Cities Have Their Own Microbial Signatures

The city where an office is located, like Toronto, seems to affect its microbiome more than other factors. (Photo: Shutterstock)

More than half of all humans now live in cities, a habitat that will house two-thirds of our species by 2050. And in developed countries like the U.S., a typical person now spends more than 90 percent of her life inside buildings or vehicles.

Yet despite all our time in built environments, there's still a lot we don't know about these enclosed habitats. They teem with tiny wildlife, for example, like the 100 kinds of bugs living in a typical American house. They're also awash in unseen microbes, which can affect the health of buildings as well as the humans who inhabit them.

Much like every human body has its own array of microbes, known as a "microbiome," so do individual rooms and buildings. These indoor microbiomes are heavily influenced by the microbiomes of people and pets, and vice versa, but they're also part of much broader microbial communities. In fact, according to a newly published study, entire cities have their own microbial signatures.

"This was especially interesting because even within each city, the offices we studied differed from each other in terms of size, usage patterns and ventilation systems," says co-author J. Gregory Caporaso, an assistant professor of biological sciences at Northern Arizona University, in a statement. The fact that city-specific microbiomes were still obvious, he adds, suggests "geography is more important than any of these features in driving the bacterial community composition of the offices."

How much did office microbiomes vary by location? Enough that a computer learning model could guess a city just by looking at its office microbes, the study explains:

"[W]e were able to predict the city of origin of unlabeled samples (where we knew the city of origin but withheld that information from the classifier) with 85% accuracy only on the basis of its microbiome composition."

Flagstaff, Arizona
Researchers found the highest microbial diversity in Flagstaff offices, but aren't sure why. (Photo: Shutterstock)

A tale of three cities

The study's authors spent a year monitoring the microbiomes of nine offices in three North American cities: Flagstaff, Arizona; San Diego, California; and Toronto. They installed three sampling plates in each office, outfitted with swatches of painted drywall, ceiling tile and carpet, as well as sensors to measure environmental variables like available light, occupancy and temperature. These plates were placed on a floor, ceiling and wall in each office, and collected in four six-week periods, one per season. The researchers then used gene sequencing to profile the microbe samples.

"Across all nine offices, human skin bacterial communities were the largest identifiable source of the office bacterial community samples, with at least 25 to 30% of the office surface microbiome being derived from human skin," they write in the journal mSystems. "The human nasal microbiome also appeared to be a small but consistent source of office surface microbial communities."

Those findings fit with another recent study from Brazil, which revealed that urban homes had more microbes typically found in people's mouths and skin, while rural homes more closely resembled the outdoor microbiomes where our ancestors evolved. "Urbanized spaces uniquely increase the content of human-associated microbes," that study reported, "and decrease exposure to the environmental microbes with which humans have co-evolved."

San Diego skyline
For some reason, microbial diversity in San Diego offices was more like Toronto's than Flagstaff's. (Photo: Shutterstock)

Small business

Despite the clear human impact on indoor microbiomes, the researchers note that office workers' personalized microbiomes were not transferred to office surfaces. (Probably because workers were asked not to touch the sampling plates directly, letting them record office-wide microbial signatures rather than localized effects of direct contact.) Instead, office microbiomes seem to be a blend of microbes from people, especially our skin, and from various nonhuman outdoor sources.

The Flagstaff offices had richer microbial diversity than San Diego or Toronto, the researchers write, although it's unclear why. And while a study of three cities offers only a hint of how urban microbiomes work, it adds to a growing field of research that's shedding vital light on the tiny neighbors and co-workers all around us.

"We suspect that in the absence of extreme conditions like flooding, microbes may be passively accumulating on surfaces in the built environment rather than undergoing an active process," Caporaso says. "As we continue to expand our understanding of the microbiology of the built environment, possibly including routine monitoring of microbial communities to track changes that may impact human health, our results will help inform future research efforts."