The Microbes We Share

Science writer Ed Yong describes the diverse ways that scientists and citizen scientists are studying our microbiomes.

The following is an excerpt from I Contain Multitudes, by Ed Yong.

The house I’m standing in is a Platonic vision of the all-American suburban idyll. Outside, there are white clapboards, a rocking chair on a porch, and kids riding around on bicycles. Inside, there’s more space than Jack Gilbert and his wife Kat know what to do with. Like me, they’re British, and are used to snugger spaces. They’re also warm and good-humoured: Jack is a dervish of energy, while Kat is poised and grounded. One of their sons, Dylan, is watching cartoons. The other, Hayden, for reasons best known to him, is trying to punch me in the bum. I am protecting myself by backing up against the kitchen counter, and nursing a cup of tea. And as I do that, I’m also passively ejecting microbes all over the cup, the counter, and the rest of this beautifully furnished kitchen.

In fairness, so are the Gilberts. As we’ve seen, along with hyenas, elephants, and badgers, we humans release bacterial smells into the air around us. But we also release the bacteria themselves. All of us are constantly seeding the world with our microbes. Every time we touch an object, we leave a microbial imprint upon it. Every time we walk, talk, scratch, shuffle, or sneeze, we cast a personalised cloud of microbes into space. Every person aerosolises around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment. When I sat in Gilbert’s car on the drive over here, I bled microbes all over his seat. Now that I’m reclining on his kitchen counter, I’m autographing it with my bacteria. I contain multitudes, yes, but only some of them; the rest, I extend into the world like a living aura.

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To analyse these auras, the Gilberts recently swabbed their light switches, doorknobs, kitchen counters, bedroom floors, and their own hands, feet, and noses. They did this every day for six weeks. They also recruited and trained six other families, including singletons, couples, and families, to do the same. The results of this study—the Home Microbiome Project—showed that every home has a distinctive microbiome that largely comes from the people who live in it. Their hand bacteria coat the light switches and doorknobs. Their foot microbes cover the floors. Their skin bugs get on the kitchen surfaces. And all of this happens with astonishing speed. Three of the volunteers moved house over the course of the study and their new abodes quickly took on the microbial character of their old ones, even when, in one case, that old accommodation was a hotel room. Within 24 hours of moving into a new place we overwrite it with our own microbes, turning it into a reflection of ourselves. When people invite you to “make yourself at home”, you and they really have no choice in the matter.

We also change the microbes of our housemates. Gilbert’s team found that room-mates share more microbes than people who live apart, and couples are even more microbially similar. (“All that I am I give to you and all that I have I share with you,” as the marriage vows go.) And if there’s a dog around, these connections become super-charged. “Dogs bring in bacteria from the outside to the inside, and they increase the microbial traffic between people,” says Gilbert. On the basis of his results, and on Susan Lynch’s work showing that dog dust contains allergy-suppressing microbes, the Gilberts got a dog of their own. He’s a ginger-and-white mix of golden retriever, collie, and Great Pyrenees, who answers to Captain Beau Diggley. “We saw the benefit in increasing the microbial diversity of the home, and we wanted to make sure that our kids had that capacity to train their immune systems,” says Gilbert. “Hayden named him; where did the name come from, Hayden?” Hayden replies: “From my head.”

Whether dog or human, all animals live in a world of microbes. And by moving through that world, we change the microbes in it. In travelling to Chicago to visit the Gilberts, I have left my skin microbes in their home, my hotel room, a few cafes, several taxis, and one aeroplane seat. The good Captain Diggley is a fuzzy conduit that shuttles microbes from the soil and water of Naperville into the Gilbert residence. A Hawaiian bobtail squid, come the dawn, flushes its luminous Vibrio fischeri partners into the surrounding water. Hyenas spray microbial graffiti onto stalks of grass. And all of us constantly welcome microbes onto and into our bodies, whether through inhalation or ingestion, touches or footfalls, injuries or bites. Our microbiomes have wide-reaching tendrils that root us in the wider world.

