9 Signs of an Unhealthy Gut

I’ve never been someone to think about my gut health.

I never considered the effect of my diet and habits on my gut. Now that I know what the signs of an unhealthy gut are, I’m paying attention to changes I might need to make.

If you’re reading this, you probably suspect something is wrong with your gut, but you don’t really know what that means. Gut health seems to be tied to everything these days, so it’s hard to know where to start. Maybe you’ve dealt with bloating, bathroom habits that keep changing, skin that keeps flaring up, or trouble sleeping. But you don’t know what’s normal and what your gut is responsible for. You just want a solid answer so you can move on with your life and take the next step.

Below are some common signs of an unhealthy gut and why they may happen. Some are well supported by the research and some are still early in the research process. Compare them with your own symptoms, and find out whether it’s time to start paying closer attention to your gut.

What is an “Unhealthy Gut”?

The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines a healthy gut as “a state of normal gastrointestinal function without active gastrointestinal disease and gut-related symptoms that affect quality of life.”

So, an unhealthy gut is one that is:

• Functioning abnormally,
• In an active disease state, or
• Causing symptoms that affect your quality of life.

The signs in this article focus on abnormal function and symptoms. Luckily, the two overlap a lot. The symptoms you feel are the visible sign of a function that’s gone wrong.

Quick Definitions

Gut Microbiome: the diverse collection of bacteria, fungi, viruses, and archaea living in the gut, along with the byproducts they produce. Gut bacteria digest fiber that your body can’t digest on its own. They also make vitamins, help regulate your immune system, and communicate with your nervous system. A healthy gut microbiome tends to have a large number of different species, which is called diversity. Higher diversity is generally associated with a resilient gut (but more isn’t always better).

Gut Barrier: the lining of your gut. It’s a thin wall of cells covered by a layer of mucus, with immune cells beneath. A functioning gut barrier decides what enters your body and lets nutrients in while keeping harmful substances out.

Short-chain fatty acids (SCFAs): compounds produced by your gut bacteria when they ferment fiber. These compounds fuel the cells of your gut barrier and help keep it strong. They have a wide variety of capabilities, including calming inflammation.

Digestive Signs

We’ll start with signs that are local to the gut itself. Each one may indicate faulty gut function and each is a common complaint whether or not someone has a diagnosed GI disorder.

Common signs local to the gut include:

1. Bloating and gas
2. Stomach pain or discomfort
3. Constipation, diarrhea, changing bowel habits
4. Heartburn and reflux

Bloating and Gas

Bloating is a feeling of fullness and discomfort in your abdomen. It can feel like something is pressing up against the inside of your stomach. It may or may not come with distension, which is a visible increase in the size of your abdomen.

Bloating is one of the most common gut complaints. About 19% of people deal with it, and in people with irritable bowel syndrome (IBS), it’s up to 90%. Two factors play into bloating: how much gas builds up in your gut, and how your gut perceives the buildup.

Gas gets into your GI tract in three ways. You swallow air as you talk, breathe, and eat. Your gut bacteria make gas as they ferment food you don’t digest. And some gas diffuses in from your bloodstream. It leaves by burping, passing gas, getting absorbed into your blood, or being used up by your gut bacteria. When gas accumulates in the gut faster than it leaves, it builds up.

So why does that build up happen? Bloating has been linked to carb intolerance, celiac disease, inflammatory bowel disease (IBD), and small intestinal bacterial overgrowth (SIBO). These conditions can change how much gas your gut makes or holds onto, which leads to more buildup.

But the amount of gas isn’t the whole story. People with IBS have about the same amount of gas in their colon as healthy people, even after eating carbs that get fermented. Yet only those with IBS feel it. That’s called visceral hypersensitivity. The pain receptors in your gut become overactive and your brain reads normally harmless signals as painful.

A visible swelling is a separate question. Normally, when your gut fills with gas, your diaphragm relaxes and your abdominal wall tightens. In some people, this is backwards: the diaphragm pushes down and the abdominal wall relaxes, which causes your abdomen to bloat outwards.

Bloating can be a sign of an unhealthy gut when gas builds up faster than your gut clears it, or when your gut reads normal amounts of gas as painful.

