What is in the Dust? Species-Level Profiling Reveals Pathogenic and Protective Potential of Microbial Communities in Daycare and Home Environments.

Abstract

Indoor environments are rich in microbial diversity, which is influenced by multiple factors, including human activities, occupancy levels and the presence of pets. Environment-associated taxa were found to be prevalent in daycare and human-associated taxa in home environments during the COVID-19 pandemic, a period marked by profoundly altered social mixing and hygiene practices. In this study, we investigated the structure of microbial communities and their ecological profiles in daycare and home dust in the post-COVID-19 era. Microbial communities in household dust remain more heterogeneous, with a higher prevalence of human-associated species, than daycare samples. Full-length 16S rRNA gene sequencing enabled species-level taxonomic resolution, yet approximately 40% of amplicon sequence variants remained unclassified, underscoring the vast, novel microbial diversity within our indoor environments encountered in everyday life. AI-assisted ecological profiling revealed a higher burden of pathogens and opportunistic pathogens in home environments than in daycares. Interestingly, the presence of pets had limited influence on microbial diversity in household dust. Finally, several species with known probiotic properties and immunostimulatory potential were present in both environments, reinforcing the notion that microbial exposure during the critical window of early childhood may confer protection against various non-communicable diseases including asthma, childhood leukaemia and other cancers.