What Causes an Unhealthy Gut?

What causes an unhealthy gut?

An unhealthy gut, known as dysbiosis, happens when the balance of microbes in your gut is disrupted. The most common causes are:

• A diet low in fibre or high in processed food and sugar
• Frequent or unnecessary antibiotic use
• Ongoing stress
• Poor or irregular sleep
• Drinking too much alcohol
• A lack of variety in your diet

Most people's gut problems come from a combination of these rather than a single cause, and they tend to add up over time.

How does diet affect your gut?

Diet is one of the most powerful everyday influences on your gut microbiome. Fibre from plant foods feeds beneficial gut bacteria, which produce short-chain fatty acids that help support the gut lining, immune balance, and normal digestion. In contrast, a low-fibre Western-style diet that is high in ultra-processed foods, simple sugars, and saturated fats is linked with lower microbial diversity, lower short-chain fatty acid production, and a greater risk of gut imbalance. Variety matters too: different microbes use different fibres and plant compounds, so eating a wider range of plant foods may help support a more diverse and resilient gut microbiome.

→ Best Foods for Gut Health: What to Eat (and Why)

How do antibiotics affect your gut?

Antibiotics affect your gut by killing harmful bacteria that cause infections, but they can also reduce helpful bacteria and disrupt the balance of your gut microbiome. Broad-spectrum antibiotics are especially likely to affect both the target bacteria and beneficial microbes that support digestion, immune function, gut barrier health, and protection against pathogens. After a necessary course, the gut microbiome may begin to recover, but recovery is not always immediate or complete, and it can vary depending on the antibiotic, the person, and how often antibiotics are used. Repeated or unnecessary antibiotic use can reduce microbial diversity more lastingly and create space for opportunistic bacteria, including Clostridioides difficile, or antibiotic-resistant strains to grow. That is why antibiotics are important when they are genuinely needed, but using them carefully also matters for protecting your gut microbiome.

How does stress affect your gut?

Stress affects your gut through the gut-brain connection, the two-way communication network between your digestive system and your brain. When stress is ongoing, it can change how your gut moves, how sensitive it feels, and the balance of bacteria living there. It can also affect gut motility, which is one reason stress may show up as cramping, diarrhoea, or constipation, and it may make the gut lining more permeable. And it works both ways: an unsettled gut can send signals back to the brain, influencing stress, mood, and how you feel.

Managing stress is not just good for your mind; it can also be part of looking after your gut.

How does sleep affect your gut?

Sleep and gut health are closely linked, and the relationship appears to run both ways. Poor or irregular sleep can disturb the gut microbiome, partly because both sleep and gut bacteria follow circadian rhythms. When your sleep schedule is disrupted, the balance of gut microbes may shift, beneficial bacteria may decrease, short-chain fatty acid production can fall, and inflammation may rise. At the same time, the gut can send signals back to the brain through the gut-brain axis, using immune signals and microbial metabolites involved in sleep regulation. That means an unsettled gut may also influence how well you sleep. Consistent, good-quality sleep is therefore not just a recovery tool for your brain; it may also be one way to support a more balanced gut environment.

What other factors can affect your gut?

Beyond diet, stress, sleep, and antibiotics, other factors can also influence your gut microbiome over time:

• Alcohol: Regular heavy drinking can disrupt the gut microbiome, reducing some beneficial bacteria and increasing bacteria linked with inflammation
• Certain medications: Some medicines, including frequent acid blockers such as PPIs, may shift the gut microbiome and reduce microbial diversity
• Lack of movement: Regular physical activity is linked with healthier digestion and greater gut microbial diversity
• Age and life changes: The gut microbiome naturally changes across life stages, including ageing, hormonal shifts, illness, and major routine changes

These influences often build gradually, which is why steady habits usually matter more than any single “gut health” fix.

What are the signs your gut is unhealthy?

If several of these causes apply to you, you may notice signs like bloating, gas, irregular bowel movements, fatigue, skin issues, or changes in mood. These are more meaningful when they appear together or keep returning.

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

How do you fix an unhealthy gut?

The good news is that most of the causes of an unhealthy gut are within your control. Eating more fibre and variety, adding fermented foods, managing stress, sleeping well, and using antibiotics carefully all help restore balance over time. Because everyone's gut is different, testing yours can show you your own starting point.

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