3
SEEING IN THE DARK
We stopped looking for monsters under our bed when we realized that they were inside us.
—CHARLES DARWIN
MY QUEST TO UNDERSTAND the life in houses has its roots in the rain forest. When I was an undergraduate student, I spent part of my sophomore year at La Selva Biological Station in Costa Rica. I was working with Sam Messier, a graduate student from the University of Colorado, Boulder, who was studying the termite species Nasutitermes corniger. Worker termites eat dead wood and leaves of the forest, foods full of carbon but low in nitrogen. To compensate for the nitrogen missing from their diet, the termites host bacteria in their guts able to gather nitrogen out of the air. Colonies of these worker termites and their queens, king, and babies are defended by soldiers with long nose cannons that expel a kind of turpentine on their enemies, primarily ants and anteaters. The nose cannons of these soldiers are so long that the soldiers are unable to eat on their own and so they must rely on nutrients given to them by workers or gathered from the air by bacteria. Some Nasutitermes corniger colonies have many of these needy, dependent soldiers, whereas others have few. Sam wanted to know whether colonies produced more soldiers after having been repeatedly attacked by anteaters. There was an easy way to test Sam’s hypothesis: simulate the effects of an anteater attack on some termite nests and not on others. This simulation was to be my job. I had a machete and would go termite nest to termite nest, day after day.
For the young boy still lurking in my twenty-year-old self, this job was great. I got to wander a trail hacking at things with a machete. For the young scientist in me, it was far better. While working, I talked to Sam about science until she tired. At lunch and dinner, I talked to other scientists until they tired. Then, when there was no one left to answer questions, I walked. At night, I walked paths with a headlamp, a flashlight, and a backup flashlight.1 The night forest was full of the sounds of life and the smells of life, but the only things that could be seen were those revealed by the light. It was as if the light, in revealing species, also created them. I learned to tell the difference between the eye shines of snakes, frogs, and mammals. I learned to recognize the silhouettes of sleeping birds. I learned to look patiently at leaves and bark where giant spiders, katydids, and insects that mimicked bird feces lurked. Some nights, I convinced a German bat scientist to take me netting for bats. I hadn’t been vaccinated for rabies. He didn’t care. I was twenty, I didn’t care. He taught me how to identify the bats. I learned the nectar feeders, the insect feeders, and the fruit feeders. I encountered the giant, bird-eating Vampyrum spectrum, so big it would rip a hole right through the net. My observations, however anecdotal, allowed me to begin to come up with my own hypotheses. I fell in love with the idea that most of what was understandable was not yet understood. I fell in love with discovery, with the way in which the unknown could be revealed with patience under nearly any log or leaf.
By the end of my stay in Costa Rica, I’d helped Sam show that the termite colonies were able to make more soldiers when bothered more often with a machete.2 That was the end of the study, but not of the influence of the experience on me. I spent much of the next decade in Bolivia, Ecuador, Peru, Australia, Singapore, Thailand, Ghana, and elsewhere, moving in and out of tropical forests, threading through them as though I was trying to sew together some big picture. I’d return to the temperate zone, to Michigan or Connecticut or Tennessee, and then someone would offer me an opportunity—a free plane ticket, a mission, and all the beans and rice I could eat—and I’d suddenly find myself once more in the jungle. In time, I found the same kinds of discoveries and joys I associated with the rain forest in other realms, be they deserts or temperate forests. I even began to find them in backyards. This shift to backyards started when a new student, Benoit Guenard, joined my lab. Benoit is fascinated by ants. When Benoit arrived in Raleigh, he searched the forests for ants, ceaselessly. He turned up a species neither he nor I could identify. It was an introduced species, the Asian needle ant, Brachyponera chinensis.3 The Asian needle ant had become common in Raleigh without anyone really noticing. In studying this ant, Benoit realized it exhibited behaviors never before seen in insects. For example, when one forager finds food, rather than lay a pheromone trail for others to follow, she returns to the nest, grabs another forager, carries her to the food, and throws her down upon it: “Here, food!”4 Benoit went to Japan to study the Asian needle ant in its native range. Once there, he found a totally new species of ant, related to the Asian needle ant, common but unnoticed across much of southern Japan, including in and around cities.5 These discoveries were just the beginning.
