Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization

Background: Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance. Objective: We sought to determine whether bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children. Methods: We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, before their developing allergic disease. Results: We found that the microbiome of infants who went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production. Conclusions: Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against the development of allergies.