Microbial transmission and ecology of human and environmental microbial communities in childcare centers.

Background: Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results: Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Conclusions: This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.