Diet shapes microbial ecology, yet consequences of this for the immune system are uncertain. Here we report that a high-fiber diet promoted a distinctive gut microbiota and high levels of short chain fatty acids (SCFAs) particularly acetate. This suppressed the development of allergic airways disease (AAD) in adult mice, a model for human asthma. Surprisingly, high fiber feeding of pregnant mice imparted on offspring an inability to respond robustly in AAD models. Similar correlations were seen in humans. The mechanism involved inhibition of histone deacetylases, increased acetylation at the Foxp3 promoter, and effects on Treg biology, as well as Foxp3 target genes expressed in the lung. Thus asthma risk may relate primarily to diet, and have its origin during development.