5 Surprising Symptoms of an Unhealthy Gut
Health ConditionsDigestive Health

5 Surprising Symptoms of an Unhealthy Gut

Find out if your diet and lifestyle habits are helping or harming your gut microbiome, and what to do about it.
5 Surprising Symptoms of an Unhealthy Gut
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Updated on April 30, 2025
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Most people think of bloating, constipation, diarrhea, and abdominal pain as the main symptoms of an unhealthy gut. While gastrointestinal symptoms can certainly indicate a gut in disrepair, they aren’t the only ones to look out for.

Your gut is home to trillions of microorganisms, an ecosystem known as the gut microbiome that researchers believe may play a significant role in gut and overall health.

 “In many ways, we are just beginning to understand how the microbiome impacts our health,” says Michael Schopis, MD, a gastroenterologist in private practice in New York City.

More research is needed to know exactly how the gut microbiome connects to certain health conditions, but some symptoms may suggest a struggling microbiome and, in turn, suboptimal gut health, he adds. Here are five surprising symptoms that might indicate an unhealthy gut, and what to do about it.

Surprising Signs Your Gut Is Unhealthy — and What to Do About It

An unbalanced gut can throw off the health of your entire body, but the symptoms aren’t always obvious. Learn to recognize — and deal with — three especially sneaky signs.
Surprising Signs Your Gut Is Unhealthy — and What to Do About It

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1. Excessive Sugar Cravings

It’s no secret that sugar has addictive qualities. “Your sugar cravings might not be coming from you — they could be coming from your gut bugs,” says Alyssa Simpson RDN, a digestive health dietitian based in Phoenix, Arizona.

Since our bodies are composed of a number of organisms competing for nutritional resources, according to preliminary studies done on mice, cravings may be the result of an evolutionary conflict between the person and their own microbiota. In other words, gut microbes may manipulate our eating behaviors to benefit their survival.

If you have a particularly stubborn sweet tooth, the best way to discourage sugar-loving gut microbes from taking over is to progressively decrease your intake of added sugars.

For example, replace sugar-sweetened beverages with herbal teas and water infused with citrus fruit. Instead of reaching for a candy bar, opt for dark chocolate and nuts. If you typically add sugar to oatmeal, tea, or coffee, instead try adding cinnamon, a naturally sweet flavoring agent.

It’s also good to read nutrition labels and ingredient lists to minimize consumption of unnecessary added sugars hiding in foods you wouldn’t expect, like pasta sauces, nut butters, condiments, and breads. Over time, these seemingly small adjustments will help restore balance to your gut microbiome.

2. Food Intolerances

Food allergies are immune reactions to proteins in foods we eat, whereas food intolerances occur when you have difficulty digesting a certain food or component of food.

 

Food allergies may cause shortness of breath, swelling, itching, or hives. Food intolerances do not create allergic reactions, but instead lead to gastrointestinal symptoms like diarrhea, abdominal cramping, bloating, and gas. “When your gut isn’t functioning properly, it can reduce how much of certain enzymes you produce, like lactase for dairy or DAO [diamine oxidase] for histamine, so you end up reacting to things you used to tolerate,” says Simpson.

Unlike food allergies, those with food intolerances may be able to tolerate small quantities of a food they are intolerant to.

 Food intolerances may affect up to 20 percent of the population, and although they are not life threatening, they can be highly disruptive.

While there are different types of food intolerances and a number of reasons why one might develop, research suggests that many food intolerances may result from changes in the gut microbiome that may be corrected through dietary adjustments.

To identify food intolerances, it’s helpful to keep a food and symptom journal, to pinpoint the offending food. Once identified, eliminate that food from your diet for several weeks. If your symptoms dissipate, consider reintroducing the food in small quantities, slowly increasing portions as tolerated. Gradual reintroduction allows your gut bacteria to shift and adjust to become more adept at breaking down this food, potentially increasing your tolerance.

Working with a registered dietitian can be particularly helpful in guiding you through this process.

