Microbial communities in rural and urban homes and their relationship to surrounding land use, household characteristics, and asthma status

Abstract

The relationships between the microbial communities that develop within homes and local outdoor features, household conditions and respiratory health outcomes are not well understood. In this study, high-throughput bacterial 16S and fungal ITS rDNA sequencing were coupled with a quantitative, GIS-based land use approach in a sample of 95 homes in adjacent urban and rural areas to investigate how local land use features surrounding homes relate to the home microbiome. Bacterial richness was higher in homes surrounded by less development while fungal richness was higher in homes surrounded by more development. Home mycobiomes in less developed areas were enriched with crop-associated taxa whereas in more developed areas human-associated bacterial taxa and wood decaying fungal taxa predominated. Not all vegetation had the same effect on the home microbiome and distinct differences were observed between bacterial and fungal communities, and the distance between home and vegetation. Crops and tree coverage were strongly related to indoor mycobiomes due to the abundance of crop-related taxa and wood decaying taxa, respectively. Regarding asthma, the microbiomes in homes with asthmatic children had greater bacterial diversity and lower fungal diversity compared to homes without asthmatic children. In addition, ‘protective’ taxa were enriched in non-asthmatic homes. The buffer-based approach used for quantitatively categorizing land use and development levels around homes identified specific outdoor environmental factors that affect the indoor microbiomes in urban and rural homes. The study also supports the growing body of scientific evidence that the indoor microbiome can affect health outcomes such as childhood asthma.