Associations between early-life exposures and the infant skin microbiome

Background Factors influencing the early-life skin microbiome, and the association with atopic dermatitis (AD), are relatively unexplored. Objective To evaluate associations with the infant skin microbiome during the first year of life. Methods 3-month-old infants from the Enquiring About Tolerance (EAT) birth cohort were examined for AD at enrolment, 1 and 3 years of age. Parent-completed questionnaires, trans-epidermal water loss (TEWL), and filaggrin mutation status were evaluated. Bacterial swabs were collected from the elbow crease and volar forearm in 148 infants at 3 months and 1 year of age, and the microbiome composition was characterized using 16S rRNA gene sequencing (V3-V4 region). Results Shannon diversity was significantly higher at the forearm compared to the elbow. Staphylococcus, Acinetobacter, and Streptococcus were the most abundant genera across time and body-site. Microbiome community composition was primarily associated with body-site and age (p≤0.001, both). Other significant associations were found with ethnicity (p=0.009), filaggrin status (p≤0.001), urban-vs-rural residence (p=0.005), older siblings (p=0.041), bath product usage at 3 months (p=0.011), but not with pets (p=0.159), systemic antibiotics (p=0.27) nor with bathing frequency (p=0.109). The microbiome was associated with elevated TEWL (3-months p=0.004, 1-year p≤0.001) and with concurrent AD (3-months p=0.027, 1-year p≤0.001). Streptococcus parasanguinis was significantly less abundant in non-lesional skin of infants with AD at 3 months. Conclusion In addition to age and body-site, the infant skin microbiome is associated with heritable factors, the home environment, hygiene practices, and with the presence of AD.