Stomach Pain or Discomfort

The most studied example of recurring stomach pain is IBS. It’s defined by abdominal pain at least one day a week on average, for three months, along with changes in bowel habits. IBS can feel like a vague, unhelpful “catch-all” diagnosis because of these broad criteria.

When people with IBS get tested there’s no visible damage, inflammation, or immune or metabolic markers. Everything looks normal despite symptoms. That’s part of why researchers have changed the way they view these conditions. Functional gut disorders like IBS are now called disorders of gut-brain interaction (DGBIs), and over 40% of people worldwide have one.

The brain and the gut are in constant communication. In DGBIs, the brain can perceive signals coming from the gut differently, which can lead to pain. This can be because of immune activation in the gut itself, or it can be an issue with how your spinal cord and brain process the signals.

A gut infection can set off these amplified pain signals. Taking antibiotics for that infection can raise that risk further. Stress and sleep matter too. In people with IBS, a night they felt they slept poorly predicted more abdominal pain the next day.

Over two-thirds of people with a DGBI also have anxiety or depression. It’s unclear which originates first, or if they both develop together.

Recurring stomach pain can be a sign of an unhealthy gut even when every test comes back normal. The problem can lie in how your gut and brain handle the pain signals.

Constipation, Diarrhea, Changing Bowel Habits

Constipation and diarrhea sit at opposite ends of the bowel-movement spectrum. Constipation is not only going less often, but also hard, lumpy stools or feelings of incomplete evacuation. Diarrhea, on the other hand, is defined by loose, watery stools.

How hard or loose your stool is mostly reflects how fast it moved through your gut. The slower it moves, the harder and lumpier it gets. The faster it moves, the looser it gets.

So what’s normal? In one study of people with no gut disease, 98% went anywhere from three times a day to three times a week. That’s a wide range, so how often you go only tells you so much. A more helpful check might be whether your bowel habits have recently changed, what your stool quality is like, and the presence of other symptoms like bloating and stomach pain.

Constipation and diarrhea can be signs that your gut is moving things along too slowly or too quickly, and a recent change from your normal habits is the part to pay attention to.

Heartburn and Reflux

Reflux is when stomach contents flow back up into the esophagus. Heartburn is the burning feeling in your chest that often comes with it. Reflux happens when the barrier between your stomach and esophagus doesn’t keep stomach contents down, like when your stomach stretches after a big meal or if there’s extra pressure on your stomach.

What you eat may also play a part. A study that followed about 183,000 adults for about 13 years found that people who ate the most inflammatory diets had about an 11% higher risk of developing gastroesophageal reflux disease (GERD). People eating a Mediterranean-style diet had about an 11-13% lower risk. The people who developed GERD also tended to have higher body-mass index (BMI), more low-grade inflammation, more NSAID use (like ibuprofen), less physical activity, and poorer sleep.

Whole-Body Signs

Your gut is a gateway to the rest of your body, so when it isn’t working properly, the signs can show up elsewhere.

This can happen in a few ways. When your gut barrier isn’t doing its job, more harmful substances get through. From there they go to your liver, and then the rest of your body.

Your gut has a few more pathways that can have far-reaching effects. For example, compounds your gut bacteria make, like SCFAs, can enter the bloodstream and act on other organs. The gut is also linked to the brain through the vagus nerve, which means the gut can influence the signals your brain receives.

Most human research on these signs reveals associations and not causation. The gut could be causing the symptoms, the symptoms could be changing the gut, or both could be true at once, creating a vicious cycle.

Skin Flare-ups

Your gut and your skin have a lot in common. Both are barriers between the outside world and the inside of your body, and both have their own microbiome. They talk to each other through immune signals, hormones, and compounds that your microbes make. This connection is commonly called the gut-skin axis.

What your gut bacteria make matters too. SCFAs can bind to receptors on skin cells and immune cells, which may help calm inflammation in the skin. People with eczema tend to have lower SCFA levels.

SCFAs help balance two types of immune cells, one of which drives inflammation behind acne breakouts. People with acne also tend to have lower gut diversity and fewer SCFA-producing bacteria. Probiotics might help reduce acne severity in some populations, but just because one probiotic strain might be beneficial, it doesn’t mean all of them are.

