disease), many gluten-free products contain additives such as refined starches and emulsifiers. Test tube studies have shown that emulsifiers in processed foods can damage the intestinal lining and cause inflammation. Additionally, many gluten-free foods are low in fiber. Since fiber is fuel for our good gut microbes, foods low in fiber are not very beneficial for our gut.
Try choosing naturally gluten-free whole foods like quinoa, brown rice, and sweet potatoes. If you’re looking for a gluten-free packaged food, read the ingredient list and try to avoid those with added emulsifiers (like carrageenan).
Protein bars


Protein bars are often full of artificial flavors and sweeteners, sugar alcohols and gums that can disrupt digestion. Sugar alcohols like sorbitol can cause bloating, gas, and diarrhea in some people. Additionally, non-nutritive sweeteners like sucralose can modify the composition of the human intestinal microbiota.
To increase your protein intake, try including more eggs, yogurt, cottage cheese, edamame, roasted chickpeas, tofu, beans, and protein-rich grains (like quinoa and farro ) in your diet.
Dairy-Free Milk Alternatives


Although plant-based milk can be a great substitute for those sensitive to dairy, some contain carrageenan or other emulsifiers, which test tube studies have been linked to intestinal irritation and inflammation.
Look for non-dairy milks with minimal ingredients, such as 8 Non-Dairy Milks made with the highest quality ingredients.
Overly processed plant-based “meats”


Vegan meats may seem healthy, but many are highly processed and contain preservatives, fillers and sodium that can harm gut bacteria. Ultra-processed foods (UPF) are ready to eat from refined ingredients like high fructose corn syrup, hydrogenated oils, and broken down proteins. They often contain additives used to improve the taste of the final food product, such as flavorings, flavor enhancers, colors, emulsifiers and thickeners. For example, Beyond meat burgers contain a long list of ingredients, including refined oils, methylcellulose, potato starch and salt.
What’s the deal with UPF and gut health? Well there is growing evidence that UPFs are linked to an increased incidence of intestinal diseases such as inflammatory bowel disease, colorectal cancer and irritable bowel syndrome (IBS). Additionally, animal and test-tube studies show that additives such as emulsifiers and sweeteners can alter the gut microbiota, increase leaky gut, and cause inflammation.
Instead of choosing plant-based processed meats, choose homemade plant-based meals made with lentils, chickpeas, black beans, or tofu instead of store-bought vegan hamburger patties.
Flavored Instant Oatmeal Packets


Instant oatmeal packets may seem like a healthy breakfast, but many contain added sugars and artificial ingredients that can disrupt gut health. Instant oatmeal also contains more refined oats than regular oatmeal, which can cause blood sugar spikes.
Choose plain oats (such as These from Bob’s Red Mill) and flavor them with cinnamon, berries and a drizzle of honey or maple syrup for a healthier alternative.
Fruit Juice With Added Sugar


Juices may seem like a simple way to increase your fruit and vegetable intake, but they often contain added sugars that can harm gut health. Additionally, even fruit juices made without added sugar are often high in fructose, a type of simple sugar found in many fruits. Although a certain amount of fructose is not a problem, our bodies have difficulty absorbing it when there is too much, which can lead to unpleasant symptoms such as gas, bloating, and diarrhea, especially in people with irritable bowel syndrome (IBS).
Instead of juice, make your own smoothies at home using whole fruits, leafy greens and unsweetened yogurt.
Final Thoughts
Supporting your gut health doesn’t mean cutting out every food on this list—it’s more about making smarter choices and striving for balance. Choose whole, minimally processed foods whenever possible and take the time to read labels and ingredient lists to spot additives or hidden sugars.
You don’t need to completely restrict these “healthy” foods, but you can keep your gut microbiota thriving by prioritizing a diet rich in whole, gut-friendly foods.
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