A healthy gut is the cornerstone of a healthy body: when your gut microbiome is balanced and diverse, almost every other system in your body benefits. Similarly, an unbalanced gut can wreak havoc on everything from your metabolism to your mood. What you eat plays a huge role in the health of your gut. Supporting your gut with good bacteria from certain foods and taking a probiotic supplement is essential. A damaged gut can lead to all sorts of digestive health issues including irritable bowel syndrome (IBS), SIBO, Crohn's Disease, irregularity, stomach pain, bloating, and more. One of the best ways to support your gut health is to eat well. Here are 13 foods with the highest potential to damage or disrupt your gut microbiome—and therefore avoid—followed by some foods you can eat to support a better gut health diet.

13 Foods to Avoid in a Gut Health Diet


Refined white sugar may have a particularly bad reputation, but it turns out that sugar in any of its forms is potentially harmful to your gut health. Participants in a study of sugar's effects on digestion reported increased constipation and poorer overall gut function while on a high-sugar diet. (1) Read our post on how to stop sugar cravings if saying no to sugar is a particular challenge for you.

Processed Foods

Most of us know that processed foods aren't exactly healthy, but the effects that they can have on your digestive system balance might surprise you. A recent study conducted on mice revealed that the emulsifiers used in heavily-processed foods disturbed their gut microbiota so much that many developed colitis and metabolic diseases. (2)


While sugar and processed foods are generally regarded as unhealthy, soy is often thought of as nutritious and beneficial. However, the high levels of processing that much of today's soy goes through have changed how it affects the body. In fact, high levels of soy in your diet can have damaging effects on your gut microbiome as the ingredient has been shown to reduce key Bifidobacteria and Lactobacillus populations, two strains that are crucial for a balanced gut. (3)


Even if you aren't lactose intolerant, dairy may not be the best choice for your stomach. Studies have shown that dairy consumption changes the bacterial makeup of your gut within days, allowing strains linked to intestinal disease and inflammation to flourish. (4)

Red Meat

Like dairy, eating red meat can encourage the growth of certain bacterial strains that can negatively impact your health, from your weight to your immune function to your emotional state. The same study that found dairy to be problematic showed that red meat had the same ill effects on study participants’ gut microbiomes.


Gluten—a protein found in a number of grains such as wheat and barley—has gotten a bad rap in recent years, and it turns out this reputation is unfortunately well-earned. While those with Celiac disease are particularly susceptible to its effects, studies have found that gluten can lead to stomach pain, bloating, and fatigue even in those without the disease. (5) Research has also indicated that going gluten-free lowers insulin resistance, inflammation, and weight gain/obesity. (6)


While concerns about eggs raising bad cholesterol levels may have been debunked, new research indicates that eating eggs may lead to heart disease in a different way. Cleveland Clinic researchers found that a certain protein in eggs encourages the growth of gut bacteria that produce a chemical compound that causes clotting and thus raises the risk of heart attack and stroke. (7)

Genetically-Modified Organisms (GMOs)

In an effort to cultivate crops that are naturally resistant to pests and disease, scientists have created what is known as genetically-modified organisms (or GMOs); wheat, soybeans, and corn are the three most common GMOs in the United States. Unfortunately, the traits that help GMOs resist disease can have terrible effects on gut health: studies have found that consumption of GMO foods can reduce the beneficial bacteria populations in the gut. (8)


The reason that corn can be so detrimental to your gut health is simple: almost 90% of all corn grown in the United States is genetically modified. (9) The prevalence of corn in the American diet—and the general fuzziness surrounding what is and isn't genetically modified—suggests that avoiding corn altogether might be the best choice for your gut health.

Farmed Fish

While the taste and availability of farmed fish and wild fish differ greatly, one major distinction between the two explains why farmed fish can be bad for your gut: the use of antibiotics in aquaculture. Huge amounts of antibiotics are included in the food that farmed fish are fed, and evidence suggests that these antibiotics can be passed along when these fish are eaten. (10) Of course, any antibiotic kills the healthy bacteria in your gut along with the bad bacteria, leading to an unhealthy balance of key strains.


