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What are the signs that your gut flora is out of balance?

There are several recognisable signals, of which abdominal complaints such as persistent pain, diarrhoea, or constipation are the best supported. If you experience prolonged bowel complaints after a course of antibiotics or an infection, discuss this with your GP.

Abdominal complaints are the most recognisable signal. Recurring abdominal pain, diarrhoea, constipation, or an alternating pattern between these all occur with a disrupted gut flora. More than a third of the population experiences this kind of functional bowel complaint, which is strongly associated with an abnormal composition of the gut flora.

In persistent constipation, stool analysis shows measurably lower levels of Bifidobacteria and Lactobacilli than in healthy individuals. Elevated methane levels in the breath can also be an indication. Note, however: these are associations from observational research, not proof that one complaint causes the other.

Excessive abdominal pain and diarrhoea after eating can also be an indication. In a specific form of irritable bowel syndrome in which diarrhoea predominates, bile acids accumulate in the gut because certain bacteria are absent. This makes the gut more irritable and more sensitive to pain.

A 'leaky gut' is another consequence that becomes visible in blood tests. The intestinal wall seals less effectively, allowing substances to leak into the bloodstream. This process appears to be linked to a disrupted gut flora, although causality has not been fully proven.

Less well-known signals are mood swings and difficulty concentrating. The gut and the brain are in constant communication via nerve pathways and hormones. Both animal and human studies show that a dysregulated gut flora can influence this connection, but whether that is also the cause of your complaints is not straightforward to establish. Finally: courses of antibiotics are a well-known but underestimated trigger. After a course of antibiotics or a gut infection, the flora can remain disrupted for a long time, sometimes resulting in new bowel complaints that persist for months.

The evidence
7 studies · 1 randomised trial

Evidence is based on multiple reviews, a systematic review, and a randomised study. Most associations are observational; causality is probable for some signals (IBS, leaky gut) but has not yet been fully demonstrated for others (mood complaints).

Last checked: September 2026 · how this was judged
Related answers

Is my gut flora linked to being overweight?

Your gut microbiome is probably linked to excess weight through multiple mechanisms, but a proven causal relationship in humans is still lacking. A varied diet that supports your gut microbiome is worthwhile, but specific supplements for weight loss have not yet been proven effective.

Can a disrupted gut microbiome weaken your immune system?

A disrupted gut microbiome demonstrably dysregulates your immune system and increases the risk of chronic inflammation. Eating fermented foods is the best-supported way to do something about it.

Yes · Moderate evidence

Can your gut microbiome influence inflammation in your body?

Your gut microbiome can influence inflammatory processes throughout your body via the gut wall. Eating more fibre and exercising regularly are the most well-supported ways to influence this favourably.

Can your gut microbiome control your appetite and hunger?

Yes, your gut microbiome can influence your hunger and eating behaviour via a direct connection to your brain. Eating more fibre is the best thing you can do right now to support that route.

Is there a real connection between your gut microbiome and your mood or brain?

There is a biologically plausible and, in animal research, robustly supported connection between your gut microbiome and your brain, but causality has not yet been proven in healthy humans. A varied, fibre-rich diet is the most concrete step you can take right now.

Can exercise improve your gut microbiome?

Moderate regular exercise demonstrably improves your gut microbiome, but you need to keep exercising because the effect disappears when you stop. Do not overdo it: very intensive training can actually put gut health under pressure.

Yes · Moderate evidence
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