3. Unintentional Weight Gain

If you experience unintentional weight gain that cannot be attributed to a medical condition or lifestyle changes, your gut microbiome may be the culprit. Gut imbalances may lead to weight gain by a few potential mechanisms: changing how your body absorbs calories, increasing cravings, or creating low-grade inflammation that tells your body to hold on to fat, says Simpson.

According to one study, gut bacteria affect energy expenditure and the amount of calories a person extracts from food. After researchers assessed the gut microbiomes of over 500 participants, they found that as diversity of participants’ gut microbiomes decreased, body mass index (BMI) increased.

 
Another study demonstrated that researchers can predict who is living with obesity by analyzing the composition of a person’s gut microbiome.

 
A potential explanation for these findings is that some gut bacteria are more efficient at breaking down food than others, allowing us to absorb more calories from eating the same exact foods, as suggested by a review.

 Additionally, as outlined in research, certain gut bacteria promote inflammation, which contributes to insulin resistance, indirectly affecting weight.

 
The link between weight and the gut microbiome is so well established that new proposed strategies to treat and prevent obesity target the gut microbiome. While the research is promising, it is too preliminary to recommend specific protocols.

In the meantime, it’s best to stick to a diet high in plant fibers from fruits, vegetables, legumes, and whole grains, to promote a healthy gut microbiome. According to research, this type of dietary pattern is associated with reduced weight gain independent of calories consumed.

4. Moodiness, Anxiety, and Depression

It’s no wonder many phrases in our vernacular associate the gut with our emotions — if you’ve ever had “butterflies in your stomach,” a “gut feeling” about something, or felt “sick to your stomach,” you’re likely familiar with the gut-brain connection. In fact, the gut is often referred to as the second brain, and for good reason.

Gut microbes communicate with the nervous system, endocrine system, and immune system, influencing mood.

 

 “A disrupted microbiome can reduce the production of mood-regulating chemicals like serotonin and increase inflammation that impacts the brain,” says Simpson.
People diagnosed with anxiety and depression are thought to have abnormal intestinal function, and a handful of studies suggest that supplementation of prebiotics (fuel that supports probiotics, the good bacteria in your gut) and specific probiotic strains may improve symptoms. One meta-analysis found probiotic supplementation to be associated with reduced depressive symptoms. That said, the ability of a probiotic supplement to improve mood is likely dependent on the specific probiotic strains and formulation.

Short of specific probiotic supplementation, adopting a diet rich in whole, plant-based foods, such as the Mediterranean diet, may promote a gut microbiome conducive to optimal mental health. According to a review, this type of dietary pattern promotes gut microbial diversity and reduces gut inflammation, benefiting mental health. Increasing dietary omega-3 fatty acids from certain fish may also have a positive effect on gut microbiome composition, and reduce risk for depression.

5. Skin Irritation

If you have ever found certain foods to exacerbate skin issues, your gut bacteria may be part of the problem. Eating foods high in saturated fat and refined sugar promotes an unhealthy balance of gut bacteria, according to research.

 This state of dysbiosis (imbalance) is associated with abnormal immune function, contributing to inflammatory skin conditions like eczema, psoriasis, acne, rosacea, and dandruff.
The research also demonstrated that those with inflammatory skin conditions have different gut bacteria compared with those without these conditions. Those with rosacea also have a higher prevalence of gastrointestinal conditions, and an estimated 7 to 11 percent of people with inflammatory bowel disease (IBD) also have psoriasis, further validating the gut-skin connection.

 
To support skin health, following the same anti-inflammatory dietary guidance for optimal gut microbiome health is recommended. According to research, this means consuming a diet rich in whole plant foods and incorporating omega-3 fatty acid sources like fish while limiting processed and animal-derived foods.

The Takeaway

  • Early research suggests the gut microbiome plays a key role in many aspects of health, including digestion, mood, immunity, and more.
  • Excessive sugar cravings, food intolerances, unintentional weight gain, mood issues, and skin irritations could all indicate issues with your gut microbiome.
  • Eating a diet rich in fruits, vegetables, legumes, whole grains, and omega-3 fatty acids while limiting animal-derived and ultraprocessed foods is one way to help boost the health of your gut microbiome.


Additional reporting by Abby McCoy.

EDITORIAL SOURCES
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
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