Gilbert wants to understand those connections. He wants to be an all-seeing border officer for the human body, who knows exactly which microbes are coming in (and their point of origin), and which ones are leaving (and their destination). But humans make his job very difficult. We interact with so many different objects, people, and places that it becomes a nightmare to trace the paths of any particular bacterium. “I’m an ecologist; I want to treat the human being like an island,” he says. “But I’m literally not allowed. I put in a proposal to take some people and lock them in a space for six weeks, and the institutional review board said no.”

That’s why he turned to dolphins.

“How many samples would you like?” asks veterinarian Bernie Maciol. “How many have you done?” says Gilbert.


“Can you do replicates of those? And maybe some from another skin site? What about the armpit? No, not armpit. Whatever that is. What do you call a dolphin’s armpit?”

We are in the Shedd Aquarium’s dolphin exhibit—a large tank, overlooked by artificial rocks and trees. Jessica, a trainer in a black-and-blue wetsuit, sits in the water and slaps its surface with her hand. A Pacific white-sided dolphin named Sagu swims up. He’s a beautiful animal, with skin like a laminated charcoal drawing. He’s obedient, too: when Jessica holds her hands palms-down and waves them to the side, Sagu rolls over and exposes his milky-white stomach. Maciol reaches across, swabs Sagu’s armpit with a cotton bud, seals it in a tube, and passes it back to Gilbert. She does the same for two other dolphins, Kri and Piquet, who are quietly mooching next to their respective trainers.

“We’ve been doing blowhole sampling, faecal sampling, and skin sampling,” Jessica tells me. “For the blowhole, I’ll rest their head in my hand, put an agar plate over the hole, and tap to make the dolphin do a forced exhale. For the faecal sample, I’ll make them roll over, insert a small rubber catheter and pull it out. We’re not short of poop around here.”

This Aquarium Microbiome Project offers Gilbert what he cannot get from his Naperville house or any of the other homes that he has sampled—a kind of omniscience. Here are animals whose environment is fully known. Everything about the water—temperature, salinity, chemical content—can be measured, and regularly is. Here, Gilbert can analyse the microbiome of the dolphins’ bodies, water, food, tanks, trainers, handlers, and air, and he has done so once a day for six weeks. “These are real animals with their own real microbiomes living in a real environment, and we’ve catalogued all of the microbial interactions they have with that environment,” he says. And that should give him an unprecedented view of the connections between the microbes in an animal’s body and those in the surrounding world.

I Contain Multitudes


The aquarium is running several such projects to improve the lives of its charges. Bill Van Bonn, the Shedd’s vice-president for animal health, tells me that the entire 3-million-gallon water supply in the main oceanarium used to pass through a life-support loop that cleaned and filtered it every three hours. “You know how much energy it takes to push that water? Why do we do it that often? Because: we’re going to make this water so clean that it’ll be absolutely the best thing,” he says, putting on a mock gung-ho tone. “But when we back it up and do it half as much, what happens! Nothing! The water chemistry and the animals’ health actually improves!”

Van Bonn suspects that in shooting for sanitation their intense cleaning regimes had gone too far. They ended up stripping the microbes from the aquarium environment, preventing mature and diverse communities from establishing themselves, and creating opportunities for weedy and harmful species to exploit. Sound familiar? That’s exactly what antibiotics do in the guts of hospital patients. They divest an ecosystem of its native microbes, and allow competing pathogens like C-diff to flourish in their stead. In both settings, sterility is a curse not a goal, and a diverse ecosystem is better than an impoverished one. These principles are the same whether we’re talking about a human intestine or an aquarium tank—or even a hospital room.

“I’m Dr. Jack Gilbert, and that is a hospital,” says Jack Gilbert, gesturing with his thumb at the massive hospital looming behind him.

We’re now at the University of Chicago’s Center for Care and Discovery, a shiny new building that looks like a giant opera gateau, with several grey, orange, and black layers. Gilbert stands in front of it, doing repeated takes for a promotional video. I’m not convinced that the cameraman’s microphone is going to pick up any decent audio over the sound of Chicago’s unforgiving wind. I’m more convinced that Gilbert is very cold. And I’m totally convinced that, yes, that is indeed a hospital.