At about this time, back in Raleigh, a high school student, Katherine Driscoll, came to the lab. Katherine wanted to study tigers. I didn’t study tigers, and so Benoit and I told Katherine to go search for and study Discothyrea testacea, “the tiger ant.” What we didn’t tell Katherine was that we had just made up the name “tiger ant” and that no one had ever found a living colony of these ants. Katherine went off looking. I imagined she would get distracted as she searched and find something else on which to focus. Instead, Katherine found the “tiger ant”; not only that, she found it in the soil behind the building that houses my lab and office. She was, at the age of eighteen, the first person to ever see a Discothyrea testacea, “tiger ant” queen alive.6 Soon, we started to engage even younger students in helping us to sample ants in backyards, but no longer just in Raleigh.7 We made kits that allowed kids across the United Stated to sample ants in their backyards. When we did, the rate of discovery accelerated even more. An eight-year-old discovered that the Asian needle ant was found in Wisconsin. Another eight-year-old found it in Washington State. No one knew it had spread anywhere beyond the southeastern United States.
This work engaging kids in the study of backyard ants precipitated a change in the lab. We began to involve the public more often in helping us to make discoveries. At first it was tens of people, then hundreds, and soon thousands of people looking where they lived for discoveries. By following these discoveries—discoveries we were making with the public—we eventually began to study the life indoors. It was thrilling to work with people to find new species and behaviors in backyards in no small part because those discoveries were immediate to people’s daily lives. We were reminding people of the mystery that remained in the world around them. We were, I hoped, offering a little of the thrill that I experienced when I was twenty in Costa Rica but that I might have also experienced where I grew up in Michigan if I’d known there were still discoveries left to be made. It would be even more exciting, we thought, for the people we worked with to find new species, behaviors, and other discoveries where they actually spend most of their time: in the wilderness indoors.
Most studies of indoor life focused on pests and pathogens, so it was easy to imagine that other species might have been overlooked. At the time, scientists had done individual studies here and there on interesting, nonpathogenic, and nonpest species in homes (such as the work on Thermus scotoductus bacteria in hot water heaters), but these were one-offs, small studies rather than larger dedicated works. There was no field station directed to the study of, well, the inside of the field station. I assembled a team to study houses, a team that has continued to grow ever since, a team that includes scientists around the world and the public—adults, families, kids. Together we would seek Leeuwenhoek’s exhilaration, the exhilarating madness of the possible. We were nearly ready. But there was still one trick, figuring out where to start and how to see. We decided to start with bacteria. I’d been interested in the bacteria in nests since my work with Sam Messier on the Nasutitermes termites—and what is a house if not a big nest? It seemed likely that it was among bacteria and other microbes, species invisible to the naked eye, that the biggest discoveries would be made. But to study these species we were going to need more than a microscope with a single lens. Times had changed. This is where Noah Fierer, a microbiologist at the University of Colorado, Boulder (in the same department where Sam Messier was a graduate student), came in. Noah provided the tool through which we would see the life inside homes. He could identify the species present in dust on the basis of their DNA; he could sequence the life in dust and in doing so reveal the invisible life we walk through and breathe.8
By training and inclination, Noah is a soil microbiologist. He is fascinated by soil; in it, he finds the same wonder I find in jungles, a way to lose himself in discovery. Fortunately, he can also be intrigued (or maybe distracted is the better word) by life elsewhere, so long as it isn’t bigger than a fungal spore. Start talking about an ant or a lizard and Noah’s eyes glaze over. Regardless of the habitat in which he is studying small life, Noah has a genius, like Leeuwenhoek’s, for using a common tool in new ways. Leeuwenhoek is often said to have invented the microscope, which isn’t true. Nor is it necessarily even true that Leeuwenhoek had particularly special microscopes. Instead, what was special about Leeuwenhoek’s microscopes was Leeuwenhoek. In the same way, what is special about Noah’s investigations is not that he has great devices for decoding the identity of microbes in samples (though he does); it is the way he uses these devices and techniques to see what others have missed. Noah would identify the species present in samples from homes by sequencing the DNA present in those samples. Noah and members of his lab would extract the DNA from each sample, make more copies of that DNA using the enzymes from Thermus aquaticus (or, by then, some other thermophilic microbe), and then decode the genetic sequence of particular genes common to all of the species in the sample. In doing so, he could reveal not only those species that scientists know how to culture but also those that no one can. Together with the public and Noah, we would be able to detect everything, living or dead, dormant or dividing, in homes.