Plants in the nightshade family such as tomatoes, eggplant, potatoes, and bell peppers are generally thought to be an important part of a healthy diet, but one key ingredient in all of these foods has the potential to cause serious gut issues. Naturally-occurring glycoalkaloids found in all nightshades have been shown to lead to intestinal inflammation and the condition known as "leaky gut" in mice, raising concerns about their effects on the human digestive tract. (11)

Tap Water

Staying hydrated by drinking enough water is obviously necessary, but you should be careful about the source of the water you drink. The water that comes from your tap is treated with a host of chemicals including chlorine, and research has found that chlorinated water can alter gut microbiota and even lead to the development of colorectal cancer. (12) Filtered water is the best option.

Artificial Sweeteners

Many people trying to lose weight turn to artificial sweeteners; after all, what could be bad about these zero-calorie treats? Quite a lot, as it turns out. Research increasingly points to a host of negative gut effects caused by artificial sweeteners, including changes to the gut microbial composition, increased glucose intolerance and higher rates of metabolic disease. (13)

Good Foods for a Gut Health Diet

After reading that list, you might feel a bit overwhelmed. Of course, avoiding all of these ingredients all the time is practically impossible, particularly if you enjoy a good pizza or bowl of ice cream every now and then. However, taking steps to reduce your intake of these foods and adding in a daily probiotic supplement to help preserve your beneficial gut bacteria can go a long way towards a healthier gut. To help you transition to a more gut-healthy diet here are some foods you can consume more of as you begin to decrease your intake of those mentioned above.

Fiber-Rich Foods

Keep in mind, the good bacteria in your gut are living organisms. That means like any other living organism, they need food to survive and thrive. High-fiber foods are great for your gut health because they provide this sustenance for the probiotic bacteria in the form of prebiotic fiber. Read our post on prebiotics and why they are important to learn more.

Foods With Inulin

Inulin is a prebiotic fiber, meaning it feeds your good bacteria, promoting healthy gut flora. Because inulin cannot be broken down in your small intestines, it is able to make its way your lower GI tract where your gut lives. Foods with inulin include:
  • Asparagus
  • Chicory root
  • Garlic
  • Jerusalem artichoke
  • Jicama
  • Onions
  • Yacon root
While these inulin-rich foods all provide prebiotic fuel for your gut bacteria, they also offer a number of other health benefits including constipation relief, weight loss, and balance blood sugar levels (helpful in managing Diabetes). (14)

Fermented Foods

Fermented foods including sauerkraut, kimchi—a Korean version of sauerkraut, kombucha, tempeh, and miso are beneficial for the gut because they have probiotics from the fermentation process. Regarding miso, you want to choose unpasteurized since the pasteurization process kills much of the naturally-occurring probiotic bacteria. Heating it has the same effect so be careful there as well. If fermented foods are new to you, here are 8 Fast and Easy Probiotic Meals for Your Family full of flavor and health benefits.

Organic Foods

Organic foods are aligned with optimal gut health because they are free of pesticides, herbicides, antibiotics, and hormones all which can be disruptive to your gut flora balance and harmful to your overall health.

Add a Probiotic Supplement to Your Diet for Extra Support

If you are guilty of eating many of the "no" foods mentioned in this post as part of your everyday diet, gradually beginning to remove these foods for more healthy options is the first step to fostering a healthy microbiome and thus improving your overall health. In conjunction with taking a high-quality probiotic supplement, these changes will help to repopulate your healthy gut bacteria. You also want to be sure the probiotic you choose as an effective delivery system. Standard capsules are not designed to withstand the harsh acidic environment of the stomach, meaning most of the most of the live organisms are killed off before they can reach your gastrointestinal tract (where your microbiome lives). Our probiotic supplements are different! We use a patented time-release coating called BIO-tract®, scientifically proven to give our pills 15x more survivability than standard veggie capsules and powders. In other words, 15x as many of our CFUs make it past your stomach acid barrier and deep into your GI tract. Probiotics also help to protect and nurture the health of your whole family right from the moment of birth. They support the pre and post-natal health of pregnant moms and the healthy development of infants and children. The overall health benefits of adding a probiotic supplement to your daily diet are vast including increased metabolism (linked to weight loss), immune system support, increased nutrient absorption, better brain health, anti-inflammatory effects, and more.
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