Gut health and immunity: How does the microbiome regulate your body’s defences?
The human digestive system harbours an extremely complex biological system known as the microbiome, comprising over 100 trillion microorganisms, including bacteria, fungi, viruses and other organisms.
In this article, we review recent scientific findings on the relationship between gut health and immunity, and how probiotics and prebiotics can contribute to promoting this health in a scientifically proven way.
What is the microbiome and how does it develop?
The microbiome is the entire microbial community that inhabits the digestive system, and its development begins from the very moment of birth. According to a comprehensive scientific review published in PMC in 2024, the microbiome accompanies humans from birth and matures gradually in constant interaction with the host’s physiological characteristics; disturbances in the microbiome are directly reflected in organs distant from the gut, such as the brain, heart, skin and joints.
The Microbiome and the Immune System
The digestive system harbours approximately 70 per cent of the immune system’s cells in the human body, making the gut the body’s largest immune hub. Beneficial bacteria regulate this immune response through three main mechanisms:
- Firstly: Strengthening the intestinal barrier: Beneficial bacteria secrete short-chain fatty acids such as butyrate, acetate and propionate, which nourish the cells lining the intestine and strengthen the tight junctions between them, thereby preventing harmful substances and pathogens from leaking into the bloodstream.
- Secondly: Regulating the inflammatory response: Beneficial bacteria balance pro-inflammatory and anti-inflammatory immune cells, and reduce the production of inflammatory cytokines such as IL-6 and hs-CRP.
- Thirdly: Protection against pathogenic microbes: Beneficial bacteria compete with harmful organisms for attachment sites on the intestinal lining and secrete antimicrobial substances that limit their growth.
A systematic review published in PMC in 2025 — which examined the evidence on the role of probiotics and prebiotics in intestinal permeability and immunity — confirmed that these compounds improve the integrity of the intestinal barrier and modulate immune responses via multiple mechanisms, including the regulation of zonulin and calprotectin levels, which are associated with intestinal permeability.
Symptoms of a dysbiotic microbiome
A dysbiotic microbiome occurs when the balance between beneficial and harmful organisms in the gut is disrupted. Its symptoms vary and may extend beyond the digestive system:
- Gastrointestinal symptoms: recurrent bloating, alternating diarrhoea and constipation, irritable bowel syndrome, persistent heartburn.
- Immune system symptoms: frequent respiratory infections, slow recovery from illness, worsening allergy symptoms.
- Skin symptoms: Recent studies have linked microbiome dysbiosis to the exacerbation of eczema and atopic dermatitis; a review published in PMC in 2025 demonstrated that multi-strain probiotic interventions helped to improve the severity of eczema symptoms in children via the gut-skin axis.
- Mental health and mood: A report published in PMC in January 2026 revealed that gut bacteria produce and modulate neurotransmitters such as serotonin and dopamine, and that strains known as ‘psychobiotics’ have been shown in clinical trials to significantly reduce levels of depression and anxiety.
Scientifically proven health benefits of probiotics and prebiotics
1. Boosting immunity and reducing inflammation
A comprehensive review published in Frontiers in Systems Biology concluded that probiotics and prebiotics stimulate the growth of beneficial bacteria, strengthen the intestinal barrier and regulate immune responses, making them promising tools in the management of inflammatory bowel diseases and the enhancement of general immunity.
2. Supporting cognitive health via the gut-brain axis
The 2025 Microbiome Achievements review, published by Gut Microbiota for Health, noted that a randomised clinical trial conducted on adults over the age of 60 found that taking a prebiotic blend containing inulin and fructo -oligosaccharides improved cognitive performance compared with a placebo group, noting that 2025 saw a quantum leap in understanding the mechanisms by which the microbiome influences the brain and behaviour.
3. Improving skin health via the gut-skin axis
A study published in 2025 in PMC, a journal specialising in the gut-skin -skin axis confirmed that multi-strain probiotic interventions based on Lactobacillus and Bifidobacterium helped to improve the severity of eczema symptoms in children and markers of skin inflammation, suggesting that gut health is literally reflected in skin health.
4. Supporting metabolic and cardiovascular health
A review in Gut Microbiota for Health (2026) documented that studies from 2025 revealed the mechanisms by which the microbiome influences the accumulation of atherosclerotic plaques in the arteries via bile acid metabolism, and that modulating the microbiome reduces visceral fat accumulation independently of diet.
Factors that compromise the health of the microbiome
- Antibiotics: These target both harmful and beneficial bacteria, and may continue to affect the microbiome for months after treatment has ended.
- A diet low in fibre: Fibre is the primary food source for beneficial bacteria; a lack of it reduces the diversity of the microbiome.
- Chronic stress: alters the microbial balance via the HPA axis and by affecting bowel movements.
- Lack of sleep: has been linked to disruptions in the microbiome’s circadian rhythm.
- Processed foods and refined sugar: feed harmful bacteria and reduce overall microbiome diversity.
Practical guidelines for promoting microbiome health
- Eat a varied diet rich in fibre: vegetables, fruit, pulses and whole grains nourish different bacterial strains.
- Fermented foods: natural yoghurt, kefir, kimchi and naturally fermented pickles are natural sources of probiotics.
- Probiotic supplements: particularly after courses of antibiotics or during periods of ongoing stress.
- Limit processed foods: reducing refined sugar and trans fats supports microbiome diversity.
- Exercise and good sleep: moderate exercise and adequate sleep have been shown to improve microbiome diversity.
Frequently Asked Questions
What is the difference between probiotics and prebiotics? Probiotics are live beneficial bacteria that are introduced directly into the body, whilst prebiotics are fibres that nourish the beneficial bacteria already present in the gut. Combining the two (synbiotics) produces a more sustainable effect.
Are probiotics safe for daily use? Yes, for healthy people; however, those with autoimmune conditions or taking immunosuppressive medication should consult their doctor before use.
How long does it take for the microbiome to recover after a course of antibiotics? Studies suggest that the microbiome begins to recover within weeks, but it may take between six months and a year to regain its full diversity. Taking probiotics during this period speeds up recovery.
Does gut health really affect mood? Yes, the gut produces around 90 per cent of the body’s serotonin, and clinical studies have shown that improving the microbiome reduces symptoms of anxiety and mild depression.
Is eating yoghurt enough to boost the microbiome? Natural yoghurt is beneficial but contains only a limited number of strains. Specialised supplements contain multiple strains in concentrations far higher than those provided by food alone, particularly in cases of obvious microbial imbalance.
Summary
The microbiome is no longer merely part of the digestive system; it has become central to our understanding of overall human health — from immunity and metabolism to skin health, brain health and mood. Scientific research in 2024 and 2025 is accumulating mounting evidence that probiotics and prebiotics are not merely digestive supplements, but precise biological tools that profoundly influence human health.
