Gut Microbiota Influence on Atopic Diseases

The gut microbiota plays a pivotal role in the development and regulation of immune responses implicated in atopic diseases, including eczema, atopic dermatitis and chronic urticaria. A balanced microbial community supports maturation of mucosal immunity, promotes regulatory T-cell function and generates metabolites—most notably short-chain fatty acids—that strengthen barrier integrity and suppress inflammatory cascades. Conversely, dysbiosis characterised by reduced microbial diversity, loss of key commensals and overgrowth of conditional pathogens is linked to heightened IgE-mediated reactions, increased gut permeability and systemic inflammation. Early-life colonisation patterns, shaped by mode of delivery, antibiotic exposure, diet and sibling or pet contact, establish long-term microbial ecosystems that can predispose to or protect against atopic manifestations. Understanding these interactions has global relevance: microbial modulation through diet, prebiotics, probiotics or faecal microbiota transplantation offers promising avenues to prevent or ameliorate atopic disease burden and to personalise therapeutic strategies across diverse populations.

Research from Nature Portfolio

Recent studies have uncovered distinctive microbial and metabolic alterations in chronic spontaneous urticaria. Patients exhibit low gut bacterial diversity, elevated Klebsiella pneumoniae abundance and diminished production of short-chain fatty acids. In murine models, transplantation of urticaria-associated microbiota or Klebsiella alone amplified IgE-dependent mast cell activation, increased intestinal permeability and promoted skin inflammation, whereas supplementation with a butyrate-producing commensal reduced these effects. In paediatric atopic dermatitis, investigation of probiotic persistence revealed that key short-chain fatty acid–producing taxa remain depleted despite supplementation, while markers of dysbiosis—such as increased Faecalibacterium and Oscillospira—persist. These findings highlight both the causal role of specific bacterial strains in driving cutaneous inflammation and the challenge of achieving durable microbiota restoration in atopic conditions.

Gut Microbiota Influence on Atopic Diseases publication trend

The graph below shows the total number of articles in gut microbiota influence on atopic diseases across all publications each year (not limited to Nature Index journals).

Technical terms

Dysbiosis: An imbalance in the composition or function of the gut microbiota that can promote inflammatory and allergic responses.

Short-chain fatty acids (SCFAs): Metabolic by-products of bacterial fermentation (e.g., acetate, propionate, butyrate) that support gut barrier integrity and regulate immune cell activity.

IgE: Immunoglobulin E, an antibody isotype central to allergic sensitisation and mast cell activation.

Mast cells: Immune cells that release histamine and other mediators upon IgE-dependent activation, driving immediate hypersensitivity reactions.

Regulatory T cells (Tregs): A subset of CD4+ T cells that suppress excessive immune responses and maintain tolerance to self and benign antigens, including commensal microbes.

References

1. Microbial network signatures of early colonizers in infants with eczema. iMeta (2023).
2. Gut microbiota facilitate chronic spontaneous urticaria. Nature Communications (2024).
3. A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs. Microbiome (2023).
4. Microbiome and Allergic Diseases. Frontiers in Immunology (2018).
5. Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture. Scientific Reports (2019).
6. Gut Microbiota, Probiotics, and Their Interactions in Prevention and Treatment of Atopic Dermatitis: A Review. Frontiers in Immunology (2021).