by Amy Stewart
In order to understand what happens when a built environment’s microbial ecosystem is wiped out, scientists have begun to study the most sterile structures on Earth—and off. For astronauts, the International Space Station (ISS) is like living inside a giant antibiotic pill. HEPA filters remove airborne germs, surfaces deter bacterial growth, and iodine and biocidal nanosilver cull microbes from water. “Everything is sterilized, except for the humans,” says Hernan Lorenzi of the J. Craig Venter Institute, which has been studying the ISS for four years.
As a result, the microbial ecosystem in the station is made up mostly of the organisms the astronauts themselves shed daily. There are no Amazon deliveries, no windows to crack—no influx of fresh microbes to balance the ecosystem. And so Lorenzi’s team is sampling the microbiome of astronauts to see how it changes after a stint in the station. A loss of gut diversity, he says, correlates with many diseases and could raise concerns for long-term space travel. Astronauts often have impaired immunity, and “if you lose your gut microflora,” Lorenzi says, “the immune system goes dormant.” It takes a space vacation. “Can you imagine a trip to Mars?” asks Eisen. “They’ve gotta be screwed.”
On Earth, the same phenomenon occurs in hospitals, only sick patients are the ones shedding microbes. Despite extensive sanitation, infections acquired in U.S. hospitals kill about 75,000 people annually—more deaths than from breast cancer and HIV/AIDS combined. The Chicago-based Hospital Microbiome Project, led by Argonne National Laboratory’s Jack Gilbert, studied the ecology of one hospital for a year and found microbes everywhere. “You can do as much cleaning as you want,” says Gilbert. “The hospital is a bloody sterile place, and a pathogen might still make you sick.”
That sounds terrifying, but everyone harbors pathogens. The dreaded Clostridium difficile, which can cause life-threatening diarrhea, is found in 66 percent of infants. Staphylococcus aureus is carried by 20 percent of adults. People who seem perfectly healthy harbor the influenza virus. These germs don’t do much harm when they’re kept in check by other organisms. Studies suggest, for instance, that the flu virus can be contained through competition with Lactobacillus.
And so Gilbert thinks the notion that we “catch” things is flawed. In a study of intensive care units, his group observed otherwise harmless microbes go rogue in four patients after drugs decimated their gut flora. “You put humans through the ringer, and we’re surprised their germs are stressed too?” he asks. Scientists suspect that in hospital rooms, sanitization can likewise pressure microbes to evolve into virulent pathogens, which then colonize surfaces cleared of competitive bacteria. Recycled-air systems help concentrate them. “We’ve gone too far,” says Gilbert. “Hygiene is good; sterility may not be.”
For Sandra Bauder, an architect in Houston, the zealous sanitation trend brings to mind a fancy horse her uncle kept in Venezuela. “He babied it—with special food, an air-conditioned barn, never let any bugs get on it. And it was always sick. Then he got a mutt horse. It lived in a pasture. It didn’t get anything, not even a stomachache. I think it’s the same for people.”
After my son was born, I received an Evite for a party entitled “Please don’t lick the baby.” Further instructions asked guests to wash their hands before arrival and not to touch the baby anyway. This seemed sensible. Parenthood can make anyone a hormonal germophobe, and I was no different. I had visitors apply botanical hand sanitizer (we lived in San Francisco, where there was hippie Purell) and remove their shoes at the door. Yet despite my vigilance, my son grew into an allergic toddler. His eyes swelled shut, his bottom turned red, and his body erupted with hives after exposure to a litany of foods, dust, pollen, and even the housecat he was raised with. Doctors warned me to prepare for a lifetime of severe immune dysfunction.
The devastating irony is that the rise of diseases of inflammation in children—often called “modern plagues”—is most likely not caused by picking up the pathogens we fear. Rather, it’s the result of not being exposed to the microbes that are key to maturing immunity. And how we enter the world determines our first colonizers.
