“We wanted to know what variables influence the microbial ecosystems in our homes, and the biggest difference we’ve found so far is whether you own a dog,” says Dr. Rob Dunn, an associate professor of biology at NC State and co-author of a paper describing the work. “We can tell whether you own a dog based on the bacteria we find on your television screen or pillow case. For example, there are bacteria normally found in soil that are 700 times more common in dog-owning households than in those without dogs.”
And these microbial differences may be important. For example, it’s known that women who have a dog in the home when pregnant are less likely to have children with allergies. This is a correlation – there’s no known causal link between the presence of a dog and the absence of allergies – but it has been hypothesized that the difference is related to the women’s exposure to a wider variety of microbes. However, to this point there were few data on what the differences in microbial populations might be. While this study doesn’t demonstrate a causal link, it sheds more light on the subject, showing that dogs have a major influence on which microbes are found in our homes.
Citizen scientists in 40 homes sampled nine common surfaces to help researchers determine what kinds of bacteria lived there, and in what relative numbers. The nine surfaces were wiped with sterile swabs from which researchers collected DNA to see which organisms were present. The nine surfaces were the television screen, kitchen counter, refrigerator, toilet seat, cutting board, pillow case, exterior door handle, the trim around an interior door and the trim around an exterior door.
The study found 7,726 phylotypes, or kinds, of bacteria in the homes. The study also found that each of the locations sampled harbored its own unique collection of bacteria. Researchers were able to group the sampled surfaces in the homes into one of three general habitats: places we touch, places our food touches and places that collect dust. For example, the types of bacteria found in refrigerators, on kitchen counters and on cutting boards tended to be similar – because they were primarily linked to our food. Meanwhile, the bacteria found on doorknobs, pillow cases and toilet seats were also fairly similar – and came from humans.
“We leave a microbial ‘fingerprint’ on everything we touch,” Dunn says. “Sometimes those microbes come from our skin, sometimes they’re oral bacteria and – as often as not – they’re human fecal bacteria.”
The research also shows that the difference between habitats is greater than the difference between homes. For example, the bacteria on my pillow case are probably more similar to the bacteria on your pillow case than they are to the bacteria on my kitchen counter.
“This makes sense,” Dunn says. “Humans have been living in houses for thousands of years, which is sufficient time for organisms to adapt to living in particular parts of houses. We know, for example, that there is a species that only lives in hot-water heaters. We deposit these bacterial hitchhikers in different ways in different places, and they thrive or fail depending on their adaptations.”
The researchers are currently processing samples from another 40 homes, and are preparing to process samples from a national survey of 1,300 homes across the United States. The national survey sampled four sites in each home, representing the various habitats.
“The larger sample size will help us better understand the range of variables that influence these microbial ecosystems,” Dunn says. “Does it matter if you have kids or live in an apartment? We expect the microbial populations of homes in deserts to be different from the populations of homes in Manhattan, but no one knows if that’s true. We want to find out.”
The paper, “Home Life: Factors structuring the bacterial diversity found within and between homes,” was published in PLOS ONE May 22. The paper was co-authored by Dunn; Dr. Holly Menninger, director of public science for the Your Wild Life program at NC State; and Dr. Noah Fierer, Jessica Henley and Jonathan Leff of the University of Colorado. The research was supported by the Sloan Foundation and the Howard Hughes Medical Institute. The dataset used for the paper is also publicly available at figshare: http://dx.doi.org/10.6084/m9.figshare.674588.
Note to Editors: The study abstract follows.
Authors: Robert R. Dunn and Holly L. Menninger, North Carolina State University; Noah Fierer, Jessica B. Henley and Jonathan W. Leff, University of Colorado
Published: May 22, PLOS ONE
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.