Signs of an Unhealthy Gut, 10 Warning Signs Your Gut Is Out of Balance

Your gut is crucial to your overall health. Everything you eat is processed in your gut, supplying the nutrients your body needs to survive and repair itself. Part of its function is down to the gut microbiome, a community of microbes living throughout your digestive tract. If these become unbalanced, it can lead to an unhealthy gut.

Too often, we ignore the signs of an unhealthy gut (and unbalanced gut microbiome). We put it down to one bad meal or blame our fatigue on stress or lack of sleep. However, the underlying causes might be related to your current gut health — something a microbiome check can help uncover.

Below, we’ll take you through the top ten signs of an unhealthy gut (and what they mean).

10 Signs of an Unhealthy Gut

1. Persistent Bloating or Excess Gas

Bloating is the most common symptom of an unhealthy gut. It can be caused by swallowing air (aerophagia) when eating or due to anxiety. However, if you’re regularly feeling swollen, tight, or gassy after eating, the cause often points to poor digestion, food intolerances, or bacterial imbalances.

High-FODMAP foods contain fructans, which can cause certain gut bacteria and yeasts to overgrow. This overgrowth can lead to increased fermentation in the intestines, resulting in excess gas.

2. Irregular Bowel Movements

Your bowel habits are a reliable indicator of your gut health. Diarrhoea or constipation are signs of disrupted gut motility — switching between the two can also be characteristic of irritable bowel syndrome (IBS).

Chronic constipation, typically defined as having three or fewer bowel movements per week, is often linked to low fibre intake or sluggish gut motility.

Frequent diarrhoea, marked by three or more loose, watery stools per day, may signal gut inflammation or impaired nutrient absorption due to damage to the gut lining.

3. Ongoing Fatigue

If your gut isn’t digesting or absorbing nutrients optimally, fatigue often follows. You might feel constantly tired, even with good sleep. Key nutrients like iron, magnesium, and B vitamins can all be low.

Gut inflammation, for example, inflammatory bowel disease (IBD), can also soak up your body’s resources, leaving you more fatigued.

4. Frequent Food Sensitivities

Food sensitivities aren’t the same as an allergy. The effects aren’t immediate and they aren’t life-threatening. Most people notice symptoms within hours (or in some cases days) after eating a particular food or food group. Symptoms often experienced include bloating, cramps, headaches, or nausea.

Since there’s no cure for food sensitivities, managing your symptoms by eliminating trigger foods, correcting enzyme imbalances, or restoring a healthy gut microbiome are typically advised.

5. Brain Fog or Poor Concentration

The gut-brain axis describes the two-way communication between your digestive system and nervous system. These systems aren’t separate or cut off from each other; they’re interconnected.

People with an unhealthy gut may report foggy thinking, low motivation, or slower cognition. In fact, it can even impact your mood (see next).

6. Mood Changes (Anxiety, Low Mood, or Irritability)

Did you know that around 95% of serotonin, the brain’s “feel-good” chemical, is produced in your gut? But that’s not all, gut bacteria also help regulate serotonin, dopamine, and GABA. This is why imbalances in the gut microbiome (dysbiosis) are increasingly linked to anxiety, depression, and mood swings.

7. Skin Problems (Acne, Eczema, or Rashes)

Your skin can reveal signs about your gut health. Inflammation in the gut often shows up on the skin, triggered by dysbiosis. Chronic acne, rosacea, and eczema can all flare up due to systemic inflammation and are linked to digestive health.

For example, coeliac disease can present with intensely itchy, blistering rashes, while inflammatory bowel disease (IBD) is often connected to psoriasis.

8. Unexplained Weight Changes

Weight changes aren’t surprising if your gut is unhealthy. This sign can occur due to poor nutrient absorption, insulin dysregulation, or a microbial imbalance. Look for difficulty gaining or losing weight despite stable habits.

Appetite is another factor. Some bacteria can influence your appetite hormones or your blood sugar levels, influencing how hungry you feel.

9. Frequent Infections or Weakened Immunity

Your gut isn’t just connected to your nervous system. It’s the frontline in the fight against infections. Around 70-80% of your immune cells are found in your gut. Recurrent colds, slow recovery, or constant run-down feelings can be traced back to gut dysfunction.

10. Reflux, Heartburn, or Indigestion

Chronic upper digestive symptoms such as reflux, burning, or heaviness after meals can be linked to low stomach acid, delayed emptying, or conditions like gastroesophageal reflux disease (GERD).

Ready to Get Answers?

If these symptoms sound uncomfortably familiar, it might be time to stop guessing and start understanding what’s really happening in your gut.

The Functional Gut Clinic’s fully integrated microbiome clinic helps uncover what’s really driving your symptoms, using advanced testing and expert clinical insights. From microbiome and breath tests to personalised treatment plans, everything is tailored to you.

Book your assessment today and take a clear, confident step towards better digestion and long-term wellbeing.