7 Signs of an Unhealthy Gut (and What They Mean)

What are the symptoms of an unhealthy gut microbiome?

There is no single symptom that proves your gut microbiome is unhealthy. But when several of these signs appear together, keep coming back, or feel unusual for you, they may point to gut dysbiosis or another digestive issue.

Abdominal pain

Abdominal pain can be one possible sign that something in your gut is irritated or out of balance. It is more meaningful when it appears alongside bloating, gas, diarrhoea, constipation or other changes in digestion. Pain alone does not prove gut dysbiosis, and ongoing or severe pain should be checked by a healthcare professional.

Bloating

Bloating can happen when digestion, gut movement or fermentation patterns change. Gut bacteria are involved in breaking down food, so shifts in the microbiome may contribute to bloating in some people. It matters more when it happens regularly or appears with other gut symptoms.

Gas

Gas is a normal by-product of digestion, but excessive or uncomfortable gas can sometimes be linked with changes in how gut bacteria ferment food. On its own, gas does not automatically mean your gut is unhealthy. It is more useful to look at whether it appears with bloating, pain or changes in bowel habits.

Diarrhoea or constipation

Diarrhoea and constipation can both be linked with gut dysbiosis or other digestive conditions. Dysbiosis may disrupt the normal gut environment, which can affect digestion, stool consistency and bowel rhythm. Track changes that are persistent, unusual for you or happening alongside other symptoms.

Fatigue

Fatigue may be associated with gut dysbiosis, especially when it appears with ongoing digestive symptoms. But tiredness has many possible causes, including poor sleep, stress, low iron, infections and other health conditions. So fatigue should be treated as a possible clue, not proof of an unhealthy gut.

Mental health changes

The gut microbiome communicates with the brain through the gut-brain axis. When the gut microbiome is imbalanced, it may be associated with changes in mood, stress response or anxiety. This does not mean the gut is always the cause, but it may be one factor involved.

Skin conditions

Skin issues such as eczema, acne or psoriasis may be associated with gut dysbiosis in some people. One possible explanation is that gut imbalance may affect inflammation and immune activity, which can also influence the skin. Skin symptoms alone do not prove gut imbalance, but they may be worth considering when they appear alongside digestive symptoms.

Overall, these signs are best viewed as a pattern rather than individually. One symptom by itself does not necessarily mean you have an unhealthy gut, but several recurring symptoms may be a reason to look more closely at your digestion, diet, stress, medication history and microbiome.

What are the signs of a healthy gut?

A healthy gut is usually linked with a balanced gut microbiome, steady digestion and fewer ongoing gut-related symptoms. In daily life, this may show up as more comfortable digestion, regular bowel habits and less frequent bloating or gas. Symptoms alone cannot show the exact state of your microbiome, but they can give you a general sense of how your gut is functioning.

Some possible signs of a healthy gut include:

Less frequent bloating Occasional bloating is normal, but a healthier gut often feels more settled after meals.

Consistent bowel habits Regular bowel movements that are normal for you can be a sign that digestion and gut motility are working well.

Less excessive gas Gas is a normal part of digestion, but frequent or uncomfortable gas may suggest your gut is struggling with certain foods or fermentation patterns.

How do you improve your gut health naturally?

Improving gut health usually starts with supporting a more balanced gut microbiome. Diet, stress, medication use and long-term lifestyle habits can all affect the balance of the gut microbiome. The basics are simple, but they work best when done consistently:

Eat more fibre and plant variety Fibre-rich foods such as vegetables, fruits, legumes, nuts, seeds and whole grains help feed beneficial gut bacteria.

Add fermented foods if they suit you Foods like yoghurt, kefir, kimchi and sauerkraut may support microbial diversity, although not everyone tolerates them well.

Manage stress and sleep Stress and poor sleep can affect gut function, bowel habits and the gut-brain connection, so recovery is not only about food.

Limit ultra-processed foods and excess sugar Highly processed, low-fibre diets may work against gut microbial balance over time.

Avoid unnecessary antibiotics Antibiotics can be important and sometimes essential, but unnecessary use can disrupt the gut microbiome.

Because many gut symptoms overlap, symptoms alone cannot show exactly what is happening in your microbiome.

A gut microbiome test can give a snapshot of the bacteria detected in your sample and may help identify patterns linked with dysbiosis, but results should be interpreted alongside your symptoms, diet, medication history and clinical context.

For a more personal view of your gut health, the Phenome gut test can help map your microbiome and show what may be affecting your gut balance.

→ Explore the Gut Microbiome Test
→ How to Improve Your Gut Health: The Complete Guide
→ What Is Gut Dysbiosis?
→ What Causes an Unhealthy Gut?
→ Constant Bloating: Why It Won't Go Away and What to Do
→ Can Your Gut Affect Your Skin?
→ Can Your Gut Affect Your Mood?