What the Research Is Finding

Allergies…one of the most common presentations I see in clinical practice. From the mild to the serious, from food to dust, animal fur, and the ‘general unknown’.

There are growing insights and evidence of the role gut microbes play in allergies. And, as we know, the microbiome plays a huge role in immune regulation – there’s the link 🙂

The gut microbiome is the community of microorganisms that live within the digestive tract. These microbes don’t simply live alongside us. They also produce substances known as metabolites as they interact with the foods and other compounds that pass through the gut.

Allergies are directly influenced by the immune system itself, but substances the microbes that live in our guts produce (metabolites) may affect immune regulation across the body, including in conditions such as asthma, hay fever, and food allergy. In particular, researchers are interested in microbial metabolites because these compounds may help shape inflammation, barrier function, and immune tolerance.

What Are Allergies?

Allergies are adverse immune responses to typically harmless substances, known as allergens. While allergies can involve diverse immune responses, type 2 immune responses that induce acute hypersensitivity mediated by mast cells, eosinophils, and basophils are the major mechanisms underlying allergic disorders. Allergic diseases include atopic dermatitis, allergic rhinitis, food allergies and asthma.

The onset and persistence of allergic disorders are influenced by:

genetic factors
pre-existing illnesses
age
environmental conditions
other lifestyle factors – diet and microbiomes considerably affect the incidence of various allergic diseases in the skin, lung and intestine.

Individuals prone to develop allergic diseases often have impaired and skewed microbial diversification over the first year of life, and this can lead to altered levels of microbial metabolites in the intestine and inflamed tissues.

Did you know – the skin, lungs and intestines possess unique immune systems tailored to their specific needs and microbial exposures?

What the Research Found

A 2026 review published in Experimental & Molecular Medicine examined how microbial metabolites may regulate allergic disease across different parts of the body. Published in February 2026, the review brought together existing laboratory and clinical research examining the relationship between the gut microbiome, the substances microbes produce, and allergic immune responses throughout the body.

The review, Regulation of allergies across the body by microbial metabolites, looked particularly at compounds such as short-chain fatty acids, indole metabolites, and bile acids, and how they may interact with tissue barriers and cells involved in the immune response.

The study reviewed existing laboratory and clinical evidence on gut microbial imbalance and its effects on metabolite production. It focused especially on compounds such as short-chain fatty acids and other immune-active metabolites, which may help strengthen tissue barriers, reduce inflammatory responses, and influence how the immune system reacts to allergens.

Researchers are interested in these metabolites because they may help explain how changes in the gut microbiome could affect the body beyond the digestive system. Metabolites produced or modified in the gut can interact with immune cells and tissues elsewhere in the body, providing a possible connection between gut microbial health and allergic responses affecting areas such as the skin and lungs.

This study suggested that reduced microbial diversity and lower levels of beneficial metabolites may contribute to allergy development or severity.

Therapeutic Approach

Approaches that improve gut microbial health, such as diet-based or microbiome-targeted interventions
Supporting the microbiome in the early years to ensure optimal diversity and richness, limit toxin exposure, and maximize immune development

About Lynn Joels

Lynn has a passion for the health and wellbeing of children, with it being at the heart of her professional life for over 20 years. A fully qualified paediatric naturopath and healthcare professional, she has always worked with the goal of improving the lives of the children and families she has the privilege of supporting.

Learn more about Lynn, her work, and her approach to children’s health and wellbeing on her website

Disclaimer: This information is not intended to be a substitute for professional medical advice, diagnosis or treatment and is for information only. Always seek the advice of your physician or another qualified health provider with any questions about your medical condition and/or current medication. Do not disregard professional medical advice or delay seeking advice or treatment because of something you have read here.

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