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.

The ecology of microscopic life in household dust

“…In particular, whether a home had dogs was the most important predictor of the relative abundances of those bacteria preferentially found within homes (electronic supplementary material, table S2). This effect of dogs on indoor bacterial communities has been noted previously [3,20,22] with some work suggesting that these bacterial differences are associated with human health outcomes rspb.royalsocietypublishing.org Proc. R. Soc.…”

“…If there was ever any doubt, it has become clear in recent years that we are exposed to many thousands of bacterial and fungal species as we go about our daily lives [1][2][3][4]. As humans become ever-more urban and we now spend the majority of our lives indoors [5], the time we spend with the microbial taxa found inside homes is increasing.…”

Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

“…The analysis of similarities (ANOSIM) test was performed in PRIMER (v.6; PRIMER-E, Plymouth, United Kingdom) to determine whether the major sample factors (MTR line, MTR line type, indoors/outdoors, time, peak/nonpeak, sampling day) had significantly different microbial communities. UniFrac distance calculations, PCoA, and ANOSIM were also performed to compare microbial communities from our study to indoor samples collected from air and surface samples from previous reports (5,36). These reports were selected because they targeted the same V4 16S rRNA gene region using the Illumina sequencing platform.…”

“…As one of the few large-scale studies investigating aerosol microbial community composition in Asia, we were interested in comparing our subway and outdoor data sets to those of indoor microbiome studies conducted elsewhere. We have chosen studies investigating the bioaerosols of a university building in Oregon (36) and the household surface microbial compositions in North Carolina homes (5). PCoA plots based on weighted UniFrac distances clearly showed that the Hong Kong cluster is distinct from the American groups (global R ϭ 0.34, P ϭ 0.001 by ANOSIM) (Fig.…”

“…Therefore, characterizations of indoor microbial compositions will provide information regarding the nature and extent to which individuals in indoor settings are exposed to microbial life and the breadth of microbial life in which transmission can occur. Given its importance, microbial community assessments have been conducted in numerous indoor air and surface environments (3,(5)(6)(7).…”