Home life: factors structuring the bacterial diversity found within and between homes

Abstract

Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity of microbial communities change across different locations within the home. Here we examined the diversity of bacterial communities found in nine distinct locations within each of forty homes in the Raleigh-Durham area of North Carolina, USA, using high-throughput sequencing of the bacterial 16S rRNA gene. We found that each of the sampled locations harbored bacterial communities that were distinct from one another with surfaces that are regularly cleaned typically harboring lower levels of diversity than surfaces that are cleaned infrequently. These location-specific differences in bacterial communities could be directly related to usage patterns and differences in the likely sources of bacteria dispersed onto these locations. Finally, we examined whether the variability across homes in bacterial diversity could be attributed to outdoor environmental factors, indoor habitat structure, or the occupants of the home. We found that the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the home can have a direct effect on the microbial communities living on surfaces within our homes. Together this work provides the first comprehensive analysis of the microbial communities found in the home and the factors that shape the structure of these communities both within and between homes.

Figure 1. Differences in mean OTU richness across the locations sampled in each of the 40 homes.

OTU richness was calculated as the number of bacterial phylotypes identified out of 1000 reads per sample. Boxes represent 95% confidence intervals. Bars denote minimum and maximum values excluding outliers.

Figure 2. Principal coordinates plot showing overall variation in bacterial community composition among habitats and homes.

Differences in the composition of the bacterial communities were quantified using the unweighted UniFrac distance metric. Symbols are colored by habitat (sample location) with symbols closer together representing samples with more similar bacterial communities.

Figure 3. Heat map of the mean relative abundances of dominant bacterial taxa across the nine sampled locations.

Each column is colored so that taxa with high relative abundances are red, intermediate relative abundances are white, and low abundances are blue. The dendrogram on the left summarizes the overall degree of dissimilarity (calculated from unweighted UniFrac values) of the bacterial communities in each of the sampled locations relative to each other. The dendrogram was created using mean UniFrac values for each of the sampled locations.

Figure 4. Source tracking analysis showing relative proportion of bacteria at each sampling site associated with given sources.

Values represent median percentages. Warmer colors indicate greater influences of particular sources across the sites. As many of the taxa at a given site could not be attributed to individual sources and some of the sources had more indicator taxa than other sources, these results show changes in the relative importance of individual sources across sites, not comparisons across sources within sites. For example, these results show that soil is a more important source of bacteria on door trims than on cutting boards, but these results cannot be used to directly compare the relative importance of soil versus leaves as sources of bacteria at individual locations.