A Prospective Microbiome-Wide Association Study of Childhood Food Sensitization and Allergy

Abstract

Alterations in the intestinal microbiome are prospectively associated with the development of asthma; it is unknown whether these differences occur in food allergy. Child intestinal microbiome samples were collected at age 3-6 months in children participating in the follow-up phase of an interventional trial of high dose Vitamin D given during pregnancy. At age 3, sensitization to foods (milk, egg, peanut, soy, wheat, walnut) was assessed. Food allergy was defined as caretaker report of healthcare provider-diagnosed allergy to the above foods prior to age 3 years with evidence of IgE sensitization. Analysis was performed using phyloseq and DESeq2; p-values are adjusted for multiple comparisons. Complete data were available on 225 children; there were 87 cases of food sensitization and 14 cases of food allergy. Microbial diversity measures did not differ between food sensitization and food allergy cases and controls. The genera Haemophilus (log2 fold change -2.10, p=0.003), Clostridium (log2 fold change -1.57, p=0.007), and Dorea (log2 fold change -1.57, p=0.03) were underrepresented among subjects with food sensitization. The genera Oscillospira (log2 fold change -2.85, p=0.02), Citrobacter (log2 fold change -3.40, p=0.02), Lactococcus (log2 fold change -3.33, p=0.03), Dorea (log2 fold change -3.05, p=0.03), and Clostridium (log2 fold change -2.55, p=0.04) were underrepresented among subjects with food allergy. The temporal association between bacterial taxa and food sensitization and allergy suggest that the microbiome may have a causal role in the development of food allergy. Our findings have therapeutic implications for the prevention and treatment of food allergy.