Skin flare-ups may be one sign that your gut microbiome has lower diversity and isn’t making the SCFAs it should.

Getting Sick Often

If it feels like you’re always getting sick, your gut may play a part.

Your gut microbiome and your immune cells are in constant contact, and your microbiome teaches those cells what’s harmful and what’s not. When the microbiome is altered by things like antibiotics or a Western-style diet heavy in ultra-processed foods, the teaching process can be affected. The result can be an overactive immune system leading to more inflammation.

Your microbiome training your immune system is a well-established pathway. The direct cause and effect leading to more sickness hasn’t been shown in humans within the research yet, but it’s possible. Your gut might not be the reason behind every cold you catch, but it might be one contributing factor.

Your gut barrier plays a part too. An imbalanced microbiome can weaken it, letting more harmful bacteria and their byproducts slip through, so your immune system has to switch on more often.

Getting sick often could be one sign that your microbiome isn’t properly training your immune system. Future research is still necessary to observe the full causes and effects in humans.

Mood Changes, Brain Fog

Your gut and your brain are constantly communicating back and forth.

The vagus nerve carries signals from your gut’s own nervous system up to your brain.

SCFAs act as signals too. They help keep the brain’s immune cells in balance and they may send signals to the brain through the vagus nerve.

Across 59 studies, people with depression, bipolar disorder, schizophrenia, and anxiety tended to have fewer bacteria that make butyrate, one of the main SCFAs.

There isn’t a microbiome pattern that’s unique to depression or anxiety, so your gut microbiome composition can’t confirm any specific diagnoses. However, the gut can be one more thing to consider in the entire mental health picture.

Gut symptoms are some of the most common physical symptoms in cases of depression, and anxiety often shows up alongside diagnosed gut disorders.

Across 13 trials, prebiotics, probiotics, and synbiotics gave small improvements in depression scores, mostly in mild-to-moderate cases when added on top of regular treatment. On their own, results varied too much from study to study to say whether they work unconditionally. Part of the reason is that probiotic effects depend on strain, and different studies used different strains.

One classic brain symptom is brain fog. It’s harder to define, but it’s common in people with gut problems. The link is clearest in diagnosed gut diseases. In a small study of 11 people newly diagnosed with celiac disease, attention and verbal skills improved over a year on a gluten-free diet as their gut lining healed. Across 12 studies, people with IBD scored lower on attention and working memory tests than healthy people did. Why this happens isn’t exactly clear yet, but the link does suggest that people with these conditions may have a harder time focusing day to day.

Mood changes and brain fog may be linked to changes in your gut microbiome, and the link can run both ways.

Poor Sleep

A study following 1,809 middle-aged and older adults for six years found that both people who had recently developed insomnia and those who had it for years tended to have lower gut diversity.

In mice, disrupted sleep has been shown to change the microbiome.

Unfortunately, research has not yet found a concrete or direct explanation for why low diversity and insomnia are commonly seen together.

Cravings

Your gut bacteria may play a role in how full you feel after meals.

Some cells in your colon release a hormone called PYY that helps you feel full as you eat.

It’s been shown in mice that these colon cells can detect a protein that originates from gut bacteria and release PYY in response. Mice that couldn’t sense that protein ate bigger, longer meals and gained more weight. The same process is yet to be researched in humans.

SCFAs can also trigger the release of PYY and another hormone that makes you feel full, GLP-1. They can dampen ghrelin, the hormone that makes you feel hungry. So a healthy gut microbiome producing these SCFAs may help your body make the hormones that keep hunger in check.

By the same logic, a gut with fewer SCFA producers could release less of these hormones which can lead to more cravings and hunger in general.

If you’re often hungry or craving food, a gut making fewer SCFAs than it should be could be part of the reason. Future research is necessary to observe the full causes and effects in humans.

Food Sensitivities and Leaky Gut

One of the most common things people point to as a sign of an “unhealthy gut” is something you may have heard called “leaky gut.”

It’s when your gut barrier stops doing its job, which can let harmful things into your body and may trigger inflammation as your immune system fights back.

Barrier problems are measurable and well documented in IBD, celiac disease, and IBS.

