D1.280 - Microbiome Signatures Associated with Food Allergy Resolution in Children

The mechanisms underlying symptom resolution and persistence in pediatric food allergy (FA) remain poorly understood. Emerging evidence suggests that microbial factors may play a key role in immune tolerance. This study aimed to identify microbiome characteristics associated with symptom resolution and persistence of FA in children through analysis of serum-derived microbial extracellular vesicles (EVs).

Twenty-nine children with FA and 29 age-matched healthy controls were enrolled. Serum samples were collected at diagnosis and during follow-up, and subjects were classified into persistent or resolving groups based on clinical outcomes. EVs were isolated from serum, and DNA extracted from the V3–V4 regions of the 16S rRNA gene was sequenced. Microbial community composition was assessed using Amplicon Sequence Variants (ASVs). Alterations in microbiome characteristics at diagnosis and follow-up were compared according to resolution status. Paired comparisons and similarity percentage (SIMPER) analysis were performed to assess differences between persistent and resolving groups. Correlation analysis was conducted to examine relationships between microbial changes at diagnosis and follow-up. Clustering analyses were performed using Bray–Curtis and Jensen–Shannon distance matrices. PICRUSt2 was used for functional pathway prediction.

Faecalibacillus and Intestinimonas showed increased abundance in the resolving group, whereas Haemophilus and Neisseria declined from diagnosis to follow-up. A distinct microbial cluster (Cluster 2), characterized by enrichment of Parabacteroides and Coprococcus and depletion of Veillonella, was commonly observed in both the resolving group and healthy controls. In the SIMPER analysis, most of the microbiota, including Haemophilus, Neisseria, Parabacteroides, Coprococcus and Veillonella, contributing to the differences between the persistent and resolution groups were intercorrelated in their changes observed at diagnosis and follow-up. Functionally, PICRUSt2 predicted increased short-chain fatty acid (SCFA) production and anti-inflammatory pathways in the resolving group. 

Symptom resolution in pediatric FA is associated with distinct serum EV-derived microbiome signatures, characterized by enrichment of tolerance-linked taxa (Parabacteroides and Coprococcus) and metabolic pathways related to SCFA production. Conversely, persistence is linked to enrichment of Haemophilus, Neisseria and Veillonella. These findings suggest that circulating microbial EVs may contribute to the acquisition or failure of immune tolerance in children with FA.