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.