9 Surprising Signs of an Unhealthy Gut (and What to Do About It)

Constipation, diarrhea, or bloating are the most obvious signs of bad gut health. But they’re not the only ones. Signs of an unhealthy gut can appear in many ways throughout your body. 

So, the first step to a healthy digestive tract is understanding how your gut affects your overall health. From there, you can better understand what your gut may be telling you — and what you can do about it. 

What is the gut microbiome?

Your gut microbiome refers to the trillions of bacteria and other microorganisms that live in your digestive tract. These microorganisms can be helpful or harmful. A healthy microbiome has the right balance of good bacteria, which help keep the bad bacteria in check.

What is gut dysbiosis? 

When the gut contains too many harmful bacteria and not enough helpful bacteria, it’s called dysbiosis. Dysbiosis is a main cause of an unhealthy gut. It can cause symptoms in the digestive tract and beyond.

How does the gut microbiome affect our health?

Your gut microbiome is connected to many different parts of your body. When there’s an imbalance of gut bacteria, it can cause inflammation in the intestine and throughout the rest of the body.

Researchers are still trying to understand exactly how this imbalance creates disease in other parts of the body. But the imbalance or overgrowth of certain bacteria in the gut has been linked to conditions such as:

• Irritable bowel syndrome (IBS) 

• Inflammatory bowel disease (IBD)

• Cardiovascular disease

• Type 2 diabetes

• Depression

• Weight gain 

• Some types of cancer

Signs of an unhealthy gut

Signs of an unhealthy gut aren’t always obvious — and they go beyond the digestive tract.

1. Poor digestion

This can include an upset stomach, gas, and/or bloating. You may also experience heartburn or acid reflux. Each of these symptoms can be a sign that your gut is having difficulty digesting food and/or eliminating waste.

2. Changes in bowel habits 

Digestive symptoms — like constipation, diarrhea, or IBS — can be easy to overlook, especially when you don’t always have “regular” bowel movements. The frequency of bowel movements varies from person to person. But stools should generally be easy to pass and soft but formed.

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• Natural ways to improve gut health: Yes, dietary changes matter. But reducing stress and sticking to exercise habits also help keep the gut microbiome happy.

3. Skin issues 

Imbalanced bacteria on the skin and/or in the gut may cause your immune system to react. This can potentially trigger skin conditions such as eczema, psoriasis, and rosacea.

4. Food allergies and/or sensitivities

A disruption of the gut’s bacteria balance can lead to food sensitivities. It can also cause food to be improperly digested. This can cause an immune reaction that can contribute to the development of food allergies. 

5. Autoimmune disorders

The health of your gut microbiome is linked to the risk of developing autoimmune disorders like Hashimoto’s thyroiditis, multiple sclerosis, or psoriasis. This is because of the role the gut plays in your body’s immune function. 

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Your gut microbes help teach your immune cells how to recognize foreign invaders. These gut microbes can also influence the way that your body activates different parts of your immune system. If this process goes wrong, autoimmune disorders can develop. 

6. Getting sick often

Dysbiosis — too much harmful bacteria in your gut — can lead to a weakened immune system. Because of this, you may get sick more frequently with things like the common cold or flu. It might also affect the severity of your symptoms when you get sick — like with COVID-19.

7. Unexplained weight changes

An imbalanced gut microbiome can cause your body to struggle to absorb nutrients, regulate blood sugar, and/or store and utilize fat. As a result, you might gain or lose weight. 

8. Sleep and mood issues 

About 95% of your body’s serotonin — a brain chemical that influences your mood and sleep – is produced in your gut. So, an unhealthy gut can affect mood and sleep. And the relationship goes both ways. Early research suggests that dysbiosis can contribute to sleep problems and depression. And depression and sleep problems can also contribute to dysbiosis. 

9. Food cravings

An unhealthy gut microbiome may contribute to food cravings and even binge eating. Scientists think this is related to the way that your gut bacteria influences the hormones leptin and ghrelin. These hormones affect hunger and fullness cues. 

How to improve gut health: Essential dos and don’ts

There are many things you can do to help improve poor gut health. Both lifestyle factors and eating habits can play an important role. 

Do eat a balanced diet

Try to eat a nutritious diet full of a variety of whole, minimally processed foods. Some specific food categories to include are:

• Fermented foods and fermented beverages: Foods like kimchi, kombucha, and sauerkraut are a natural source of probiotics that are excellent for gut health.

• Foods high in fiber: Dietary fiber gets fermented in your intestinal tract, which helps create a nice environment for the good bacteria that supports your microbiome. Fruits, vegetables, beans, and nuts are examples of high-fiber foods. Many foods high in fiber — like asparagus, bananas, and onions — contain prebiotics. Prebiotics have lots of health benefits, including acting as “fuel” for probiotics to help them do their job effectively. 

• Anti-inflammatory foods: Since dysbiosis can cause inflammation, eating foods that lower inflammation can help your gut health. Examples of anti-inflammatory foods are salmon, berries, and olive oil.

Do cut back on ultra-processed foods

The Western diet often contains lots of highly processed foods. And these foods are closely linked to changes in your gut microbiota. These changes can lead to the development of chronic conditions like diabetes and heart disease. 

Do manage your stress levels

Stress can be harmful to your gut. It can affect your gut motility, which refers to how quickly food moves through your digestive tract. It can also cause inflammation in your intestinal lining. This can lead to issues, such as:

• Abdominal pain

• Diarrhea

• Nutrient malabsorption

• Ulcers

Managing stress isn’t easy to do. And it isn’t always in your full control. But try these when you can:

• Ask for help.

• Remove yourself from known triggers.

• Spend time doing things you love.

Do prioritize sleep

Getting enough sleep can improve your stress levels. It also can improve your gut health by supporting a balanced microbiome.

Do stay hydrated

The amount of water you drink can help balance your gut microbiome. Not drinking enough water can also lead to constipation. 

Do exercise

Studies suggest that exercise increases the amount of good bacteria in your gut. To help get enough exercise, find a movement practice that works for your body and lifestyle. 

Don’t eat too much added sugar

Sugar can alter the gut microbiome and contribute to inflammation. Even if you don’t often eat desserts, you could be getting excess sugar from other places, like snack foods, cereals, and condiments. 

Don’t drink a lot of alcohol

Alcohol can increase the number of harmful bacteria in your gut. This can lead to many types of disease. 

Don’t overuse antibiotics

Antibiotics work by killing the bad bacteria that cause bacterial illness. But they also kill the good bacteria along with it. So take antibiotics only when necessary and as instructed by a healthcare professional. If you do take antibiotics, consider taking probiotics alongside them to help reduce possible side effects.

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Written by:

Joanna Foley, RD

Joanna Foley, RD, is a registered dietitian (RD) and the owner of joannafoleynutrition.com, a private nutrition consulting business. She has previously worked as a clinical dietitian and outpatient renal dietitian.

Edited by:

Meredith Hoffa

Meredith Hoffa is a senior health editor at GoodRx, where she leads journalists and clinicians covering various well-being topics, particularly in diet and nutrition.

Reviewed by:

Mandy Armitage, MD

Mandy Armitage, MD, has combined clinical medicine with her passion for education and content development for many years. She served as medical director for the health technology companies HealthLoop (now Get Well) and Doximity.

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