Constant fatigue. That stubborn cluster of pimples on your forehead that won’t budge no matter how many patches you apply. The low mood that hits even when you’re supposed to be having fun with friends. At first, these might seem unrelated—or even unrelated to your health—but they could share one common factor: the state of your gut microbiome.
Quick refresher: the gut microbiome is a vast community of bacteria and other microorganisms living in your digestive system. “There are more living organisms inside us than the total number of our cells,” says Vincci Tsui, a Canadian dietitian and intuitive eating coach, highlighting just how massive this system is. Since it’s linked to the gut, it’s easy to think it only affects digestion. But when the balance is off—too few good bacteria and too many harmful ones—it can show up in surprising ways.
“The microbiome has been one of the hottest topics in nutrition and health research over the past decade, and we’re still just scratching the surface,” says Tsui. “But we already know its impact goes far beyond the gut.”
In fact, Dr. Robert Burk, professor of microbiology and immunology at Albert Einstein College of Medicine, says the microbiome practically acts like a separate organ. Constipation or diarrhea are clear signs something’s off—but there are sneakier symptoms, too. Here are the most common ones.
You might not realize some of these issues could be symptoms of dysbiosis—an imbalance in your gut.
Struggling with acne or other skin issues?
The gut–brain axis is well-known—it connects your gut and brain through a network of nerves—but there’s also a gut–skin axis. “Inflammation triggered by a compromised microbiome often shows up as skin problems,” says Tsui.
This can appear as acne, dandruff, atopic dermatitis, seborrheic dermatitis, psoriasis, eczema, rosacea, or hair loss.
Sometimes, the connection can be even more serious. For example, eczema flare-ups have been linked to a drop in beneficial Lactobacillus and Bifidobacterium strains.
Unexplained changes in your weight
Your gut microbiome seriously influences your metabolism.
“The microbiome affects feelings of fullness, when and how much we eat, and how efficiently we process nutrients,” says Dr. Alice Cheng, a gastroenterologist at the University of Chicago. “It also impacts how sugars, glucose, and fats are metabolized.”
This can lead to weight loss or gain, depending on how your body responds. These shifts can affect blood sugar, blood pressure, cholesterol, triglycerides, and even the risk of type 2 diabetes or heart disease.
Trouble sleeping?
“The gut microbiome plays a key role in regulating our circadian rhythm,” says Dr. Orlando “Landon” DeLeon, a researcher at the University of Chicago.
If the balance is off, our internal clock can get disrupted. Most of the serotonin in your body—which regulates mood and sleep—is produced in the gut, so dysbiosis can easily cause insomnia, restless sleep, or frequent nighttime awakenings.
Feeling tired all the time?
Chronic exhaustion—even when you’re getting enough sleep—can also signal gut issues. Tsui points to H. pylori infection as a possible cause; it damages the stomach lining and upper small intestine, reducing iron absorption. And iron is crucial for keeping your energy up.
Unexplained low mood?
The gut–brain axis is a prime example of how your mood can be affected.
“Because the gut is in constant communication with the brain, an imbalanced microbiome can lead to anxiety and depressive symptoms,” says Tsui.
Research has found links between generalized anxiety, major depression, and shifts in certain gut bacteria.
For example, depressed patients often have higher Eggerthella levels, while Faecalibacterium and Coprococcus bacteria decrease.
Struggling to concentrate?
It’s not just mood—cognitive functions can suffer too. Although direct research on brain fog and the microbiome is limited, Tsui notes many people report concentration issues when their gut is out of balance.
Frequently falling ill?
“The gut microbiome plays a key role in training the immune system,” says Dr. Burk.
Observations show that people who often catch infections usually have weaker microbiome health. If you get sick regularly—especially more than others—it’s a warning sign.
Cause and effect?
As microbiome research rapidly evolves, experts don’t always know exactly why things happen. Often, symptoms appear together, so clear cause-and-effect isn’t always established. For example, studies on certain patient groups—like those with depression—show their microbiomes differ from healthy controls.
One study found that over half of people with irritable bowel syndrome also struggled with chronic fatigue. Another showed rosacea patients had higher rates of SIBO, and treating it nearly eliminated their skin symptoms. Cause or consequence—the connection is undeniable.