In the birth canal, babies acquire Lactobacillus, which helps them digest milk and begins the process of lowering the gut’s pH to the normal range. But babies born by cesarean miss out. Studies show they instead often end up with bacteria that are commonly found on the skin (sometimes not even the mother’s), such as Staphylococcus—and in the case of one neonatal intensive care unit, antibiotic- and disinfectant-resistant bacteria. Abnormal colonization may explain why C-section babies seem to have a heightened risk for obesity, allergies, and asthma, which are linked to gut inflammation.
My son was not a C-section baby. But he did grow up in an apartment that might have been too clean. According to one theory, environmental exposures contribute to our development after birth, and recent studies seem to back that up. They suggest germs might actually help prevent children from developing various maladies.
“A house with a more bacteria-rich environment is a healthier one,” says Susan Lynch, a microbiologist at the University of California at San Francisco. Her group profiled 104 infants inside their homes and found that the babies exposed to house dust with the greatest bacterial diversity before age one were the least likely to have asthma symptoms as three-year-olds. In addition to mouse and cockroach droppings, the dust was heavily colonized with microbes found in a healthy Western gut. Toddlers exposed to fewer types of bacteria, on the other hand, turned into hyperallergic wheezers. “We found that in homes with very little bacterial diversity,” she says, “there was a very large number of fungi present.”
Because studies show pet exposure might protect kids from allergies, Lynch also fed young mice meals from homes with germ-rich dogs. The mice grew up to be less allergic than those used as controls. She isolated one of their gut microbes, Lactobacillus johnsonii, and fed it to more mice. They were protected, too, but less so. Lynch suspects that L. johnsonii is a “keystone” species: it has an outsize role in determining which microbes move in and how they behave—guiding the immune response.
I’ve met Lynch before, when my son was morphing into one of her asthmatic superwheezers. She helped line up a medical referral. “How’s he doing?” she now asks.
I tell her we moved to Oakland, where I countered my son’s rather unscientific medical diagnosis of “allergic gut” with an equally unscientific prescription of dirt, dogs, chickens, and cultured foods. After school he tends to his bean tepee, and grows the strawberries he once couldn’t eat. A fine sprinkling of soil often rings his mouth, like cookie crumbs. Surprisingly, most of his allergies have disappeared.
“He sounds like a perfect case study,” Lynch says, completely nonplussed. “I would have liked to have gotten samples from him before and after. My guess is that his microbiome looks more like a normal gut.” Lynch recently left San Francisco, too; it turns out we’re neighbors. “We have a great picture of our 10-month-old daughter eating soil off a rock,” she says.
In a remote corner of Northern California, on a steep slope of knotty oaks, sulfur and steam rise in plumes from Wilbur Hot Springs. It’s the perfect place, says Eisen, to investigate the ghost limbs on the tree of life, the ones that contain multitudes of microbes we haven’t yet identified. This microbial dark matter, as he calls it, is best pursued in isolated locales, such as deep mines and underground aquifers—or a nearby pool of absinthe-colored spring water, by which a sunbather lounges in a broad hat, and not much else.
This place is weird, and it is Eisen’s milieu. He enters a creaky wooden shack, where water from a spigot feeds the pool. His colleagues from the Department of Energy’s Joint Genome Institute, where he is an adjunct scientist, were here months earlier with collection jars. They were taking the waters, to echo an old phrase referring to the devotees of spa towns—only quite literally. They took samples back to the lab, where they amplified the microbial DNA a billionfold.
As we hike along a creek toward the source water, Eise
n is in a good mood. The view’s nice; the chaparral smells great. Here, he makes his final case for microbial diversity: dark matter is special, he tells me. By 2009 scientists had sequenced the DNA of only about a thousand microbes, those important to medicine or with clear applications. They mainly came from the same three branches of the evolutionary tree. And so Eisen led a team that set out to sequence a thousand more, with an emphasis on “neglected” species. The work has begun to fill in the tree with many more branches, revealing how microbes evolved and how species are related.
