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Study discovers households marked by 'signature' bacteria

Families and roommates share plenty — food, bathrooms, dishes. A study published Thursday adds a less visible but ubiquitous item to the list: bacteria.

Households carry a common community of bacteria, populating surfaces such as doorknobs, counters and floors, and shared by humans and pets alike, the study found. It travels with us like another member of the family and quickly takes over new environments, such as a new home or even a hotel room, with a distinct signature like fingerprints.


The findings, published in the journal Science, could help improve understanding of the role environments play in child development, including conditions like food allergies, the researchers said. They also could suggest applications in forensics, perhaps offering evidence of who has inhabited a home and how recently they left.

The study followed seven families for six weeks, requiring them to constantly swab their household surfaces and themselves. Researchers at the University of Chicago and Argonne National Laboratory, with help from a team at the University of Maryland, College Park, said they were surprised at how quickly the bacterial fingerprint spread. Three of the families moved over the course of the study.


"We leave a unique fingerprint in our homes in less than 24 hours after we move into it," said Jack Gilbert, a microbiologist at Argonne who led the study.

The research was conducted as part of the Home Microbiome Project, a larger scientific effort to explore how microbial communities are shaped by environmental factors. While a lot of research on microbes in the home focuses on how hygiene affects them and how long they survive, the researchers sought to explore what types of bacteria are present over an extended period of time and what shapes any changes.

The 18 research subjects were required to take regular samples from their doorknobs, light switches, floors and counters, as well as their hands, noses and feet. Four dogs and a cat also were included. Sampling involved firmly rubbing a cotton swab on each surface for about 15 seconds each time, said Gilbert, who jokingly added that his family may or may not have been one of those studied.

The samples were carefully packaged and kept in a freezer before being processed using DNA sequencing equipment. Researchers tested for bacteria types they suspected might be present, and then passed the genomic data along to University of Maryland microbiologist Rita Colwell to analyze them further.

Colwell and colleagues at both the University of Maryland Institute for Advanced Computer Studies and the company she founded, CosmosID, have spent the past five years building a massive database of bacteria genomes, along with algorithms that can analyze samples and classify them to a specific degree of confidence. Using the technique on the household samples revealed many different species of known gut bacteria as well as some pathogens that are always lurking but usually harmless, she said.

It also revealed the presence of bacteria that likely could only be found with such a mathematical approach, as opposed to more traditional lab-based techniques like cultures.

"We were able to show the presence of species and strains of enterobacteria that hadn't really been described before," Colwell said.

The data showed some interesting patterns.


All three households that moved over the course of the study caused rapid colonization of their new homes by their own bacterial communities — including one group that moved from a hotel room.

Familial relationships weren't a requirement for shared bacteria — one of the households was made up of a couple and a third roommate who lived in a separate area of the house. The two subjects who were in a relationship had more bacteria in common with each other than with the third person, however.

In one household, when one subject left for several days, the contributions that person would have made to the household surfaces disappeared, suggesting that while it is pervasive, the microbial community is also ephemeral. That could offer a way for forensic analysts to use the decay of a person's bacterial signature to say how long ago they were in a particular environment, Gilbert said.

Overall, the researchers found "evidence for substantial interaction among human, home, and pet microbiota," they wrote in the study. "Such interactions could have considerable human and animal health implications."

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The findings help confirm theories microbiologists have long held but faced difficulty confirming, said Ivan Erill, an associate professor of biological sciences at the University of Maryland, Baltimore County, who was not involved in the research. For example, scientists once wondered whether diet or ancestry determined what type of bacteria was present in mammals' guts, he said — they ultimately determined it was the former.

The study answers a similar question about the relationships among humans, their environments and bacteria, he said. Mathematical approaches like Colwell's could help explore new questions the study poses, such as what happens in a shared environment like an office or dormitory.


"Obviously there's a battle for dominance in that shared space," Erill said. "That's probably something they already have in the pipeline" to study.

The researchers also intend to explore how the bacterial environment affects health, particularly in young children, Gilbert said. It could lead to discoveries about what contributes to food allergies, for example, he said.

"As a child, you have a very malleable and adaptable microbiome that is constantly equilibrating until you reach the signature," Gilbert said. "We don't know the impacts of environments on that microbiome."