Nature

28
Feb

Mapping the Microbiome

You probably think you know who shares your home. But other than the very largest organisms—your family, your pets, some occasional unwelcome rodents, perhaps the odd earwig or cockroach—the truth is, you really have no idea. For thousands of years, humans have lived indoors, spending the bulk of our time in an environment we built ourselves. And yet, it turns out, we know virtually nothing about the organisms with whom we interact every day, in our living rooms, kitchens, bedrooms, and bathrooms.

Rob Dunn and Noah Fierer are out to change this. Dunn, a biologist at North Carolina State University, and Fierer, an ecologist at the University of Colorado, are cataloging the diversity of our houseguests—those of the microscopic variety. Their project, called “The Wild Life of Your Home,” is exploring the microbial makeup of 1,000 homes around the country.

Kitchen sink faucet
We know little about what microbes live in our homes.

The technology fueling the project is distinctly 21st-century—genetic sequencing at a scale which wouldn’t have been feasible just a couple of years ago—but the questions at its heart are far more basic. “We’re doing 19th-century ecology,” Fierer says. By which he means basic natural history: What are the species that live with us?

“How have they evolved to live here?” Dunn wonders. “What are they doing to us, and how do our decisions affect which ones we’re exposed to?” It’s a series of questions Dunn’s been asking repeatedly in his lab. “Consistently,” he says, “we find we know extremely little about these species. Unless they kill us, we don’t study them.”

Finding New Frontiers

In their search to catalog the invisible world around us, Dunn and Fierer are a bit like modern-day Lewis and Clarks. Except unlike that long-ago duo who traversed the West together, Dunn and Fierer, despite several collaborations, have never met in person.

They have, though, traveled together into America’s biodiversity frontiers. In a pilot project involving 40 homes, their team found three main trends: that the presence of dogs had a big influence on the dominant types of microbes, that frequently cleaned surfaces had lower diversity than their less-clean counterparts, and that microbes living outdoors directly influenced those living indoors.

Not long ago, Dunn surveyed the insects in 50 houses in the Raleigh-Durham area. “In one house,” he says proudly, “we found 50 species of arthropods just in the living room.” That number included one extremely rare species in which “the only way larvae becomes a male is if it eats its own mother.” Dunn says he has not yet told the homeowners.

If we’re that in the dark about housemates we can see, imagine the gazillions of microscopic life forms that might be sharing our beds and cutting boards. “If we don’t know what’s going on with the visible stuff,” Dunn says, “once we get to the invisible, all bets are out the door. So part of what we want to do is get a sense of what the heck is living with us.”

Swabbing for Species

Eager to participate, I signed up for the study, which relies on citizen scientists to collect the data. A few days later, my swabbing kit arrived in the mail: four extra-long Q-Tip-style swabs each encased in its own plastic tube. Following the instructions, I swabbed a kitchen countertop, a pillowcase from my bed, and the tops of the doorframes inside and outside my front door. Then I mailed my embarrassingly dirty—and presumably microbe-coated—swabs to North Carolina.

I also filled out a detailed questionnaire that covered things like how often I vacuum, whether I have pets (and what kind and how many), whether I’ve recently suffered from dry skin or fatigue. That information will help the team begin to understand how microbes affect us—and vice versa.

My samples will eventually come back to Colorado, where Fierer’s lab (which happens to be down the street from my house) will extract the DNA from all 4,000 swabs in the study and run them through DNA sequencing machines. Ultimately, the genetic information will show what groups of microbes are present in each home and at what concentration. The results will show the genus of microbes, though not the exact species, which might prove frustrating for participants hoping to know exactly what’s living in their homes and how good or bad those neighbors might be. Staphylococcus, for instance, is a genus of bacteria that’s common on our skin and around our homes, and many types of staph are completely harmless. But the genus also contains MRSA (methicillin-resistant Staphylococcus aureus), which causes dangerous and potentially deadly infections.

“There’s a disconnect,” Fierer admits, “between what people want to know and the information scientists can give them.” What the researchers can do, though, is start making correlations between types of microbes and practical implications—like, for example, how the presence of certain bugs affects asthma rates.

“Studies show that people with dogs have a lower risk of allergies,” Fierer says. “So now maybe we can show that it’s because they’re exposed to these specific bugs.”

Mapping the Microbiome

The researchers also want to understand regional differences in our microbial neighbors: Is a house in Phoenix, say, filled with different creatures than one in Miami? If you move from Los Angeles to Cleveland, do you take your household microbes with you? And how do our daily actions—the cleaning products we use, for instance—impact our home microbiome?

A study released last year found that in one community in Finland, the plants people grew in their backyards affected their children’s health. When scientists compared the microbes on the skin of teenagers whose yards contained native plants with those whose yards grew nonnatives, they found completely different diversity. What’s more, teens growing up with native plants were at four times lower risk for allergies than their exotic-plant peers. “We’re seeing more and more associations between particular groups of microbes and health issues,” Dunn says.

Over the next few years, he hopes to help unravel and clarify those associations with the ultimate goal of understanding how we can create healthier homes. “We know that some microbial taxa are really drought tolerant,” Dunn says. So in desert houses, he expects to see different groups of bacteria than in wetter environments. That finding could help the team focus on health impacts. Imagine that the abundance of Staphylococcus varies based on local climate (outside, not inside). That could influence the risk of finding a harmful strain of staph that’s resistant to antibiotics. “It tests what we know about where these resistant strains are evolving,” Dunn says.

Once the more mundane environments of our homes are conquered and chronicled, Fierer plans to push on to new frontiers. He wants to know what lives in extreme environments of the domestic variety: your dishwasher, your salt shaker, your soap dish. He’s beginning to sample these places, curious to learn what they’ll yield.

“You don’t have to travel to some alkali hot spot in Kenya to find novel environments,” Fierer says. “They’re mimicked by your dishwasher. The biomass is low, but there might be some interesting diversity.”

Tell us what you think on Twitter #novanext, Facebook, or email.

Hillary Rosner

Hillary Rosner

Hillary Rosner writes about science and the environment for The New York Times, Wired, National Geographic, Scientific American, and many other publications. She lives in Boulder, Colorado.