Infant Gut Microbiome is Enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites With Traditional Farming Lifestyle

Abstract

Growing up on traditional, single-family farms is associated with fewer early manifestations of asthma and possibly other atopic conditions. This study examined gut microbiome and metabolome composition in rural Old Order Mennonite (OOM) infants at low risk and Rochester, NY infants at high risk of atopic conditions.This cohort included OOM mother-infant pairs from the Finger Lakes region of New York State (N = 65) and urban or suburban mother-infant pairs from Rochester, NY (N = 39); most infants were exclusively breastfed.Microbiome composition was evaluated by 16S rRNA gene sequencing of 101 infant stool and 61 human milk samples. Bifidobacterium spp. and B. longum ssp. infantis (B. infantis), a consumer of human milk oligosaccharides, were quantified using quanititative polymerase chain reation. Fatty acids (FAs) were analyzed in 34 stool and 24 human milk samples. Symptoms and diagnoses of atopic conditions were assessed by telephone.At a median age of 2 months, stool was enriched with Bifidobacteriaceae, Clostridiaceae, and Aerococcaceae in OOM compared with Rochester infants. B. infantis was more abundant (P < .001) and prevalent (P < .001) in OOM (70%) compared with Rochester (21%) infants. Stool colonized with B. infantis had higher levels of lactate (P < .05) and several medium-to long or odd-chain FAs (P < .05). Human milk α diversity was similar between the groups. Paired human milk was enriched with a distinct pattern of FAs, including butyrate. At age 3 years, fewer atopic conditions, particularly eczema and food allergy, were reported in OOM children (6.5%) compared with Rochester children (35%, P < .001). Atopic conditions were not associated with B. infantis presence (P = .08), or enrichment of gut or human milk microbiome α diversity.In this small, cross-sectional, pilot study, OOM infants had a high rate of B. infantis colonization, similar to infants in developing countries, and were at lower risk of developing early atopic conditions.OOM infants have a distinct gut microbiome and metabolome composition and fewer early-onset atopic conditions. Prospective examination of the associations in the gut and human milk microbiome and presence of B. infantis in a larger cohort of OOM infants may help to further elucidate the mechanisms of these associations.URL: www.pediatrics.org/cgi/doi/10.1542/peds.10.1111/all.14877