Prenatal Indoor Dog Exposure and Early Life Gut Microbiota in the Microbes, Asthma, Allergy and Pets Birth Cohort

Rationale: Early-life indoor dog exposure associates with lower atopy and asthma in childhood and may be related to altered gut microbial profiles among dog-exposed infants. Methods: Pregnant women living with either an indoor dog(s) or living in pet-free homes were recruited in southeast Michigan. Stool samples (n=490) were collected from 131 children at five intervals beginning at 1 week until approximately 18 months of age. 16S ribosomal RNA sequencing was used for stool bacterial characterization; community characteristics were compared between infants born into dog-keeping versus pet-free homes. Mixed effect models were fit for alpha diversity longitudinal trajectory analyses. Compositional differences over time were assessed using the first component from a principle coordinates analysis, again subjected to mixed effect modeling. Results were adjusted for potentially confounding covariates. Results: Richness and Faith’s diversity were higher among children from dog-keeping homes (β±SE=12.9±5.9, p=0.029; β±SE=0.83±0.34, p=0.016; respectively). Following adjustment for household income or breastfeeding duration, associations were diminished and often no longer statistically significant. Longitudinal compositional differences were observed using unweighted UniFrac and Canberra metrics (β±SE=0.039±0.017, p=0.021; β±SE=0.026±0.12, p=0.027; respectively) in unadjusted analyses. However, effects were similarly diminished following covariate adjustment. Conclusions: Infants living with dogs have more rich and diverse early-life gut microbial profiles and distinct overall compositions. However, our data indicate this relationship may be at least partially associative rather than causative. Additional work is needed to determine if specific taxa differ by dog exposure after accounting for confounders, which may not be captured by overall diversity metrics.