Influence of the gut microbiome on IgE and non-IgE-mediated food allergies

Abstract

Background: The prevalence of food allergy (FA) in children has been increasing in last decade. Recent studies show changes in gut microbiome with FA. However, whether gut microbiome may differ between IgE and non‐IgE‐mediated FA is not defined. The aim of this study is to examine the intestinal microbiome composition in infants with IgE and non‐IgE‐mediated FA and healthy infants. Method: Infants younger than 1‐year‐old, breastfed and diagnosed with FA by a physician were included in the study. DNA was isolated from stool samples of infants with non‐IgE‐mediated FA (n = 25) and IgE‐mediated FA (n = 11) and healthy infants (n = 7). Whole genome shotgun sequencing was applied to identify the composition of microbial DNA (an average depth of 3.1 ± 0.8 million paired end reads and 0.9 ± 0.2 gigabase pairs). Results: There were compositional differences among 3 different groups. Shannon index was significantly higher in IgE‐mediated FA compared to non‐IgE‐mediated FA group (Kruskal‐Wallis test, P = 0.034). Even though β‐diversity was similar, the Sparse Partial Least Square Discriminant Analysis (sPLS‐DA) demonstrated that there were taxa‐level differences among three groups. In species level, Veillonella parvula was in a significantly higher density in healthy infants compared to IgE and non‐IgE‐mediated FA groups. Rahnella aquatilis and Lactobacillus salivarius were significantly lower and Treponema succinifaciens significantly higher in IgE‐mediated FA group compared to other groups. Additionally, Prevotella sp. oral taxon 299 was significantly lower in non‐IgE‐mediated FA group compared to others. Prevotella sp oral taxon 299 was related to mucus in stool whereas urticaria related species were Olsenall uli, Bactreoides thetaiotaomicron, Klebsiella variiocola, Rahnella aquatilis, Treponema succinfaciens, Ethanoligenens harbinenese. Conclusion: Analysis of microbiome differences in FA patients may aid in the understanding of the disease process. The present data suggest that there are compositional variations mostly in species‐ level among infants with FA and healthy ones. Our results suggest that the gut microbiome has a stronger relationship to IgE‐mediated than non‐IgE‐mediated FA. Further functional analysis of the microbiome may help better understand the changes seen in the gut microbiome in FAs and improve our knowledge in the disease etiopathology.