Characterizing bacterial and fungal communities in childcare environments: a study overview

Indoor environments harbor diverse microbes to which occupants are constantly exposed. Exposure to environmental microbes has been shown to have both negative and positive health impacts, particularly relating to children’s immune maturation during early development. Many preschool-aged children spend 7 to 10 hours per day in childcares, almost as much as at home, yet the environmental microbes associated with childcares have yet to be fully elucidated.
The first component of this study is to characterize viable microbial communities in the childcare environments. While high-throughput sequencing provides powerful methods for surveying microbial communities, it remains challenging to differentiate biochemically active (“viable”) microbes that are often outnumbered by their “dead” counterparts in the built environment (BE) due to its unusual chemical makeup. Critically, the functions of a microbial community are defined by these viable microbes, therefore, the distinction of microbial viability is essential for understanding indoor microbial impacts on occupant health. To date, few studies could reliably distinguish viable community members, which hinders the interpretation of health implications. Here, we will use paired metagenomics and metatranscriptomics to characterize viable BE microbial communities, including functional molecular mechanisms responsible for microbial persistence and antimicrobial resistance burden in childcare environments.
The second component of this study is to identify indoor fungal communities with higher resolution using full-length internal transcribed spacer (ITS) amplicon sequencing. The traditional fungal identification marker ITS ranges from 500-1200 base pairs in size, which cannot be sequenced as a single DNA fragment with short-read sequencing. There have been controversies in the selection of ITS1 or ITS2 (both are subregions of the full-length ITS) for sequencing, and using either alone often results in lower taxonomic resolution, higher proportion of unidentified taxa and greater extent of underclustering. This study will utilize the single molecule real-time (SMRT) technology from Pacifici Biosciences to sequence the full-length ITS region. Here will also include substantial full-length ITS reference database curation and evaluation to improve our fungal taxonomic resolution.