Our plan was to enlist the public to help us sample the dust from ten habitats in each of forty houses using cotton swabs. The houses would all be in Raleigh, North Carolina, the city in which I lived and live. We needed to start somewhere and we knew so little about the indoor environment that Raleigh was as good a place as anywhere. We chose to sample refrigerators—not the food in them but instead the growth alongside the food. We sampled the dust on door frames, both inside homes and outside. We sampled pillowcases on beds, also toilets and door knobs, and kitchen counters too. Rather, we had the participants sample all of these places.
We sent each participant9 the cotton swabs that they were to use to sample the habitats in their homes. The dust on the used swabs would contain what Hannah Holmes has called “fragments of a disintegrated world”: bits of paint, clothing, snail shell, couch fibers, dog fur, shrimp shell, marijuana residue, and skin. The dust would also contain bacteria, living and dead.10 The participants would then seal the swabs in airtight tubes and send them to Noah’s lab, where nearly every bacterial species in each and every dust sample would be identified. Noah’s lab would be the light through which we saw the hidden life in dust.
I’M NOT SURE what Noah expected from this survey of houses, but I can tell you what was known in the scientific literature when we began, what had been learned since the work of Leeuwenhoek in the 1600s. Beginning in the 1940s, studies had shown that bodily bacteria can be found around houses. Bodily bacteria thrive in the places humans spend more time, especially those places they touch with their naked skin, be they toilet seats, pillowcases, or remote controls. These studies focused on discovering problem species, the fecal bacteria in the cauliflower and the skin pathogen on the pillowcase, and their eradication. Anything that wasn’t worrisome wasn’t of much interest. More recent studies from the 1970s revealed other kinds of species in homes: Thermus in water heaters and unusual bacteria lurking in drains, for example. These newer studies hinted at the possibility that we might find many new life-forms as we explored homes. We did.
Across the forty houses, we found nearly eight thousand kinds of bacteria, roughly as many bacterial species as there are species of birds and mammals in all of the Americas. The species we encountered were not just well-known species from human bodies but also many other life-forms, some of them very unusual. We turned over the metaphorical leaves of forty houses and beneath them found a wilderness. Many of the species didn’t match up with anything yet known to science. They were new species, or even new genera. I was ecstatic, back in the jungle again, albeit the jungle of everyday life.
We decided to engage more participants to sample more houses. It took a while, but we were able to convince the Sloan Foundation, which had by then begun an ambitious effort to fund studies of the life in homes, to pay for a broader study. We also persuaded an additional one thousand people across the United States to swab four sites in their houses.11
In samples from those one thousand houses, we once more identified the bacteria. One might expect that we would have seen, in this second set of houses, species similar to those we saw in Raleigh. We did, to some extent. Many of the species found in Raleigh could also be found in Florida houses and even Alaska houses. But we also found species that were not seen in Raleigh, new species in each house and in each region. We saw, in total, some eighty thousand kinds of bacteria and archaea, ten times more than in the first sample of Raleigh.
The eighty thousand species we found included species from nearly all the most ancient branches of life. Species of bacteria and archaea are grouped into genera which are grouped into families which are grouped into orders which are grouped into classes which, in turn, are grouped into phyla. Some phyla, while ancient, are very rarely encountered. Yet, in homes, we found nearly all of the bacterial and archaeal phyla so far known on Earth. We found phyla that, a decade earlier, were not even known to exist, and we were finding them on pillows or in refrigerators. Here, then, was a humble moment amid the grandeur of life on Earth and in life’s history. To really make sense of the life in our homes, we would need to study, in detail, the natural history of tens of thousands of species. (We aren’t there yet; we won’t be for decades.) But even before we attempted that, we began to see broad patterns, ways of grouping this mass of life to make it a little more intelligible.
