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. OBJECTIVES: To evaluate associations with the infant skin microbiome during the first year of life. METHODS: Three-month-old infants from the Enquiring About Tolerance (EAT) birth cohort were examined for AD at enrolment and at 1 and 3 years of age. Parent-completed questionnaires, transepidermal water loss (TEWL) and FLG mutation status were evaluated. Bacterial swabs were collected from the elbow crease and volar forearm from 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 with 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 for both). Other significant associations were found with ethnicity (P = 0.009), FLG status (P ≤ 0.001), urban vs. rural residence (P = 0.005), older siblings (P = 0.04) and bath product use at 3 months (P = 0.01) but not with pets (P = 0.16), systemic antibiotics (P = 0.27) or bathing frequency (P = 0.11). The microbiome was associated with elevated TEWL (P = 0.004 at 3 months and P ≤ 0.001 at 1 year) and with concurrent AD (P = 0.03 at 3 months, P ≤ 0.001 at 1 year). Streptococcus parasanguinis was significantly less abundant in the nonlesional skin of infants with AD at 3 months. CONCLUSIONS: 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. An author video to accompany this article is available online.