Host-Childcare Microbiome Interactions Highlighted by Using Long Read Sequencing

Early-life exposure to microorganisms plays a crucial role in shaping children’s health by instructing immune maturation and modulating the risk of disease development. Most preschool-aged children spend seven to ten hours a day in childcare centers, yet the microbial communities in childcare settings and how they interact with human and human-associated microbiomes have yet to be fully elucidated. A limited number of previous studies have primarily focused on bacterial communities, using amplicon-based profiling methods, largely due to the low biomass of these communities in this built-environment setting. These studies thus omit functional or genetic information and non-bacterial community members. Additionally, none of the prior research has incorporated host-associated phenotypes and microbial profiles to investigate transmission. Expanding upon these efforts, we collected a variety of indoor and outdoor environmental samples from two childcare centers, as well as nasal and oral swabs from 34 participating children aged two to four. We profiled all samples using PacBio full-length 16S rRNA gene and internal transcribed spacer (ITS) sequencing, respectively, for bacterial and fungal community members, and a subset of pooled samples using shotgun metagenomic sequencing including both short- and long-read metagenomics. This approach not only offered enhanced resolution to identify previously unknown aspects of the microbial communities in childcare environments, but also provided additional insight regarding the functional potential in the ecosystem. Current results revealed distinct microbial profiles associated with different host-associated and environmental communities. Most of shared species between host and environmental communities were identified to be specific host-associated ones, including those associated with host food consumption, such as Lactococcus lactis and Streptococcus thermophilus. These results suggest potential microbial transmission and interactions via host shedding. Our work thus expands the understanding of microbial ecology in childcare environments and these communities’ relevance to childhood health. The knowledge gained from this study can allow us to identify potential environmental reservoirs of pathogens, track microbial transmission routes, and develop targeted interventions to benefit early-life human health.