Some of the bacterial species we found in homes were those that had already received some attention: bodily bacteria. But most of these species were not pathogens but instead detritivores, living off the awkward reality that our bodies are slowly falling apart even while we are alive. We leave a cloud of life everywhere we go. As we wander through our homes, our skin flakes off in a process called desquamation. We all fall apart at a rate of about fifty million flakes a day. Each flake floating through the air has thousands of bacteria living and feeding on it. Riding their skin flake parachutes, these bacteria fall from us like a steady snow. We also leave bacteria on the bits of bodily fluids—saliva and more—and feces deposited here and there. As a result, the places where we spend time in our homes bear the marks of our presence. Every place we put our bodies in every house we have ever studied offers microbial evidence of lives lived.12
That we leave bacteria in our wake is not surprising. It is inescapable and largely harmless, or at least harmless in settings in which modern waste treatment facilities and a supply of “clean” drinking water (we will return to just what that means later on) are available. The vast majority of species that you or someone else leaves on a chair when you sit down are beneficial or benign species that, for a brief moment of time, eat whatever bit of you has fallen off, before dying. They are gut bacteria that help you digest your food and that produce necessary vitamins. They are skin bacteria that grow all over your body and help you fight off pathogens. They are armpit bacteria that help your body fight off pathogens when they arrive on your skin. Hundreds of studies have now considered this trail of microbes we leave wherever we go. You see these studies in the news. Human bacteria are found on cell phones, on subway poles, and on door handles. They are found everywhere we go in proportion to population density. They always will be and that is fine.
In addition to the species associated with the falling apart of our bodies, we also saw species associated with the decay of our food—rot. These species were, unsurprisingly, most abundant in the refrigerator and on cutting boards, but they were elsewhere too. One of the samples taken from a television was composed almost entirely of food-associated bacteria. Sometimes we are left to guess at what a sample like that means. Science is full of enigmas.13 Regardless, if the species that rot our food and live off of the slow decay of our bodies were the only species we found in houses, it would have been scientifically unremarkable, akin to going to Costa Rica and “discovering” that the rain forest contains trees. But the microbes of bodies and rotten food were not the whole story, not hardly.
As we looked in more detail, we found other kinds of microbes, bacteria and archaea like those for which Brock might have searched, extremophiles, species that “love” and thrive in extremes. For an organism the size of an archaeon or a bacterium, your home contains incredible extremes. Most of these extremes are new habitats we have unintentionally invented. Homes contain refrigerators and freezers that can get as cold as the coldest tundra. They contain ovens hotter than the hottest desert and, of course, hot water heaters as hot as hot springs. But homes can also include very acidic conditions, such as in some foods (like sourdough bread starters), and very alkaline (basic) conditions, such as in toothpaste, bleach, and cleaning products. In these extremes of homes, we found species once thought to live only in the deep sea, on glaciers, or in remote salt deserts.
The soap dispensers in dishwashers appear to be a unique ecosystem filled with microbes able to survive hot conditions, dry conditions, and wet conditions.14 Stoves contain bacteria able to live in extreme heat. Recently, one species of archaea has even been found to survive in autoclaves, the superhot devices used to sterilize equipment in laboratories and hospitals.15 Long ago, Leeuwenhoek showed that pepper can contain unusual life-forms. We found salt does too. Freshly purchased salt contains bacteria typically found only in salt flats out in deserts and areas that were formerly oceans. Sink drains contain a mix of species seen nowhere else that includes both bacteria and tiny drain flies, whose larvae feed on the drain bacteria. (You see drain flies often, probably without realizing it. Their wings make a heart shape and each wing is patterned with what looks like lace.) The pipes of showerheads—pipes that get dry, then very wet, then dry again—are covered in films of unusual microbes seen typically in swamps. Such new ecosystems are often physically small. In addition, the niches of their species are often narrow. The species often require very particular conditions. As a result, they are easy to miss, just as species with narrow niches can be easy to miss outdoors as well. That “tiger ant” that Katherine found, for example, is hard to find because it lives only in the egg cases of spiders, spiders that hide their egg cases underground.
