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Can a disrupted gut microbiome weaken your immune system?

Yes · Moderate evidence

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.

Around 70 to 80 percent of all immune cells in your body are located in your gut. Your gut microbiome works closely together with the immune system in your gut wall and also influences immune responses elsewhere in your body. A healthy, diverse gut microbiome is needed for the normal development and regulation of your immune system, both locally and throughout the body1.

When your gut microbiome becomes unbalanced, a condition called dysbiosis, your immune system can be thrown into disarray. This increases the risk of chronic inflammatory diseases. Review studies also link dysbiosis to a higher likelihood of cardiovascular disease and cancer, although for these conditions the cause-and-effect relationship has not been proven in every case2,3.

Your gut microbiome also appears to influence how well cancer patients respond to immunotherapy, specifically to so-called immune checkpoint inhibitors. This relationship has been described in multiple studies, but the precise mechanism is still being investigated. Doctors do not yet routinely act on this in clinical practice4,5,6.

For those who want to support their gut microbiome, fermented foods offer the strongest evidence base. In a 17-week study of 36 healthy adults, microbiome diversity increased and inflammatory markers in the blood decreased in people who consistently ate more yogurt, kefir and fermented vegetables7. A high-fiber diet did not show a clear or consistent immune effect: the effect depended strongly on each person's existing gut microbiome composition. Fiber is still healthy for other reasons.

Finally, your immune system also appears to form a bridge between the gut and the brain. Disruptions in the gut microbiome have been linked to inflammation in the brain and possibly to psychiatric and neurological conditions. This field of research is still in its early stages and the associations have not yet been proven to be causal8.

The evidence
8 studies · 1 randomised trial · ≈ 36 participants

The claims are based on review studies, multiple associative studies and one randomized study in humans (36 participants, PMID 34256014). The strength of the evidence is moderate to limited: consistent in direction, but causal pathways have not been fully proven for all outcomes. No meta-analyses were used as a direct source.

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

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 influence your risk of heart disease?

Your gut microbiome influences your heart health through metabolic by-products that can promote arterial hardening, high blood pressure and blood clots. The association is plausible, but how best to modify the gut microbiome to protect your heart has not yet been sufficiently proven: always discuss major interventions with your doctor.

Yes · Moderate evidence

Can your gut microbiome influence how long you live?

There are clear associations between a healthy, diverse gut microbiome and older age, but whether that microbiome promotes longevity or is itself a consequence of being healthy has not yet been proven. For now, a varied diet rich in fibre is the most concrete tool for supporting your gut microbiome.

Preliminary evidence

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.

Can your gut microbiome affect your cholesterol?

Your gut microbiome influences your cholesterol through bile acid conversion and the fermentation of fibres. Eating more fibre is the most concrete and safe step to take; supplements such as berberine are not yet sufficiently substantiated for daily use.

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
Related research
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Gut bacteria in infancy reshape the developing intestine
01 Sep
A bacterial enzyme boosts cell energy in aging animals
31 Aug
Exercise cuts a gut metabolite that harms bones
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