Signs Your Gut Is Unhealthy and How to Restore It

Gut health is more than just a wellness buzzword — it’s a cornerstone of your overall health. From digestion to mental clarity, the trillions of microbes living in your gut, collectively known as the gut microbiome, influence countless processes throughout your body. Whether you’re dealing with being bloated, low energy or skin health, your gut might be trying to send you a message.

Composed of bacteria, viruses and fungi, the gut microbiome primarily resides in the large intestine and acts as a silent powerhouse. According to Cleveland Clinic microbiome expert Gail Cresci, these microbes help break down food, regulate inflammation, support immunity and even produce essential compounds like vitamins and hormones. If your gut is out of balance, the effects can ripple throughout your body, which is why recognizing the early signs of an unhealthy microbiome is so important.

Read more: Best Healthy Meal Delivery Services of 2025

Think of your gut microbiome as “little pets living inside your intestinal tract,” Cresci told CNET in 2023. What we eat feeds them, and our internal environment dictates how well they thrive.

As data on the gut microbiome becomes clearer, there are a few basic tips you can follow to keep it as healthy as you can.

Read more: 12 Probiotic Foods That Can Improve Your Gut Health

Signs of an unhealthy gut 

“If you’re bloated or you have lots of gas, you may have a disrupted composition and function of the gut microbiome,” Cresci said, adding that the only way to know for sure is to have it measured.

Other signs of an unhealthy gut may include vomiting or stomach upset, fatigue, trouble sleeping, food intolerance and other symptoms. Skin irritation or problems may be one particularly visible sign, as some research links skin issues like acne and psoriasis to the gut. 

Researchers are also looking into how it impacts reproductive health and hormone levels. 

Read more: The ABCs of Apple Cider Vinegar: Benefits, Precautions and Proper Dosage

How to help your gut 

It’s important to see a doctor to get to the root cause of your health concern and rule out other conditions. Making changes to your diet or routine that may improve your gut, and your overall health is a good first step. 

It’s also important to keep in mind that there’s no exact standard for the perfectly healthy gut microbiome, Cresci said, since everyone’s composition is so different. Bearing that in mind, here are four things you can do to help keep it on the right track. 

1. Eat these gut-friendly foods

The gut microbiome prefers foods we can’t digest. This includes foods with a lot of fiber, such as fresh fruits, vegetables, whole grains, legumes, seeds and nuts; foods we already know we should eat for their nutritional properties.

According to Cresci, foods to remove from your gut, or eat in lower amounts, include foods high in sugar and fat and low in fiber.

“These are all associated with the consumption of a Western diet, which is also associated with a disrupted microbiome,” she said. 

Beyond a gut-healthy diet, which not-so-coincidentally coincides with a heart-healthy diet, eating fermented foods can help replace the good microbes and their metabolites. Cresci lists yogurt, kombucha and kefir as examples. 

Here’s our full list of the best probiotic foods for gut health. 

2. Make note of the medications you’re taking

It’s a well-known fact that taking antibiotics disrupts, at least temporarily, the family of “good” bacteria thriving in your body. Some common side effects of taking antibiotics include nausea, diarrhea and developing yeast infections. If you’re prescribed an antibiotic or have recurring infections that have you taking antibiotics often, ask your doctor about what you can do to help minimize the disruption to your microbiome.

Other medications that can disrupt our microbiomes, Cresci says, include those that alter the PH of the stomach and take away acid. Examples include proton pump inhibitors, aka PPIs, and histamine H2-receptor antagonists, or H2 blockers, which are used to reduce acid reflux symptoms and might be available over the counter. 

By keeping track of the medications you’re taking, you can help pinpoint the cause of your symptoms and (with sign-off from your doctor) take the appropriate steps or substitutions if gut health is an issue.

3. Find the right probiotics or supplements 

In addition to incorporating more yogurt or fermented foods into their diet, some people may seek a probiotic in hopes of balancing their gut, as they’re designed to mimic an intact microbiota. If you’re considering taking a supplement, including probiotics, Cresci told CNET it’s important to know that probiotics are strain-specific, and “each strain has their own method of action.” 

For example, some probiotics are designed to help people with antibiotic-induced diarrhea, but that won’t work for a person taking it for bowel regularity. 

“You want to take the one that has been studied for whatever it is your problem is,” she said. 

Also, unfortunately, keep in mind that probiotics will not completely override what you eat. 

“If you have a bad diet, and you want to keep eating a bad diet but want to improve your microbiome, a probiotic isn’t gonna help you,” Cresci said. “You have to do the other part too.” 

4. Move your body every day and prioritize sleep 

“Get better sleep” or “exercise more” might sound like tired advice, but improving your sleep hygiene and squeezing in more physical activity are tried and true ways to improve your health, including your gut health. 

Exercise may help your gut in different ways, including by improving your circulation, helping your metabolism and aiding your digestive muscles, according to information from the Cleveland Clinic. If you dread running or don’t have time to go to the gym, don’t worry: There are small ways you can get your body in the habit of moving every day or at least more frequently. 

Getting good sleep is another general piece of wellness advice tied directly to the health of our guts. According to Cresci, our microbiome adheres to the circadian rhythm too. So if we’re eating when our gut microbiome isn’t ready, we won’t be set up to properly process the nutrients of our food. 

Lacking sleep also triggers an increase in stress and cortisol, which have negative mental and physical impacts. 

“There’s a lot going on with the gut-brain interaction, so that signals back to the microbiome, and vice versa,” Cresci said. 

Perhaps most fundamental is the fact that when we’re exhausted, we don’t have the energy to check off many of the things that keep us healthy, including exercising or finding a nutritious meal — both of which impact our gut health. 

“When you’re sleepy, tired, exhausted, you tend not to do the things we know are good for microbiomes,” Cresci said. “So it kind of perpetuates itself.”