Just before it opened in February 2013, Gilbert’s student Simon Lax led a team of researchers through the eerily empty hallways, armed with bags of Q-tips and a plan. They swept through ten patient rooms and two nurse stations, spread over two floors: one for short-stay patients recovering from elective surgery, and another for long-term ones like cancer patients and transplant recipients. But none of the rooms were home to any humans yet. Their only residents were microbes, which Lax’s team collected. They swabbed the pristine floors, the gleaming bedrails and taps, and the perfectly folded sheets.

They collected samples from light switches, door handles, air vents, phones, keyboards, and more. Finally, they fitted the rooms with data loggers that would measure light, temperature, humidity, and air pressure, carbon dioxide monitors that would automatically record if a room was occupied, and infrared sensors that could tell when people entered or left. After the grand opening, the team carried on their work, collecting more weekly samples from the rooms and the patients inside them.

Just as others have catalogued the developing microbiome of a newborn baby, Gilbert has, for the first time, catalogued the developing microbiome of a newborn building. His team is busy analysing the data now, to work out how the presence of humans has changed the edifice’s microbial character, and whether those environmental microbes have flowed back into the occupants. Nowhere are those questions more important than in a hospital. There, the flow of microbes can mean life or death—a lot of deaths. In the developing world, around 5 to 10 percent of people who check into hospitals and other health-care institutions pick up some kind of infection during their stay, falling ill in the very places that are meant to make them healthier. In the United States alone, this means around 1.7 million infections and 90,000 deaths a year. Where do the pathogens behind these infections come from? Water? The ventilation system? Contaminated equipment? Hospital staff? Gilbert plans to find out. Through the mammoth set of data that his team have amassed, he should be able to trace the movements of pathogens from, say, a light switch to a doctor’s hand to a patient’s bedrail. And he should be able to work out ways of curtailing that life-threatening traffic.

This isn’t a new problem. Ever since the 1860s, when Joseph Lister instigated sterile techniques in his hospital, cleaning regimes have helped to curb the spread of pathogens. Simple measures like hand-washing have undoubtedly saved countless lives. But just as we have gone overboard in taking unnecessary antibiotics or lathering ourselves in antibacterial sanitisers, we have also gone too far in cleaning our buildings—even our hospitals. As an example, one U.S. hospital recently spent around $700,000 to install flooring that had been impregnated with antibacterial substances, despite having no evidence that such measures work. They might even make things worse. As in the dolphin enclosure and the human gut, perhaps the quest to sterilise our hospitals has created dysbiosis in the microbiomes of our buildings. By removing harmless bacteria that would otherwise impede the growth of pathogens, perhaps we have inadvertently constructed a more dangerous ecosystem.

“You want to bring in microbes that are benign or aren’t interacting very much, and just populating surfaces,” adds Sean Gibbons, another of Gilbert’s students. “Diversity is good.” And sanitation, when taken too far, can cause diversity to collapse. Gibbons showed this by studying public toilets. He found that thoroughly scrubbed toilets are first colonised by faecal microbes, which are launched into the air by roiling, flushed water. Those species are eventually out-competed by a diverse range of skin microbes, but once the toilet gets scrubbed again, the communities go back to square one. So, here’s the irony: toilets that are cleaned too often are more likely to be covered in faecal bacteria.

Jessica Green, an Oregon-based engineer-turned-ecologist, found a similar pattern among the microbes that float inside air-conditioned hospital rooms. “I assumed that the microbial community of the indoor air would be a subset of that of outdoor air,” she says. “It really surprised me that we saw little to no overlap between the two.” Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world, but had been launched from the mouths and skins of hospital residents. The patients were effectively stewing in their own microbial juices. And the best way of fixing that was remarkably simple: open a window.

From I Contain Multitudes: The Microbes Within Us and a Grander View of Life by Ed Yong. Copyright 2016 Ed Yong. Excerpted by permission of Ecco, an imprint of HarperCollins Publishers.

Meet the Writer

About Ed Yong

Ed Yong is a science writer and author of An Immense World: How Animal Senses Reveal The Hidden Realms Around Us.

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