Comparison of dust-based sampling methods for assessing indoor microbial communities in Nunavik dwellings

ABSTRACT While indoor microbiota have been increasingly studied, microbial communities in subarctic and Arctic Canadian housing remain poorly characterized. In this sub-study, we did a methodological comparison of microbial community composition across different dust-based matrices (indoor settled dust, heating and ventilation system filter dust, and activated air) in six Inuit homes of Nunavik, Québec, Canada. Activated air sampling, which involves resuspension of settled dust, remains underexplored in indoor microbiota research and has rarely been compared directly with dust-based matrices using high-throughput sequencing. Fungal biomass was assessed with quantitative PCR (qPCR) targeting the indoor fungal markers Penicillium and Aspergillus spp., as well as the outdoor marker Cladosporium spp. The Environmental Relative Moldiness Index (ERMI) metric was used to assess fungal contamination, and microbial communities were described using high-throughput amplicon-based sequencing of the ITS2 and 16S rRNA genes. Activated air samples exhibited relatively low biomass, preventing the calculation of the ERMI metric. However, house dust and heating and ventilation system filter dust showed similarities in terms of ERMI-species detected. ITS2 amplicon-based sequencing revealed broadly similar fungal communities across the three matrices, whereas 16S sequencing showed that bacterial communities differed more strongly, with activated air enriched in human-associated and transient taxa. This sub-study provides one of the first integrated comparisons of activated air and other dust-based matrices combining ERMI-like assessment with fungal and bacterial high-throughput sequencing. This work highlights the strengths and limitations of dust-based sampling methods and supports the selection of appropriate methodological strategies for indoor microbiota assessment in remote northern housing.