Infant gut microbiome is enriched with Bifidobacterium longumssp. infantis in Old Order Mennonites with traditional farming lifestyle

Abstract

Background: 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. Methods: In a cohort of 65 OOM and 39 Rochester mother-infant pairs, 101 infant stool and 61 human milk samples were assessed by 16S rRNA gene sequencing for microbiome composition and qPCR to quantify Bifidobacterium spp. and B. longum ssp. infantis (B. infantis), a consumer of human 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.

Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition

“…For this cross-sectional study, we recruited a cohort of infants at low risk and those at high risk for allergies, as described before ( 41 ). The low-risk OOM of the Western NY reside in Penn Yan 65 mi southeast of Rochester and were recruited by a nurse midwife among prenatal visits in her clinic.…”

“…Analysis of HMO composition and original data has been previously described by us ( 41 ). In brief, we measured the absolute concentrations of 19 most abundant HMOs (see Supplementary Table 2 ) by HPLC including type 1 and type 2 chains, branching, all types of fucosylation (α1-2, α1-3, and α1-4), which will allow determination of the mother’s Secretor and Lewis status, as well as all types of sialylation (α2-3 and terminal and internal α2-6).…”

“…Results and analysis of human milk and infant gut microbiota has been previously described ( 41 , BioProject accession number PRJNA746977). In brief, genomic DNA from human milk samples was extracted using phenol-chloroform technique.…”

“…One way breastfeeding impacts infant's gut microbiota composition includes human milk oligosaccharides (HMOs), complex glycans that provide the main substrate for infant's gut microbiota, particularly for Bifidobacteria and some Bacteroides (29,30), and HMO compositional differences were detected in children protected against food allergy (31)(32)(33) and IgE-associated eczema (34). In addition, human milk contains microbiota, but the data are conflicting to which extent human milk may act as a source of bacterial species that colonize the infant gut (35)(36)(37)(38)(39)(40)(41). Human milk is also a rich source of short-chain fatty acids (SCFAs) (42), the function of which is unknown.…”

Bifidobacteria-mediated immune system imprinting early in life

“…It is also important to note that this current study does not directly assess health outcomes and benefits of expanded B. infantis or other HMO-metabolizing bacteria but this is inferred from a wealth of previous associations between microbiome development and immunemediated diseases (Arrieta et al, 2015;Vatanen et al, 2016), and a more recent study pointing specifically at B. subsp. infantis associated with a reduced risk of atopy (Seppo et al, 2021).…”