Ultimately, Eisen hopes, this knowledge will provide “a field guide to all microbes, including what is normally seen in the built environment.” Much of the DNA found in recent studies lacks context. In addition, many microbes have genes with completely unknown functions. Finding similar genes on different branches could explain what they do—and eventually help us select microbes to create healthier surroundings. Emily Landon, an epidemiologist at the University of Chicago, envisions one day replacing antimicrobial paint with probiotics-infused walls. She calls it a fecal transplant for the built environment, wherein we infuse a space with beneficial bacteria that outcompete harmful ones. Or somewhere in Lynch’s pile of anonymous DNA could be a clue to a microbe that eliminates my son’s remaining allergy, to our cat.
Near the ruins of a bathhouse, milky bubbles well up from an aquifer. Garishly colored films have formed on rocks poking out of the water. “This is pretty awesome,” Eisen says, wading toward a red-and-purple blob. “That’s a nice mat. Touch that.” As he inspects the photosynthetic bacteria, a cloud of tiny winged insects hovers at his ankles. These bugs, too, are taking the waters. Chances are they evolved to be at home with their own set of microbes. As we have.
OLIVER SACKS
My Periodic Table
FROM The New York Times
I LOOK FORWARD EAGERLY, almost greedily, to the weekly arrival of journals like Nature and Science, and turn at once to articles on the physical sciences—not, as perhaps I should, to articles on biology and medicine. It was the physical sciences that provided my first enchantment as a boy.
In a recent issue of Nature, there was a thrilling article by the Nobel Prize–winning physicist Frank Wilczek on a new way of calculating the slightly different masses of neutrons and protons. The new calculation confirms that neutrons are very slightly heavier than protons—the ratio of their masses being 939.56563 to 938.27231—a trivial difference, one might think, but if it were otherwise the universe as we know it could never have developed. The ability to calculate this, Dr. Wilczek wrote, “encourages us to predict a future in which nuclear physics reaches the level of precision and versatility that atomic physics has already achieved”—a revolution that, alas, I will never see.
Francis Crick was convinced that “the hard problem”—understanding how the brain gives rise to consciousness—would be solved by 2030. “You will see it,” he often said to my neuroscientist friend Ralph, “and you may, too, Oliver, if you live to my age.” Crick lived to his late 80s, working and thinking about consciousness till the last. Ralph died prematurely, at age 52, and now I am terminally ill, at the age of 82. I have to say that I am not too exercised by “the hard problem” of consciousness—indeed, I do not see it as a problem at all; but I am sad that I will not see the new nuclear physics that Dr. Wilczek envisages, nor a thousand other breakthroughs in the physical and biological sciences.
A few weeks ago, in the country, far from the lights of the city, I saw the entire sky “powdered with stars” (in Milton’s words); such a sky, I imagined, could be seen only on high, dry plateaus like that of Atacama in Chile (where some of the world’s most powerful telescopes are). It was this celestial splendor that suddenly made me realize how little time, how little life, I had left. My sense of the heavens’ beauty, of eternity, was inseparably mixed for me with a sense of transience—and death.
I told my friends Kate and Allen, “I would like to see such a sky again when I am dying.”
“We’ll wheel you outside,” they said.
I have been comforted, since I wrote in February about having metastatic cancer, by the hundreds of letters I have received, the expressions of love and appreciation, and the sense that (despite everything) I may have lived a good and useful life. I remain very glad and grateful for all this—yet none of it hits me as did that night sky full of stars.
I have tended since early boyhood to deal with loss—losing people dear to me—by turning to the nonhuman. When I was sent away to a boarding school as a child of 6, at the outset of World War II, numbers became my friends; when I returned to London at 10, the elements and the periodic table became my companions. Times of stress throughout my life have led me to turn, or return, to the physical sciences, a world where there is no life, but also no death.
And now, at this juncture, when death is no longer an abstract concept, but a presence—an all-too-close, not-to-be-denied presence—I am again surrounding myself, as I did when I was a boy, with metals and minerals, little emblems of eternity. At one end of my writing table, I have element 81 in a charming box, sent to me by element-friends in England: it says, HAPPY THALLIUM BIRTHDAY, a souvenir of my 81st birthday last July; then, a realm devoted to lead, element 82, for my just-celebrated 82nd birthday earlier this month. Here, too, is a little lead casket, containing element 90, thorium, crystalline thorium, as beautiful as diamonds, and, of course, radioactive—hence the lead casket.
