Environments rich in microbes, such as daycare centres, are thought to affect respiratory health in early life. However, few studies have examined the association between bacterial composition in the indoor environment and respiratory health in children.

We investigated the associations between dust bacterial microbiota in daycare and wheezing in children from the French CRESPI cohort (Respiratory health of Children in daycare).

The composition of dust microbiota was assessed by 16S rRNA gene sequencing of floor dust samples collected in 85 randomly-selected daycare centres in the Paris region. Dust microbiota profiles were determined by a clustering approach (partitioning around medoids, using weighted UniFrac distance). Cross-sectional associations between microbiota profiles and ever wheezing (evaluated by questionnaire in 409 children attending these daycare centres) were assessed using generalized estimating equations to account for daycare centre effect.

The children were on average 23.2 months-old (SD 10.7) at enrolment and 29% reported ever wheezing. Four environmental microbiota profiles were identified: (1) “Streptococcus, Neisseria, Haemophilus and Prevotella” (reference profile, n=49 daycare centres), (2) “Streptococcus and Lactococcus” (n=21), (3) “Mixed with rare (relative abundance <1%) taxa” (n=11) and (4) “Lactococcus-dominant” (n=4). After adjusting for age and the number of children per daycare centre, profile (2) was associated with a higher risk of wheezing (adjusted OR 2.29, 95% CI 1.06–4.96). No association was found for the other profiles.

Our results suggest that the composition of dust microbiota in daycare is associated with the risk of wheezing in early childhood.