One study of 1,420 relatives of people with Crohn’s disease, who had no symptoms themselves, showed that those with higher permeability markers were about three times more likely to develop Crohn’s.

Your microbiome shapes your barrier. SCFAs fuel the cells lining your gut. Some bacteria make a compound, LPS, that can loosen the seal between barrier cells. Your barrier can also shape the microbiome.

Healthy barrier cells use up oxygen, which keeps the gut environment friendly towards helpful bacteria and makes it harder for harmful species to take over.

Leaky gut isn’t a formal diagnosis. To measure permeability, researchers have people drink certain sugars and track how much shows up in their urine, and how fast. But there’s no permeability test, at home or through your doctor, that’s been validated to diagnose it. There are no agreed normal values and no standard way to run the test. Your gut’s permeability can also shift with stress and the time of day.

What we do know is that certain things increase permeability, like NSAIDs (such as ibuprofen) and some food additives like emulsifiers. When permeability increases, your immune system has more harmful substances to deal with. That can mean more inflammation. Future research is needed to show the full effects of treating barrier permeability and subsequent symptom and disease improvement.

Leaky gut also comes up with food sensitivity tests. In one study of 111 adults, people with more positive food sensitivity tests also had more markers of a leakier gut barrier. But people with gut symptoms didn’t have more positive tests than people without them. So a long list of sensitivities may say more about your gut barrier than about which foods are actually bothering you.

Can You Test For an Unhealthy Gut?

Your gut does a lot of different jobs. The microbiome alone ferments fiber into SCFAs, makes vitamins, helps regulate your immune system, and competes with harmful bacteria.

To study it, researchers look at its diversity, composition, function, outputs, pH, and inflammatory markers. And yet, no single picture of a “healthy” microbiome has been agreed upon. Everyone’s is different.

Then, there’s the gut barrier. It has its own parts: epithelial cells, the mucus layer, antimicrobial compounds, and immune cells. Both the barrier and microbiome are affected by age, diet, activity, stress, and other diseases.

To really test for an unhealthy gut, you’d have to measure all of these aspects, plus consider your symptoms to get the full picture. There’s plenty of variation in these markers from person to person, so it gets complicated fast. Getting the full picture isn’t cheap or easy. That’s why an at-home stool test has questionable value for diagnosing what’s going on in your gut. Anyone who focuses on one piece over the others is missing the point. It’s all woven together.

Your best bet is to look at the signs above and take an honest look at yourself. Are you dealing with these symptoms often? Is there anything else going on in your life that could explain them? You don’t need a test to tell you something is wrong. You might even be reading this after a test came back negative while you still have symptoms every day.

Your body is the biggest signal you have, and it’s where you should start. So, it might be time to turn your attention to your gut. Those same signals are also what tell you when it’s time to get checked.

When to See a Doctor

Several red flags can point to something more serious going on in your gut:

• Rectal bleeding
• Unexplained weight loss
• Iron-deficiency anemia
• Trouble swallowing
• Vomiting blood
• Black stools
• Major changes in bowel habits
• Family history of GI cancer

Red flag symptoms are more common than you’d think. In a study of more than 54,000 people across 26 countries, over half of adults reported at least one. People with gut-brain disorders reported them even more often. One red flag on its own doesn’t guarantee something serious is going on, but the more you have, the more they matter. Risk of colorectal cancer before age 50 can increase in the presence of multiple red flags.

If any of these sound like you, get checked by a doctor. The signs in this article focus on abnormal function and symptoms. Active disease is the part that only a qualified medical professional can check for.

Take another look at the signs above. The ones local to your gut, like bloating, stomach pain, changing bowel habits, and heartburn, are the most likely to be related to your gut health. The whole-body signs are real possibilities, but the evidence is still within early phases of research.

Occasional symptoms can be normal, and they happen to everyone from time to time. Your gut doesn’t live in a static environment. It’s constantly adapting to the input you give it. But if you notice the same symptoms coming back again and again, it might be time to give your gut the attention it needs.

Like me, a lot of people don’t think about their diet and habits until there’s a problem. Luckily, there’s a lot you can do to improve your gut health. Remember: your body is the biggest signal you have and listening to it can be the first step towards improvement.