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 Ford Explorer. Two blocks east of a strip mall in Longmont, Colorado, one of the world’s last underexplored ecosystems had come into view: a sandstone-colored ranch house, code-named “Q.” A pair of dogs barked in the backyard.
Fierer, 39, a microbiologist at the University of Colorado Boulder and self-described “natural historian of cooties,” 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 fibers, dog hair, skin flakes, particulate matter and microbial life.
Ecologists like Fierer have begun peering into an intimate, overlooked world that barely existed 100,000 years ago: the great indoors. They want to know what lives in our homes with us and how we “colonize” spaces with other species — viruses, bacteria, microbes. Homes, they have found, contain identifiable ecological signatures of their human inhabitants. Even dogs exert a significant influence on the tiny lifeforms living on our pillows and television screens. 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.
However, the first step is simply to take a census of what is already living with us, Fierer said. Only then can scientists start making sense of their effects.
“We need to know what’s out there first. If you don’t know that, you’re wandering blind in the wilderness,” he said.
Here is an undeniable fact: We are an indoor species. We spend close to 90 percent 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. (“When you train as an ecologist, you imagine yourself tramping around in the forest,” Fierer said. “You don’t imagine yourself swabbing a toilet seat,” he said.)
However, as humdrum as a home might first appear, it is a veritable wonderland. Ecology does not stop at the front door; a home to you is also home to an incredible array of wildlife.
Besides the charismatic fauna commonly observed in North American homes — dogs, cats, the occasional freshwater fish — ants and roaches, crickets and carpet bugs, mites and millions upon millions of microbes, including hundreds of multicellular species and thousands of unicellular species, also thrive in them. The “built environment” doubles as a complex ecosystem that evolves under the selective pressure of its inhabitants, their behavior and the building materials. As microbial ecologists swab DNA from our homes, they are creating an atlas of life much as 19th-century 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 journal 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.
A hotspot of unrivaled biodiversity was discovered on the stove exhaust vent, probably the result of forced air and settling. The counter and refrigerator, places seemingly as disparate as temperate and alpine grasslands, shared a similar assemblage of microbial species — probably less because of temperature and more a consequence of cleaning. Fierer’s lab also found a few potential pathogens, like Campylobacter, lurking on the cupboards. There was evidence of the bacterium on a microwave panel, too, presumably a microbial “fingerprint” left by a cook handling raw chicken.
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,” he added. (Spoiler alert: The microbes living on your pillowcase are not all that different from those living on your toilet seat. Both surfaces come in regular contact with exposed skin.)
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 US. 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. (Full disclosure: I am a volunteer participant in the study, sending in swabs from my home.) 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 favored this whole suite of species that we know very, very little about,” he said.
So little is known of what is in the home that a small sample can reveal something new. In their first study of 40 homes around Raleigh-Durham, North Carolina, published last week 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,” he said.
The data from the 1,400 homes are still being analyzed, 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 asked. “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,” he said.
The effort to catalog the creatures of the great indoors began in earnest in 2004, when Paula Olsiewski, a program 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?” she added.
No one knows what the natural microbial life of a building should be.
The foundation has put up US$28 million for projects to date, including continuing explorations into the microbial ecology of older two-story homes in the northeast, train ticket kiosks in Boston and the opening of a new hospital wing in Chicago. The Hospital Microbiome Project, led by Jack Gilbert of the University of Chicago, began sampling microbes in patients’ noses, armpits, hands and feces in February, along with those taking up residence in the newly constructed nursing stations and 10 patient rooms — a total of 12,000 swabs.
The yearlong investigation will tackle a pressing concern: One in every 20 patients acquires infections in a hospital, to the tune of an estimated 1.7 million infections and 60,000 deaths annually, according to the US Centers for Disease Control and Prevention.
“The whole reason for doing this study is to stop people from dying,” Gilbert said.
His preliminary findings suggest that the longer a patient stays in a given room, the more likely it is to acquire his or her unique microbial signature. The new hospital is being infected by its inhabitants.
“You start to be colonized by bacteria from your mother in the amniotic sac,” Gilbert said. “If you use that as an analogue, we’re looking at the birth of a hospital,” he said.
Another study, published last year in The ISME Journal, found that hospital patients were more likely to encounter potential pathogens in mechanically ventilated rooms than in ones with access to fresh air from outside.
Jessica Green, the study’s author, a theoretical ecologist at the University of Oregon and director of its Biology and Built Environment Center, said she expected buildings to eventually be redesigned with a view toward managing their microbial impact on human health.
Architects and engineers also could try to cultivate benign or beneficial species, favoring certain conditions and altering our chronic, long-term exposure. For example a study last year in Finland found that plant diversity outside was linked to a greater variety of bacteria on human skin inside homes; moreover, teenagers with this increased biodiversity were at lower risk for allergies.
We are different to other species, like leaf-cutter ants or termites, that garden beneficial organisms close by 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,” he said.
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 University.
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,” he said.
We do not have a choice about whether to share our homes with microbes, then, but soon we may have an opportunity to open them up to better company.
Back in Colorado, Fierer talked with Amanda Phillips, 61, who lives at Home Q with her husband, Chester, 67, and their dogs Hunter and Chase. Phillips admitted she did some extra cleaning before the team’s arrival. As she got up to leave, she said she was wary about the effort.
“I don’t know if I really want to know what you’re finding,” she said. “But I’m excited to learn,” she said.
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