Microbial jungle

Microbial jungle


Microbial jungle

A recent study has found that humans rapidly infect the spaces in which they live. We leave bacteria by touching surfaces with our exposed skin, and at room temperature, a healthy human kicks up a convective plume of about 37 million bacteria per minute that disperse throughout the home and can survive for extended periods, writes Peter Andrey Smith

On a sunny Wednesday, with a faint haze hanging over the Rockies, Noah Fierer eyed the field site from the back of his colleague’s car. Two blocks east of a strip mall in Longmont, one of the world’s last underexplored ecosystems had come into view: a sandstone-coloured ranch house, code-named Q. A pair of dogs barked in the backyard.

Fierer, a microbiologist at the University of Colorado, Boulder walked across the front lawn and into the house, joining a team of researchers inside. One swabbed surfaces with sterile cotton swabs. Others logged the findings from two humming air samplers: clothing fibres, dog hair, skin flakes, particulate matter and microbial life. Ecologists like Fierer have begun peering into an intimate, overlooked world that barely existed 1,00,000 years ago: the great indoors. They want to know what lives in our homes with us and how we “colonise” spaces with other species — viruses, bacteria, microbes. Homes, they’ve found, contain identifiable ecological signatures of their human inhabitants.

Once ecologists have more thoroughly identified indoor species, they hope to come up with strategies to scientifically manage homes, by eliminating harmful taxa and fostering species beneficial to our health. But the first step is simply to take a census of what’s already living with us, said Fierer. Here’s an undeniable fact: We are an indoor species. We spend close to 90 per cent of our lives in drywalled caves. Yet traditionally, ecologists ventured outdoors to observe nature’s biodiversity, in the Amazon jungles, the hot springs of Yellowstone or the subglacial lakes of Antarctica. As humdrum as a home might first appear, it is a veritable wonderland.

The “built environment” doubles as a complex ecosystem that evolves under the selective pressure of its inhabitants, their behaviour and the building materials. As microbial ecologists swab DNA from our homes, they’re creating an atlas of life much as naturalists like Alfred Russel Wallace once logged flora and fauna on the Malay Archipelago.

Take an average kitchen. In a study published in February in the Environmental Microbiology, Fierer’s lab examined 82 surfaces in four Boulder kitchens. Predictable patterns emerged. Bacterial species associated with human skin, like staphylococcaceae or corynebacteriaceae, predominated. Evidence of soil showed up on the floor, and species associated with raw produce (enterobacteriaceae, for example) appeared on countertops. Microbes common in moist areas — including sphingomonads, some strains infamous for their ability to survive in the most toxic sites — splashed in a kind of jungle above the faucet.

Samples of microbial wildlife

If a kitchen represents a temperate forest, few of its plants would be poison ivy. Most of the inhabitants are relatively benign. In any event, eradicating them is neither possible nor desirable. Fierer wants to make visible this intrinsic, if unseen, aspect of everyday life. “For a lot of the general public, they don’t care what’s in soil,” he said. “People care more about what’s on their pillowcase.” Fierer has teamed up with Rob Dunn, a biologist at North Carolina State University, to sample the microbial wildlife in 1,400 homes across the United States.

The project — known as The Wild Life of Our Home — relies on volunteers who swab pillowcases, cutting boards and doorjambs, then send samples in for analysis. Dunn hopes that the project will begin to unravel the consequences of moving from caves to creating environments around us in a haphazard way. “For the entire history of humanity, we have created environments around us, in our daily lives, in a very unintentional way. The control that we’ve exerted is predominantly one in which we kill the ones that might be bad,” Dunn said. “That’s saved a lot of lives. It’s also favoured this whole suite of species that we know very, very little about.”

In their first study of 40 homes around Raleigh-Durham, North Carolina published recently in the journal PLoS One, they found that humans rapidly “infect” the spaces in which they live. We leave bacteria by touching surfaces with our exposed skin, and at room temperature, a healthy human kicks up a “convective plume” of about 37 million bacteria per minute that disperse throughout the home and can survive for extended periods. Species living outdoors find their way indoors, Fierer and Dunn found.

Outdoor microbes are more frequent in homes with dogs, where fur-associated bacteria were found adhering to TV screens and pillowcases. “My expectation is that the effect of dogs on allergies is similar to the effect of getting your kid playing in the dirt,” Dunn said. “They end up being a surrogate for dirty nature in some ways, one dirty paw at a time.” The data from the 1,400 homes are still being analysed, but the team expects to learn how building materials, ventilation rates and cleaning habits affect the microbial map. “If you’re a vegetarian, do you have different microbes in your house than if you’re an omnivore?” Fierer said. “If you live in a forest, do you have different microbes than if you live in a desert? These are the types of questions that we don’t actually know the answer to. Yet.”

The effort to catalogue the creatures of the great indoors began in 2004, when Paula J Olsiewski, a programme director at the Alfred P Sloan Foundation in New York, sent out a call to examine buildings as a first line of defense against bioterrorism. “If there’s a biological threat,” she said, “you’re probably looking for a needle in a haystack - but what’s the haystack? What’s going on in a building?” No one knows what the natural microbial life of a building should be.

Case of the outliers

We are outliers among species, like leaf-cutter ants or termites, that garden beneficial organisms for their own benefit. “We keep beautiful forests far, far away. Crops that we can eat are far, far away,” Dunn said, adding that our cities are full of waste treatment plants. “An ant would never do that.”

The future of indoor ecology, now in its infancy, hinges on answering questions about what we should intentionally surround ourselves with. “Right now, we don’t understand how buildings work” as ecosystems, said Jordan Peccia, an environmental engineer at Yale. Peccia is examining the link between increased fungal diversity indoors and reduced rates of asthma. Someday, he said, managing indoor biodiversity will run up against traditional concerns about building cost and energy efficiency.

“We’ve seen it as an improvement to make homes more insulated, but maybe that’s a mistake from the standpoint of ecological diversity,” he said. “We’re far from making a quantitative analysis of the trade-off. And once it’s shown, it’s another huge step to convince architects and engineers that this is important enough.”