At the start of the year, in the weeks after I learned that I had cancer, I felt pretty well, despite my liver being half-occupied by metastases. When the cancer in my liver was treated in February by the injection of tiny beads into the hepatic arteries—a procedure called embolization—I felt awful for a couple of weeks but then superwell, charged with physical and mental energy. (The metastases had almost all been wiped out by the embolization.) I had been given not a remission, but an intermission, a time to deepen friendships, to see patients, to write, and to travel back to my homeland, England. People could scarcely believe at this time that I had a terminal condition, and I could easily forget it myself.
This sense of health and energy started to decline as May moved into June, but I was able to celebrate my 82nd birthday in style. (Auden used to say that one should always celebrate one’s birthday, no matter how one felt.) But now, I have some nausea and loss of appetite; chills in the day, sweats at night; and, above all, a pervasive tiredness, with sudden exhaustion if I overdo things. I continue to swim daily, but more slowly now, as I am beginning to feel a little short of breath. I could deny it before, but I know I am ill now. A CT scan on July 7 confirmed that the metastases had not only regrown in my liver but had now spread beyond it as well.
I started a new sort of treatment—immunotherapy—last week. It is not without its hazards, but I hope it will give me a few more good months. But before beginning this, I wanted to have a little fun: a trip to North Carolina to see the wonderful lemur research center at Duke University. Lemurs are close to the ancestral stock from which all primates arose, and I am happy to think that one of my own ancestors, 50 million years ago, was a little tree-dwelling creature not so dissimilar to the lemurs of today. I love their leaping vitality, their inquisitive nature.
Next to the circle of lead on my table is the land of bismuth: naturally occurring bismuth from Australia; little limousine-shaped ingots of bismuth from a mine in Bolivia; bismuth slowly cooled from a melt to form beautiful iridescent crystals terraced like a Hopi village; and, in a nod to Euclid and the beauty of geometry, a cylinder and a sphere made of bismuth.
Bismuth is element 83. I do not think I will see my 83rd birthday, but I feel there is something hopeful, something encouraging, about having “83” around. Moreover, I have a soft spot for bismuth, a modest gray metal, often unregarded, ignored, even by metal lovers. My feeling as a doctor for the mistreated or marginalized extends into the inorganic world and finds a parallel in my feeling for bismuth.
I almost certainly
will not see my polonium (84th) birthday, nor would I want any polonium around, with its intense, murderous radioactivity. But then, at the other end of my table—my periodic table—I have a beautifully machined piece of beryllium (element 4) to remind me of my childhood, and of how long ago my soon-to-end life began.
KATHRYN SCHULZ
The Really Big One
FROM The New Yorker
WHEN THE 2011 EARTHQUAKE and tsunami struck Tohoku, Japan, Chris Goldfinger was 200 miles away, in the city of Kashiwa, at an international meeting on seismology. As the shaking started, everyone in the room began to laugh. Earthquakes are common in Japan—that one was the third of the week—and the participants were, after all, at a seismology conference. Then everyone in the room checked the time.
Seismologists know that how long an earthquake lasts is a decent proxy for its magnitude. The 1989 earthquake in Loma Prieta, California, which killed 63 people and caused $6 billion worth of damage, lasted about 15 seconds and had a magnitude of 6.9. A 30-second earthquake generally has a magnitude in the mid-7s. A minute-long quake is in the high 7s, a two-minute quake has entered the 8s, and a three-minute quake is in the high 8s. By four minutes, an earthquake has hit magnitude 9.0.
When Goldfinger looked at his watch, it was quarter to three. The conference was wrapping up for the day. He was thinking about sushi. The speaker at the lectern was wondering if he should carry on with his talk. The earthquake was not particularly strong. Then it ticked past the 60-second mark, making it longer than the others that week. The shaking intensified. The seats in the conference room were small plastic desks with wheels. Goldfinger, who is tall and solidly built, thought, No way am I crouching under one of those for cover. At a minute and a half, everyone in the room got up and went outside.