Nor was the life in extreme habitats the last big discovery we found in homes. There was something else: a set of species in some but not all homes, species that, though not always common, accounted for much of the total biological diversity we found. These were species associated with wild forests and grasslands, typically found in soil, on the roots of plants, on leaves, and even in the guts of insects. This wild biodiversity was most common on outer door sills, then on inner door sills, and then it turned up here and there in other habitats in some (but not all) houses. These species may be living in the air on the bits of soil and other substances on which they have come in. They may be quiescent, waiting for just the right food, or they may be dead. Just which of these outdoor species drift indoors seems to depend on what is outdoors. The wilder the life outside a house, the wilder the life drifting through the air and settling on the doors is.16 It would be easy to think of these drifting wild species, the flotsam and jetsam of homes, as irrelevant trespassers. Easy but very wrong.
LET’S PAUSE HERE before I tell you the stories of the individual species you are breathing in right now and the stories of what happens in houses with lots of outdoor bacteria and the stories of the rest of life (the arthropods, the fungi, and more). Let me first put what we are finding in homes in a little bit more context. To really make sense of what is living with you in your home, you need to consider it relative to a longer history, the history of homes.
For most of human prehistory, we slept in nests built of sticks and leaves. We can infer this on the basis of the lives of modern apes. We share a common ancestor with these apes. Those characteristics that are different from one ape to the next say relatively little about our common ancestor, but those traits that are shared speak to habits our ancestors likely shared as well. All living apes build nests out of loosely interlaced sticks and leaves. Chimpanzees build them, as do bonobos, as do gorillas, as do orangutans.17 Apes tend to use their nests for a single night and then abandon them. They use nests more like beds than like homes, beds constructed in ephemeral settlements sometimes described, quaintly, as “dormitories.”
Recently, Megan Thoemmes, a graduate student in my lab at North Carolina State University, studied the bacteria and insects in chimpanzee nests. One might predict that these nests would be full of species associated with the bodies of chimpanzees, be they chimpanzee bodily bacteria or maybe even larger species that sneak in to take advantage of the chimpanzees. (Sloths, after all, have an entire ecosystem of arthropods and algae that live in their fur,18 why not chimps?) Fur mites. Dust mites. Maybe hide beetles. Spider beetles too. This is what we find in human beds.19 We humans are exposed, when we sleep, to the ecosystem of our decay. Instead, Megan found the nests of chimpanzees to be occupied, nearly exclusively, by environmental bacteria, bacteria from the soil and leaves.20 Just which bacteria depended on whether Megan’s samples were from the dry season or the wet season. It is likely that these were the same sorts of species that would have been found in the nests of our ancestors until they first began to build homes. The bacteria to which our ancestors were exposed for millions and millions of years would have been environmental, with the precise mix different from season to season and place to place.
When our ancestors needed something more permanent than nests, they may have initially moved into caves. Eventually, though, they began to build houses. The oldest evidence of a structure built by our ancestors is from a campsite near a beach at Terra Amata (near modern Nice).21 There, an archaeologist found evidence of at least twenty homes along an ancient shore. The most intact of these homes showed a ring of stones surrounding a floor of ash. In the floor, the location of posts used to support the roof were still visible. Around the stones, in a second ring, were the marks of stakes, each of which apparently ran from the ground and bent in to form the room. These houses were built by an ancient hominid (probably Homo heidelbergensis) more than 300,000 years ago.22 We know little about how common such houses were, how varied they were, or when they first appeared. The archaeological record offers us little, just clues here and there. For instance, shelters attributed to hominids (in this case, modern humans) at a 140,000-year-old site in South Africa. Beds at a 70,000-year-old site in South Africa.23 Whatever was going on, at least some of our ancestors were sleeping indoors, separated a little from the world outside.
By twenty thousand years ago, house sites start to turn up around the world. In nearly every case, the houses appear to have been round and domed. They were simple, like the chamber that a termite king and queen, out on their own, might build for themselves. In some places, they were made of sticks; in others, mud. Others, still, in the far north, were made of mammoth bones. Some of these homes were more ephemeral than others, used for just a few days or weeks, but I suspect that already, in these homes, we had begun to alter the species present around us. The best evidence of this change comes from studies of modern peoples living in houses similar to those our ancestors used. In Brazil, for instance, traditional, open-walled, palm-roofed Amazonian houses built by the indigenous Achuar are dominated by environmental bacteria.24 Similarly, Megan Thoemmes found that even though the houses of the Himba in northern Namibia were but a single round dome, the places where people slept contained different microbes than those where they cooked. Even simple houses tend to allow the buildup of body microbes. Yet, whereas the Himba and Achuar homes include body microbes, they are also, like chimpanzee nests, as diverse with environmental bacteria as is the air around the houses. Indoor microbes build up in contemporary Himba homes, and contemporary Achuar homes, but environmental microbes are still present as well. The modern homes of the Himba and Achuar are imperfect proxies for our historic dwellings. Yet it seems safe to suggest that exposures of our ancestors in homes like those found in Terra Amata, France, would have been similar to the Achuar and Himba homes in terms of the preponderance of environmental microbes.
