10 Warning Signs of an Unhealthy Gut

Do you often feel bloated or gassy? Do you have trouble digesting certain foods? These are just a few of the signs of poor gut health. And while digestive symptoms may seem obvious, there are several other hidden symptoms that should set off alarm bells for gut issues—if you know how to recognize them. Poor gut health is a risk factor for serious health problems, including inflammatory bowel disease, hormone imbalances, and even autoimmune conditions. Let’s find out what you should be on the lookout for to spot an unhealthy gut, and then go over the basic tips you need to maintain or improve gut health.

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Why gut health matters

Your gut is the ultimate ground zero for your health, and much of that depends on a healthy gut microbiome. Gut bacteria help us make nutrients and neurotransmitters, process hormones & toxins, and neutralize harmful pathogens—so it’s crucial to take care of your gut in order to feel well.

We know now that the nervous system that resides in the GI tract connects to almost every other system in the body, and these connections rely on a healthy microbiome to do their job. The microbial balance–or the ratio of good and bad bacteria—in your digestive system is crucial for the health of your whole body, including about 70% of your immune system, and nearly all of the feel-good neurotransmitters like serotonin.

When your gut is out of whack, it usually means there’s inflammation going on, or an imbalance between the good and bad bacteria in your microbiome.

Related: Hormone Problems That Start in Your Gut

Do you have gut issues?

Symptoms of gut problems can be easy to spot (like gas, bloating, or irregular bowel movements), but sometimes poor gut health manifests in other ways. Things that you may not immediately link back to your gut—like fatigue and skin issues—are also big red flags for trouble in your gut microbiome.

Here are some signs that your gut needs some extra support:

1. Gas, bloating, or excessive burping

When you eat food, the bacteria in your gut break down the food and release gas in a process called fermentation. But if this gas is excessive, or accompanied by stomach pain, it could be a sign of a bacterial imbalance, or dysbiosis, in your microbiome. Fermentation usually happens in the large intestine, where the majority of the body’s good bacteria reside. But if you have an overgrowth of gut microbes in other places in your digestive tract, bacteria could be fermenting foods too rapidly which produces a lot of excess gas.

SIBO, or small intestinal bacterial overgrowth, is a type of imbalance caused by having too much or the wrong type of bacteria present in the different parts of your digestive system. If you’re producing more gas than usual, it could mean that your gut isn’t breaking down food as efficiently as it should.

Read more: How to Get Rid of Bloating Fast, Tips from an Integrative MD

2. Frequent heartburn or reflux

Heartburn occurs when stomach contents backs up into your esophagus. Contrary to popular belief, the root cause of most cases of heartburn is actually not too much stomach acid, but too little (1). Low stomach acid may be a sign of an underlying condition, including H. pylori infection or vitamin deficiency.

Inflammation in your gut can cause chronic irritation, or gastritis, that can also damage the cells in your stomach to cause them to stop producing acid as well as they should.

3. Diarrhea or constipation

It probably comes as no surprise that having an unhealthy gut often leads to digestive issues, like constipation, diarrhea, or just irregular bowel movements. But what most people may not know is what constitutes an irregular bowel movement.

If you’re having fewer than three bowel movements per week, or 3 or more per day, this may be a sign that your gut is not functioning properly. Poor gut health can lead to chronic dehydration, which leads to constipation. On the other hand, an imbalance of bacteria in the small intestine can cause loose stools and excess gas. The bottom line is that trips to the bathroom should be regular, comfortable, and consistent.

4. Mood swings

Poor gut health can increase the risk of mood disorders like anxiety and depression (2).  The gut-brain connection between the central nervous system (your brain) and enteric nervous system (your gut) plays an important role in regulating mood and emotions. When this connection is disturbed by inflammation or a bad bacteria in the gut, it can lead to symptoms that affect behavior and mood. 

Additionally, if your gut isn’t absorbing nutrients properly, mood issues may be due to vitamin and mineral deficiencies.

Related: Eating This for Breakfast Can Trigger Anxiety

5. Unexplained fatigue

An unhealthy gut can cause trouble sleeping, which leads to fatigue. The majority of your body’s serotonin, which affects mood and sleep, is produced in the gut. So if your gut isn’t able to produce adequate serotonin, you may not be sleeping well.

Bad bacteria can also disrupt the production and absorption of vital nutrients necessary for energy production. Studies find that nearly half of people with IBS also struggle with fatigue or exhaustion (3). 

6. You’re sick all the time

About 75% of the immune system resides in the gut, so when it’s not functionally optimally it can put you at risk for getting sick, with longer recovery times. Immune cells in the gut make antibodies that fight infection and send signals to mobilize other immune cells if necessary. An imbalance of bacteria can weaken your immune system and make you vulnerable to infections. 

Feeling like you catch every cold or flu that comes around, or taking weeks to get better when you’re sick is a sign that your immune system needs extra attention. The best place to start to improve immune health is within your gut.

7. Skin issues

An unhealthy gut has been linked to a variety of skin conditions, including acne, eczema, psoriasis, and rosacea. The skin is often a great barometer for what’s going on inside the gut (4). 

