The enteric DNA virome differs in infants at risk for atopic disease.

Enteric bacteriophage communities significantly differed by farm-life versus urban lifestyle at six weeks and six months of age, but not at 12 months.

• Study analyzed the enteric virome in 131 infants from high-atopy-risk urban/suburban environments and low-atopic-risk single-family farming communities.
• Significant differences in phageome communities were observed at six weeks and six months of age between farming and urban infants.
• By 12 months of age, the enteric bacteriophage communities were similar between the two lifestyle groups.
• The farming lifestyle is described as traditionally protective against atopic disease including atopic dermatitis, food allergy, asthma, and allergic rhinitis.

A farming lifestyle protective from atopic disease demonstrated higher colonization rates of Bifidobacterium longum subsp. infantis (B. infantis).

• B. infantis is described as 'an important beneficial commensal.'
• Phageome communities differed in infants colonized by B. infantis at all time points studied.
• The association between B. infantis colonization and phageome differences was observed across six weeks, six months, and 12 months.

Mastadenovirus and Bocaparvovirus were more prevalent in urban infant stools at six months of age.

• These eukaryotic viruses were found at higher prevalence in urban infants compared to farming infants.
• The difference in prevalence was specifically observed at the six-month time point.
• Urban infants were from high-atopy-risk environments, while farming infants were from low-atopy-risk single-family farming communities.

Sparser phage-phage networks were found at all time points in infants who later developed atopic disease.

• Phage-phage network analysis was conducted across all three time points: six weeks, six months, and 12 months.
• Infants who later developed atopic disease consistently showed sparser phage-phage interaction networks compared to those who did not develop atopic disease.
• This finding spans all time points examined, suggesting an early and persistent difference in virome network structure associated with atopic disease risk.

The influence of the early enteric virome on atopic disease development had not previously been characterized, representing a gap in knowledge.

• While established epidemiologic connections exist between childhood respiratory viral infections and the infant gut bacterial microbiome with allergic disease development, the influence of the early enteric virome was described as 'unknown' prior to this study.
• Atopic disease prevalence 'has risen dramatically in industrialized countries.'
• Traditional, single-family farming lifestyles protect against atopic disease, 'but the mechanisms are incompletely understood.'