Where once there were only round houses, humans began to build square houses roughly twelve thousand years ago. Though square houses had less usable area inside than did round houses, they were easier to make modular. Large numbers of houses could be stacked side by side or even on top of each other. The shift from round houses to square houses happened in nearly every place humans began to farm and live in greater densities. With this change, houses came to be slightly more isolated from the outside world. There was, to a greater extent, an inside and an outside. The old-style houses didn’t go away though. Both round houses and square houses existed side by side.
Fast-forward twelve thousand years. Today, the vast majority of humans live in cities, a trend that is only accelerating, and, in cities, ever more people live in apartments. The distance an outdoor bacterium needs to travel to get inside an apartment can be lengthy. If the windows of the apartment stay closed, a bacterium must make its way up the stairs, down the hall, past some doors, and then quickly inside. We imagine we can create a world that is sterile. But in apartments with closed windows, where the route up from the park is far, what we instead create is a world filled primarily with microbes associated with our falling apart, our food’s falling apart, and even the building’s falling apart. Once, we lived in nests in which the microbes around us were all just environmental microbes and our imprint on the places we sat or slept was so modest as to be almost undetectable. Now, in some apartments, the imprint of the environment, of nature, is all but undetectable. But here is the key: our study’s results show that life inside apartments varies as it does among houses. Some dwellings are really cut off from the environment; others, like those of the modern Himba or Achuar, less so. We have choices, choices as to how much of life’s richness we allow in.
IN MY EXPERIENCE, upon learning they live among thousands of kinds of bacteria in their homes—be they detrital species, extreme species, or species of wild forests and soils—people have one of three responses. Microbiologists, whom I hang out with fairly often, are a little more impressed than they were initially, but still not overwhelmed. “Eighty thousand? I would have thought more. Did you sample in winter too? Did you swab a dog?” Microbiologists are immersed every day in the grandeur and vulgarity of the unknown; they get numb to it. Let’s ignore the microbiologists for now.
Some people feel awe. I feel awe. Awe is what I hope to also inspire in others. It is awesome to walk about in a diversity we have yet to even begin to contemplate. It took four billion years for the microbial diversity we encounter in our homes to evolve. Each home is filled with unnamed species about which we know nothing; some we might have been living alongside for millions of years, others have more recently colonized the nooks and crannies of our modern lives. There are discoveries yet to be made all around you even without leaving home. New species. New phenomena. New everything.
But many people feel disgust. How do I know this? Because when we make discoveries in homes, we report those discoveries back to their denizens. When we do, people email us questions. I enjoy the questions. Sometimes they are like the questions I asked field biologists when I was at La Selva Biological Station in Costa Rica: What do we know about this species? What does it do? Often, the answer I can provide is similar to what the tropical biologists could provide me: “We don’t know. You should study it.” Or, “We don’t know. Let’s study it together.” Sometimes, though, the questions are more along the lines of, “Okay, there are a thousand kinds of bacteria in my house dust. How do I get rid of them all?” The answer is that you shouldn’t.
What we ideally want in our homes is a kind of garden. In a garden, you kill the weeds and pests, but you take care of the diverse species you are trying to grow. The species we need to get rid of from our houses are those that can make us really sick or even kill us. But such species are far fewer than you might imagine. Fewer than a hundred species of viruses, bacteria, and protists cause nearly all of the infectious illnesses in the world. As individuals, we keep those species at bay by washing our hands, which interrupts the opportunity for fecal microbes to inadvertently move from feces to hand to mouth. Washing hands doesn’t disrupt the thick layer of microbes on your skin; it just removes the most recent arrivals. As individuals, we also keep pathogenic species at bay through vaccination. In turn, our governments and public health systems help to keep the bad species at bay by implementing policies and building infrastructure that provide drinking water devoid of pathogens (but not devoid of life). Our governments and public health systems also help to control the pathogens spread by insects, such as yellow fever and malaria. Finally, doctors should administer antibiotics when (and only when) a bacterial pathogen becomes a problem that can’t be controlled in some other way. Together, these approaches to controlling the problem species have saved hundreds of millions of lives and, used appropriately, can continue to do so.
