Growing up on traditional, single-family farms is associated with protection against asthma in school-age, but the mechanisms against early manifestations of atopic disease are largely unknown. We sought determine the gut microbiome and metabolome composition in rural Old Order Mennonite (OOM) infants at low risk and Rochester, NY urban/suburban infants at high risk for atopic diseases.
In a cohort of 65 OOM and 39 Rochester mother-infant pairs, 101 infant stool and 61human milk sampleswere assessed by 16S rRNA gene sequencing for microbiome composition and qPCR to quantifyBifidobacteriaspp. and B. longum ssp.infantis (B. infantis), a consumer ofhuman milk oligosaccharides (HMOs). Fatty acids (FAs) were analyzed in 34 stool and human 24 milk samples. Diagnoses and symptoms of atopic diseases by 3 years of age were assessed by telephone.
At a median age of 2 months,stool was enriched withBifidobacteria, Clostridiaceae and Aerococcaceaein the OOMcompared toRochester infants. B. infantis was more abundant (p<0.001) and prevalent, detected in 70% of OOM compared to 21% of Rochester infants (p<0.001). Stool colonized with B. infantishad higher levels oflactate and several medium- to long/odd-chain FAs. In contrast, human milk was enriched with a distinct set of FAs including butyrate. Atopic diseases were reported in 6.5% of OOM and 35% of Rochester children (p<0.001).
A high rate of B. infantis colonization, similar to that seen in developing countries, is found in the OOM at low risk for atopic diseases.

This article is protected by copyright. All rights reserved.