A gut with warning signs surrounding it | Signs of poor gut health

These Are the Hidden Signs of Poor Gut Health, According to MDs

Leaving these symptoms unchecked can harm your health in the long run.


loating, stomach cramps, and constipation are just some of the no-brainer ways an unhealthy gut rears its ugly head. But other signs of poor gut health can manifest outside of your digestive system, making them harder to tie back to the source. 

Many of your body’s systems—like your immune system and nervous system—have a bidirectional relationship with the gut, meaning that the health of both systems can influence the health of the other.

“Your gut health can dramatically influence your overall physical health,” warns regenerative medicine doctor Daniel Monti, M.D. A healthy gut contributes to proper digestion, nutrient absorption, immune function, and even mental well-being.

Your gut health plays a crucial role in the functioning of your immune system, your nervous system, your cardiovascular system, and your endocrine system, he explains. The health of your gut microbiome—the delicate balance of bacteria, fungi, and microorganisms that live in your digestive tract—plays a major role. Left unchecked, poor gut health can put your longevity at risk by upping your chances of developing dementia, diabetes, obesity, and cancer, per Monti. 

These are the stealth signs that your gut is in need of a tune up that you’ve probably missed, according to two longevity experts.

About the Experts:

Dr. Daniel A. Monti, M.D., is an internationally-recognized expert in regenerative medicine and natural lifestyle therapies. He is the founding chair of the department of Integrative Medicine & Nutritional Sciences at Thomas Jefferson University, where he also is CEO & Medical Director of the Marcus Institute of Integrative Health.

Dr. Menka Gupta, M.D., is a functional medicine physician with over 20 years of experience.

Sneaky Signs of Poor Gut Health

You’re feeling depressed

Ever felt butterflies in your stomach? Or felt the urge to go before a big interview? That’s your gut-brain axis at work. The gut-brain axis is made up of the enteric nervous system (ENS), which “consists of a vast network of neurons in the gut and communicates with the brain through the vagus nerve,” according to Gupta. An unbalanced gut microbiome can cause chronic inflammation and trigger a stress response via the vagus nerve—leading to depression, anxiety, and brain fog (1). 

You’d think that neurotransmitters mostly hang out in your brain—but GABA, dopamine, and serotonin are mainly produced in the gut. When your gut microbiome is imbalanced—making it harder to absorb nutrients—your body has a tough time producing these mood-boosting neurotransmitters. The potential result: conditions like anxiety and depression, says Gupta.

You’re having trouble sleeping

Running to the bathroom at 3 a.m. isn’t the only way an unhealthy gut can rob you of a good night’s sleep. 

According to Monti, sleep disturbances and chronic fatigue are common symptoms of an unbalanced gut—once again thanks to the gut-brain axis. In fact, a 2022 study found that certain microbiome imbalances were linked to physical and mental fatigue in young, physically active people (2). 

On top of regulating mood and digestion, serotonin also plays a role in regulating sleep—which is why experts suspect this gut-inhabiting neurotransmitter could cause gut-related sleep issues. 

You’re breaking out

Foods high in saturated fat and processed sugars can throw off your gut microbiome, which messes with you another bidirectional communication pathway: the gut-skin axis (3). “Poor gut health is often the root cause of skin conditions like eczema, acne, and psoriasis,” says Gupta. 

When your gut microbiome is out of whack, it can trigger an inflammatory response in the skin. Research shows that skin conditions like psoriasis, rosacea, and eczema are especially sensitive to changes in your gut microbiota and the inflammation flare-ups that follow (4).

You’re gaining weight

Inflammation from an unbalanced microbiome can make it harder to manage your weight, according to Gupta. Research has linked chronic inflammation to increased risk of metabolic disease and obesity (5).

Imbalances in gut bacteria can also contribute to insulin resistance—a condition in which makes it difficult for you to absorb glucose—which is associated with weight gain and increased fat storage (6).

You get sick frequently

If flu season hits you harder than most—or you struggle with chronic illness—it could be a sign that your gut is at odds with your immune system.

“Our gut bacteria hosts a significant portion of our immune system,” says Gupta. “An imbalanced gut microbiome can trigger unhealthy immune responses and inflammation across the whole body.”

Your gut microbiome helps your body create antimicrobial peptides, which are small proteins that help defend against harmful microorganisms (7). These peptides act as a local defense system to help fight infections from conditions like the common cold and the flu and inflammation from chronic bowel diseases alike. 

How Do I Know If My Gut is Causing My Symptoms?

“I usually conduct a comprehensive gut microbiome test. This gives a very accurate picture of the gut microbiome and their gut health including leaky gut,” says Gupta. “If the test reveals a gut dysfunction, we work on improving gut health to treat those symptoms.”

You can get tested at a GI office or order an at-home test like the GI Map test, which Gupta recommends and offers through her practice, Nutranourish. These gut microbiome tests look at the different bacteria and pathogens present in your gut and identify which may be causing inflammation or digestive issues.

After identifying what’s throwing you off, your doctor might suggest these lifestyle changes to heal your gut: