7 Clear Signs You Might Have an Unhealthy Gut

Updated: Aug. 02, 2023

You need the right balance of bacteria to maintain gut health—here’s how to know when your microbiome might be out of whack.

The mighty gut health benefits of bacteria

Your gastrointestinal, or GI, tract is inhabited by microbes collectively called the microbiome, which includes bacteria, fungi, and even viruses. Though it sounds gross and maybe even unhealthy, it’s actually the complete opposite. Gut bacteria perform many important functions in the body including aiding the immune system; producing the feel-good brain chemical serotonin; making energy available to the body from the food we eat; and disposing of foreign substances and toxins, according to Lisa Dreher, RDN, a registered dietitian at the UltraWellness Center in Lenox, Massachusetts. Though most of us have a mixture of good and bad bacteria, sometimes the bad guys get the upper hand, causing dysbiosis, or an imbalance in gut bacteria, which can play a role in a number of health conditions. So, how do you know when you have an imbalance? These clear signs point to a dysbiosis that has the potential to make you sick.

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Man clutching aching belly

Your stomach doesn’t feel right

Diarrhea, constipation, bloating, nausea and heartburn are classic symptoms of problems with gut health. “Gastrointestinal discomfort—especially after eating carbohydrate-rich meals—can be the result of poor digestion and absorption of carbohydrates,” Dreher says. Reflux, inflammatory bowel disease, irritable bowel syndrome, and colitis have all been linked to an imbalance in the microbiome. Here’s how to tell if your belly bloat is something serious.

chocolate cupcake
iStock/Vincent Shane Hansen

You have a hankering for certain foods

Craving foods, especially sweets and sugar, can mean you have an imbalance of gut bacteria. Although unproven, some experts believe that if there’s an overgrowth of yeast in the system, which might happen after a course or two of antibiotics where you wipe out all the good bacteria, then that overgrowth of yeast can actually cause you to crave more sugar.

The 6 Best Probiotic Foods for Your Gut (That Aren’t Yogurt)

woman on scale

The scale is going up or down

Certain types of gut bacteria can cause either weight loss or weight gain—especially when they colonize in the small intestine, a condition called SIBO (small intestine bacterial overgrowth). Too many microbes in the small intestines can mess with gut health by interfering with absorption of vitamins, minerals, and fat. “If you’re not able to digest and absorb fat normally, you can actually see some weight loss,” Dreher says. Other types of bacteria have been linked to weight gain, as certain microbes are able to harvest more calories from foods than others.

Exasperated man with his hands on his face

You’re anxious or feeling blue

Roughly 80 to 90%  of serotonin, a neurotransmitter that affects mood, social behavior, sleep, appetite, memory and even libido, is produced in the gut. When less serotonin is produced, it can negatively impact mood. “Gut imbalances of the microbiome can trigger depressive symptoms,” says Todd LePine, MD, a physician at the UltraWellness Center in Lenox, MA.

12 Silent Signs Your Microbiome Could Be in Trouble

Tired man unable to sleep

You’re not sleeping well

Not having enough serotonin can lead to bouts of insomnia or difficulty getting to sleep, according to Dreher. And Dr. LePine says chronic fatigue and symptoms of fibromyalgia can be tied to gut bacteria imbalances as well. Learn more about the 7 conditions you might be mistaking for fibromyalgia.

woman scratching her arm

Your skin is acting up

Skin rashes and eczema, a chronic condition characterized by inflamed and itchy red blotches on the skin, can be a sign of poor gut health because they develop when there is an imbalance in gut bacteria, according to Victoria Maizes, MD, executive director of the Arizona Center for Integrative Medicine and professor of medicine, family medicine and public health at the University of Arizona in Tucson, AZ.

older man talking to his doctor

You have an autoimmune condition

An imbalance in the microbiome can cause more than just GI symptoms. According to Dr. LePine, diseases affecting the immune system, known as autoimmune diseases, can also indicate an imbalance. “Rheumatoid arthritis and multiple sclerosis are tied in with imbalances in gut bacteria,” he says.

How a Healthy Gut Microbiome Could Add Years to Your Life

iStock/Ivan Bajic

How to build better gut health

Eating right is the first step in improving gut health. In fact, the types of foods we eat can change our microbiome in as little as 24 hours, according to Ali Keshavarzian, MD, professor of medicine and director of the Division of Digestive Diseases and Nutrition at Rush University Medical Center in Chicago, IL.

To feed your good bacteria and starve the less desirable bacteria, swap out processed foods, breads, and pastas for plants, fruits, seeds, and nuts. And consider adding fermented foods into your diet, including yogurt containing live, active cultures, kombucha, tepache, kimchi, and kefir, which naturally contain probiotics, or healthy bacteria. It’s also a great idea to fill up on prebiotic foods, which actually feed the good bacteria. Try leeks, asparagus, onions, garlic, chicory, oats, soybeans, and Jerusalem artichokes.

Lastly, avoid unnecessary use of antibiotics. “Any time you take an antibiotic, you’re going to knock out a lot of the healthy bacteria,” says Dr. Maizes. If you must take antibiotics, consider taking a probiotic supplement to help maintain a healthy and balanced bacterial community in your gut. Learn about 21 more health secrets your gut is trying to tell you.

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