All of these measures work best, though, when they target problem species. When they inadvertently also kill off other species (the other 79,950 or so kinds of bacteria in homes, for instance), the consequences tend to be negative. I’ll return often in this book to the question of just what happens when we try to get rid of all of the biodiversity in our houses. Suffice it to say for now that when we do, it tends to make it easier for pathogens to spread, succeed, and evolve, easier for dangerous pests to spread and succeed, and harder for our immune systems to function normally. In the vast majority of cases, it is actually healthier to have more biological diversity, particularly the wild biodiversity of soils and forests, in your home rather than less, so long as the dangerous species are under control. It isn’t quite that simple (nothing in biology ever is), but nearly so.25
This is where some people think to themselves, “I’m still going to try to kill all of it.” One of the benefits of the nonpathogenic microbes on our bodies and in our homes is that they help to fight off the pathogens. But you might imagine that if you kill all of the bacteria in your home, there will no longer be any pathogens, nothing the microbes need to fight on your behalf, a clean slate. Cleaning products often advertise that they kill 99 percent of germs (leaving only the truly tough and problematic behind), but maybe you could get that last 1 percent. If there is any home in which this has really been attempted, an indoor space that might offer an example of what is possible, it is the International Space Station (ISS). If you imagine you might scrub your home entirely of bacterial life, the ISS is a perfect illustration of what you will achieve.
EARLY IN ITS HISTORY the National Aeronautics and Space Administration decided it was important to prevent the transport of microbes into space. Initially, the concern was that space shuttles might inadvertently seed the solar systems with Earthly microbes26 or seed Earth with extraterrestrial life. These remain the primary concerns of NASA’s Planetary Protection Office. But with time, NASA scientists also became worried about the potential for astronauts on space shuttles and later the ISS to be trapped for extended periods alongside pathogens. Space itself worked in NASA’s favor. The potential for chance colonization of any additional life from space in the space shuttles or the ISS was nonexistent. Open a window in a home on Earth, and outside microbes blow in. Open the hatch on the ISS, and the vacuum of space sucks you (and any life around you) out. In addition, the total volume of air inside the ISS is relatively small, compared, for example, to an apartment building, such that the potential for controlling humidity and the flow of air is, relatively, great. Finally, NASA was able to build a state-of-the-art facility where each bit of food and material headed to the ISS could be cleaned before transport. In short, you are unlikely to get your house to be any more lifeless than is the ISS. The question, then, is whether anything but humans lives on the ISS.
The life on the ISS has been studied in detail and more studies are ongoing. Recently, a new study even searched for life on the ISS using the same approaches we used to study homes in Raleigh. This isn’t chance. In 2013, not long after our study on the forty homes was published, Jonathan Eisen, a microbiologist at the University of California, Davis, wrote to me, asking if he could use our protocol to sample the ISS. Much as we had invited participants to sample their own houses, he would invite the astronauts to sample theirs. The same swabs would be used. Similar sites would be swabbed, though there would have to be a few alterations. We had asked participants to swab the dust on their door frames to measure the airborne life that settles around homes. In the low-gravity environment of the ISS, dust doesn’t settle. Instead of door frames, the astronauts swabbed air filters. The study also used consent forms similar to those we had used (which gave permission for scientists to examine the data), but with an exception. In studies in homes on Earth, we keep the results of our sampling anonymous (people can see their own results, but no one else can see their results). On the ISS, this wasn’t possible. Astronauts are many things but anonymous is seldom one of them. The people living on the ISS at the time were NASA astronauts Steve Swanson and Rick Mastracchio, cosmonauts Oleg Artemyev, Alexander Skvortsov, and Mikhail Tyurin, and the commander, Koichi Wakata, from the Japan Aerospace Exploration Agency. Koichi Wakata swabbed the ISS. The swabs were then brought back to Earth and taken to Jonathan’s lab at the University of California, Davis, where they would be studied by Jonathan’s student, Jenna Lang.