The connection between the gut and skin is known as the gut-skin axis—and yes it’s a real thing! Dysbiosis, or an imbalance in the gut microbiome, can lead to inflammation that then pops up on the skin (no pun intended). As we learn more about the gut-skin connection, studies show that an unhealthy gut leads to symptoms on the skin. One study found that patients with IBD experience a greater number of skin disorders (5). 

Read more: Acne Begone! How to Get Rid of Hormonal Breakouts

8. Food intolerances or sensitivities

If you find that you’re suddenly reacting poorly to certain foods, it could be due to an unhealthy gut. Food sensitivities occur when your digestive system can’t properly break down food, causing bloating, diarrhea, constipation, or other symptoms. 

Studies show a connection to reduced beneficial bacteria or the presence of underlying infection with an increase in food sensitivities (6).

9. Sugar cravings

If you constantly crave sweets, or always want something sweet after a meal, this could signal a kind of fungal overgrowth in the gut from Candida albicans. Candida is a regular resident of your digestive tract, but certain factors—antibiotics, hormone imbalance, stress—can cause it to proliferate to a point where it interferes with healthy gut function.

Some studies also show that an absence of certain kinds of gut bacteria may cause cravings for sweet foods. Researchers noticed that overeating sweet foods happened more often after the use of antibiotics, which can alter the composition of the gut microbiome (7). 

Learn more: White Coating on Your Tongue? Signs You’re Dealing with Candida Overgrowth

10. Weight gain

In many cases, unexplained weight gain, or difficulty losing weight is a sign that something isn’t right in your gut. Your microbiome plays a big role in regulating hormones that control metabolism, so any imbalance can cause an increase in fat storage or a slowing of overall metabolism.

Additionally, low microbiome diversity in those who are overweight was also associated with impaired blood sugar balance and higher levels of inflammation, which can also make weight loss difficult (8). 

What causes gut health to decline?

There are a number of reasons your gut can get thrown out of whack, but diet and lifestyle are the biggest contributors.

In terms of diet, bad bacteria and Candida thrive on sugar and processed foods, while good gut bacteria prefer whole foods and plenty of prebiotic fiber, which most people don’t eat nearly enough of. 

You should also consider any potential food intolerances that may be unique to you—for example, lactose intolerance or gluten sensitivity. 

Poor gut health can lead to intestinal permeability, aka leaky gut. And if you’re dealing with increased intestinal permeability, you allow bacteria and other unwanted particles like undigested food to enter the bloodstream along with the nutrients. This sets the stage for more serious downstream problems like autoimmune disease, food allergies, or joint aches & pains.

Some other things that can negatively affect your gut include:

  • A poor diet
  • Lack of sleep
  • Travel
  • Alcohol intake
  • Prolonged stress
  • Antibiotic use

Related: Fiber Making You Bloated? Here’s How to Skip the Bloat & Keep the Benefits

Tips to Improve Gut Health

Eat a balanced diet rich in fiber

Eating a balanced diet is key for good gut health. Make sure that you’re getting plenty of fruits, vegetables, and other high-fiber foods. This will help to promote the growth of beneficial bacteria in your gut.

Avoid processed foods

Processed foods are often high in refined sugars and unhealthy fats, which can disrupt the balance of bacteria in your gut. To keep your gut healthy, stick to unprocessed, whole foods as much as possible.

Healthy hormones start in the gut.

Increase your intake of probiotics

Probiotics are live microorganisms that can help to restore the balance of bacteria in your gut and improve digestion. You can get them from fermented foods like yogurt, kefir, sauerkraut, kimchi, and kombucha. You can also take a probiotic supplement if needed.

Reduce stress

Stress has been linked to gut issues like leaky gut syndrome and irritable bowel syndrome (IBS). To keep your gut healthy, reduce stress as much as possible and take steps to manage it with activities like meditation, yoga, and journaling.

Exercise regularly

Exercise can help to promote the growth of beneficial bacteria in your gut and improve digestion. Aim for at least 30 minutes of moderate-intensity exercise per day.

What to remember

Keeping your gut healthy is a lifelong process that never involves just one step or one singular change. That’s why it’s important to recognize the signs of poor gut health so you can step in and support your gut back to an optimal state. A healthy gut is essential for a strong immune system, healthy hormones, and overall wellness. Eating a balanced diet, avoiding processed foods, taking probiotics, reducing stress, and exercising regularly are all great ways to support your gut.


  1. https://www.ncbi.nlm.nih.gov/books/NBK441938/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469458/
  3. https://journals.sagepub.com/doi/full/10.1177/1099800418806055#
  4. https://www.frontiersin.org/articles/10.3389/fmicb.2018.01459/full
  5. https://www.frontiersin.org/articles/10.3389/fphys.2012.00013/full
  6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767923/
  7. https://www.cell.com/current-biology/fulltext/S0960-9822(22)01750-X
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082693/
Dr. Taz Bhatia M.D.