Your Tiny Roommates: Meet the Microbes Living in Your Home

Every home you've ever lived in has had a population in the billions—and in many cases, that's a good thing

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There’s no such thing as living alone. Never mind if you’re the only person in your house and have no dog, no cat, not even fish. You’ve still got at least several billion roommates—and so do we all. Some of them are harmless, some are actually helpful and some could, in the right concentration and the wrong circumstance, kill you. They are, of course, bacteria, fungi and viruses, and like it or not, they’re on you, around you and deeply within you.

The fact that bacterial life is everywhere is not surprising. It’s something you learned practically from babyhood, every time your mom told you not to drink out of someone else’s glass during flu season. But when mothers say everywhere, even they don’t  know the full meaning of that word. There are the thriving bacteria more commonly found in hot springs that are living in your tea kettle, perhaps migrating to you through the water supply and settling down in the steamiest place possible. There are the underarm bacteria living atop your door frame. And yes, there are the fecal bacteria (maybe not yours) sleeping with you on your pillowcase. Sit with that one for a while.

Increasingly, scientists are coming to appreciate the richness of what’s known as the microbiome, a microscopic—or, in the case of viruses, submicroscopic—ecosystem every bit as complex as the ones found in oceans, rainforests, deserts and woodlands. Your house has a microbiome and so do you. Up to 90% of the cells in your body are organisms that come from outside, though that population represents at most a few pounds of your mass. (Guest cells are much smaller than your own.)

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None of that is necessarily a bad thing. Indeed, much of the time it’s a very good thing. Gut bacteria living in harmony with you can fortify your immune system, help you digest your food, protect you from certain diseases. We need our billions of houseguests, but it would be nice if we could at least get to know them better. To that end, investigators like Rob Dunn, a biologist at North Carolina State University and head of a project called the Wild Life of Your Home, have taken to conducting microbial expeditions through people’s houses and apartments, trying to discover new life forms, identify familiar ones, and figure out which ones live in which niches and why.  Eventually, he’d also like to learn how each species of bacterium affects us—interacting with our own microbial ecosystems and perhaps even joining them in our innards. (Disclosure: I contributed an article to Dunn’s educational website on household microbes, for which I was paid.) In early 2012, I asked Dunn if he would take a census of my household, in Brooklyn, New York.

The sampling kit I received in the mail contained sterile cotton swabs to wipe over six regions, selected because Dunn and his collaborators suspected they would represent several different ecosystems: my computer screen, front door knob, inner doorframe, toilet seat, kitchen counter, and pillowcase. I filled out a questionnaire about myself and my habits, including the cleaning chemicals I use and any allergies I might have. Then I ran the cotton swabs over the specified regions and sent the samples, sealed in plastic vials, to North Carolina.

It took a year before I got my results. (Dunn does a lot of sampling and identifying all the species collected by any one swab can be painstaking work.) The spreadsheet the lab sent me listed more than 1,400 different bacteria, identified by their DNA, and the team arranged the names to display the inhabitants of three places representing the three most common household ecosystems: the kitchen counter (an IKEA butcher block), the doorframe, and the pillowcase.

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On the doorframe, the most abundant bacterial DNA came, surprisingly, from plants. Chloroplasts, the structures that allow plants to draw energy from photosynthesis, were originally free-floating cyanobacteria that took up residence in plant cells, and the cyanobacteria DNA strewn around my apartment are a signature of pollen. I have a slightly heavier pollen load than most, perhaps because of my proximity to Prospect Park, less than a block away.

The other prominent citizens of my door frame, probably having settled there after floating through the air like the pollen, are skin bacteria, including many from the genus Corynebacterium, which includes the diphtheria bacterium. There are also some from the genus that includes the underarm microbes responsible for body odor. In general, the frame’s trend towards skin bacteria is characteristic of apartments, while houses tend to have more soil there. “In apartments you’re losing a lot of this stuff that you would see in a house,” says Dunn, “a lot of the soil stuff goes away, and in some cases it really becomes this whole world dominated by the stuff that falls off of us.”

My pillow, to my delight, was statistically distinguishable from a toilet seat—which is to say skin bacteria outweigh gut, or fecal, bacteria there. But that was by no means a sure thing. Fecal microbes are everywhere, constantly spreading from our nether regions—perhaps carried on our hands, but also perhaps by themselves, since clothes are not a microbe-tight barrier. The ones on my pillow may not even be mine: “You touch the fecal bacteria of strangers ALL THE TIME,” wrote Dunn in an email, with unsettlingly capitalized emphasis. “And so long as you aren’t talking about pathogens, that isn’t actually a big deal.”

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On the butcher block, 40% of the bacteria are associated with plants or produce, which puts me in about the normal range for the kitchen counters the team has looked at so far. The most intriguing find there was something called Hydrocarboniphaga effusa. When I search for it, I turn up a 2004 paper announcing the discovery of this bacterium not too far from where I live, in soil contaminated by a fuel oil leak in New Jersey, where it was happily digesting the spill. What it was eating at my house is not clear. Perhaps it stowed away on a fossil-fuel-based substance, a fertilizer or a pesticide that was contaminating produce I brought in.

Of all the houses the team has so far examined, about 40, I am the only person with H. effusa around. But outlier homes like mine—with a bacterium no one else seems to have—are not unusual. They’re actually very, very common, Dunn says. It’s in the nature of microbes that some sneak in unexplained; a different flavor for everyone.

As creepily fascinating as it is to discover just which microorganisms are living in our homes, there is also hard, perhaps even lifesaving science that can come from it. Our immune systems are highly evolved bacteria-killing machines, but often, we can forge a mutually beneficial truce with the microbes that invade us. Studies have shown that people with Crohn’s disease, for example, have less-diverse gut bacteria than controls, and that mice lacking gut bacteria have higher rates of autoimmune diseases and more immune cells in certain tissues than controls. Biologists hypothesize that the microbes that colonize us might train and toughen the immune system, and in the absence of the right complement of them, autoimmune diseases develop. How each of us acquires our own microbiome—and what the right mix of microbes is—is a subject of much research. Young children’s systems get microbial infusions right from the start, even during birth, when they receive a good dose of the mother’s vaginal microbes, provided they’re not born by Cesarean section. Breast milk is another way of taking in both the germs and antibodies mom is carrying. If this were bad, we’d have evolved a different way.

None of that means you want the rhinovirus a sniffling guest left on your doorknob, the pathogenic e. coli you picked up in a restroom, the salmonella that found its way to your kitchen counter from a package of not-quite-right chicken. It does mean that you live in at least a semi-permeable world, with tiny critters you’ve never heard of—and perhaps science hasn’t heard of either—passing onto you, into you and out of you all the time. The better we understand them, the better we’ll know which ones to ignore, which ones to avoid and, more often than we think, which ones to welcome.

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