Earlier studies of the ISS had revealed environmental bacteria to be largely absent on board. Wild species of forests and grasslands were absent. Food-associated species were also absent. If the goal was to get rid of life on the ISS, these were successes. The ISS is not free of bacteria, though. It actually abounds in bacterial life. Nearly all that life just happens to be of one basic kind: bacteria associated with the bodies of the astronauts. This was a key finding of the early studies of the ISS. It was true, too, in Lang’s study. To really bring this point home, and give it some context, we can map the ISS and its bacteria relative to other habitats, particularly the forty homes in Raleigh. On this map, samples that are similar in terms of the kinds of bacteria they contain are placed closer together. Samples that are less similar are spaced farther apart. On this map you can see some of what I’ve already told you about the homes in Raleigh: samples from door sills tend to include both indoor and outdoor species and tend to be similar to each other. Samples from kitchens tend to clump because they contain food-associated bacteria. Also, samples from pillowcases and toilet seats are different from each other, but perhaps not as different as you might hope. The ISS samples are at the bottom of the map, all of them, regardless of which site in the ISS they came from. To the extent that they match anything on Earth, they are like pillowcases or toilet seats.27
Like pillowcases and toilet seats, the ISS samples contained fecal microbes. Lang found species related to Escherichia coli and Enterobacter.28 She also found a kind of fecal bacterium that has been poorly studied back on Earth, so poorly studied that it doesn’t have a name. For now it is called “Unclassified Rikenellaceae/S24-7.” The ISS samples weren’t identical to those of toilet seats or pillowcases; they tended to have fewer species of bacteria associated with saliva than do pillows, for example, and more of the bacteria associated with skin than do toilets. Previous studies found that stinky-feet bacteria of the species Bacillus subtilis are very common on the ISS. Lang found such bacteria to be present, but she found even more bacteria of the genus Corynebacterium. Corynebacterium species are responsible for armpit odor. What with its Bacillus and Corynebacterium, it is perhaps not surprising that the ISS has been described as smelling of a mix of plastics, garbage, and body odor.29 On Earth, we tend to find more Corynebacterium armpit bacteria in houses where men live. At the time, the ISS was a house with just men in it. This brings me to something else that was different between the ISS and houses on Earth, namely, the relative rarity of vaginal bacteria, or, rather, the kinds of bacteria that tend to be common in vaginal communities, such as Lactobacillus species. One might attribute this reality to the absence of women on the ISS at the time it was sampled.
In nearly every way, the bacteria of the ISS are the sorts of bacteria we would expect in a house on Earth if all the environmental influences were removed. ISS is what you get when you scrub and scrub and close the windows, doors, and hatches. But there was something more. The samples from different sites on the ISS were all very similar to each other. Everything was everywhere. In this one regard, the ISS is like small, traditional homes made of mud or leaves. In such homes, everything is also (compared to other houses) everywhere. But with a difference. In the small traditional houses, be they in Namibia or the Amazon, microbes throughout the home tend to be relatively similar because of the ubiquity of environmental microbes. Environmental microbes are everywhere. In the ISS, Lang found that different sampling sites were similar, but it was because they were all just covered in human bacteria, human bacteria spread evenly in the relative absence of gravity, the absence of gravity and the absence of the rest of life. If you scrub and scrub your home, this is what you may achieve too. It is not unlike what we see in some apartments in Manhattan. And as we and others have begun to study such apartments, we have found a problem. The problem is not what is present but instead what is absent. The problem has to do with what happens when we create homes devoid of nearly all biodiversity except that which falls from us and then, for twenty-three hours of the day, we don’t go outside.
Figure 3.2 Shapes represent different habitats that have been sampled for bacteria in our study of Raleigh homes and in a recent study of the International Space Station (ISS). The larger the shape, the more the bacterial composition of a particular habitat varies from one sample to the next. The closer together two shapes are, the more similar they are in their composition of bacteria. Habitats at the bottom of the figure tend to be dominated by bodily bacteria, those at the top right by food-associated bacteria, those at the top left by soil and other environmental bacteria. (Figure by Neil McCoy.)