by Dan Ariely
Compelling evidence for our biota’s role in our immune system comes from the laboratory’s quick-breeding little helpers: mice. It’s possible, Vance says, to breed sterile—as in germ-free—mice, ones with absolutely no gut biota. These mice live in sterile cages, eat special food, and breathe filtered air. If they are taken out of their cages, their immune systems collapse when exposed to the meekest pathogens, and the mice die.
Unfortunately, there are cases when the body’s biota and its immune system stop their friendly scrimmage and start playing like the 1970s Oakland Raiders. This is thought to cause or play a role in autoimmune illnesses, including environmental allergies, Crohn’s disease, and inflammatory bowel disease.
Vance’s lab at Cal uses mice to study how our body’s innate immune system distinguishes between pathogens and our normal gut bacteria. So far, it seems that our body is guarded not so much by watchdogs as by burglar alarms: they can’t differentiate friend from foe. All they can do is make themselves known if something gets in.
Vance is looking at one particular burglar alarm, a protein in the cell that under certain circumstances will signal the immune system to attack all bacteria, including healthy gut bacteria. It’s not clear exactly when those circumstances might occur, but the fact that this protein doesn’t distinguish between good and bad bacteria could help us understand what triggers autoimmune diseases.
Life, however, is struggle, and our immune system and friendly gut bacteria are not the only players in the game. Sometimes a pathogen causes our immune systems and our biota to turn against each other. Research by Andreas J. Bäumler at the University of California, Davis, shows that Salmonella typhimurium, a bacterium that causes gastroenteritis, actually benefits from our immediate immune response. This reaction is a flood of antimicrobial agents and an overall change in your intestinal environment that is very noticeable to you and the person in the bathroom stall next to you. This changed environment is hostile to all bacteria, including your own. In fact, it is more harmful to your biota than it is to salmonella. Because your immune system is better at thrashing your biota than it is at thrashing salmonella, the salmonella suddenly has more nutrients to eat and more space to grow.
We are just beginning to understand the role our biota plays in human health and disease, says Rob Knight, a biophysics researcher at the University of Colorado, Boulder. Knight works on the Human Microbiome Project, sequencing and analyzing the genetic makeup of our biota, work that has only recently begun to take off as gene sequencing has become much cheaper and faster.
Right now, he says, we’re still not sure how many species we play host to. In our gut alone there may be anywhere from one hundred to a thousand species. (The answer depends not only on how many we can discover but on how finely one defines “species.”) And the particular makeup of the community living in one’s gut varies wildly from individual to individual.
It seems we acquire our first colonists literally at the moment of birth. You get most of it from your mother, but even identical twins don’t end up with identical biota, and a sibling born by cesarean section will have a very different set than his vaginally birthed brother—the C-section child is exposed to the biota on his mother’s skin, while the child passing through his mother’s vagina meets biota more like those in mom’s guts. The differences between unrelated strangers are even more pronounced, Knight says. Two unrelated North Americans will share only 10 percent of their intestinal bacteria, and a North American and a South American will share only 5 percent.
And the differences in our biota have a wide-ranging effect on our health. For one, it could even be that our biota is making us fat.
Knight points to a series of experiments in which the gut biota is transplanted out of obese mice and into healthy ones, whereupon the healthy mice either become obese or develop colitis. This is why Knight is interested in the potential of healthy bacteria called probiotics to treat human obesity and other conditions. “We’re probably where, I don’t know, radium was in 1910, where people thought making everything radioactive would just be great,” Knight says. “And while that wasn’t true, it doesn’t proscribe the important uses of radiation in, say, cancer therapy.”
So far probiotics are more popular as a marketing term for nutritional supplements and bacteria-enriched yogurt than as recognized medical treatments. In the coming years, Knight says, probiotics will likely become an increasingly legitimate medical tool. But not quite yet. There have been some very promising studies where mice were successfully treated with probiotics for inflammatory bowel disease. “We’re really good at curing diseases in mice and somewhat less good at curing them in humans.”
Scientists are only now beginning to figure out just how important our biota can be. For instance, Knight says, one study has shown that these harmless bacteria can change our metabolism in a way that affects our behavior, and not only behavior related to eating.
Again, mice are involved. Take some lab-grown sterile mice. Take some normal bacteria-infested mice. Run them both through a maze that includes a high beam without rails. It turns out that the sterile mice are much bolder and will spend more time on the beam than their normal cousins.
Even more interesting, if you introduce normal bacteria into adult sterile mice, their behavior doesn’t change. If, however, you take mice that are still growing and colonize them with the same bacteria, they will develop more typical fear responses. This suggests that our biota can influence brain development. It makes a certain amount of sense, Knight says, considering that our guts produce many of our neurotransmitters, including 90 percent of our serotonin, a linkage that, in a term of complete scientific awesomeness, is called the “gut-brain axis.”
In other words, it’s looking increasingly likely that it’s not so much that you are mostly not you as that you are also the slime sloshing around your innards. If the medical advances of the twentieth century taught us to stop thinking of our minds and bodies as separate entities, the twenty-first may teach us to include our symbiotic biota: Our Bacteria, Ourselves.
VIRGINIA HUGHES
Our Body the Ecosystem
FROM Popular Science
WHEN JAKE HARVEY VISITS the clinical center at the National Institutes of Health in Bethesda, Maryland, he is usually dirty, itchy, and wheezing—not the happiest state of affairs for a fourteen-year-old boy. But his doctors require that for twenty-four hours prior to each visit, he refrain from bathing, using the inhaler that soothes his asthma, or applying the ointment that softens his eczema. In order to study his illness, they need him to be as close to his natural state as possible.
Jake’s discomfort could lead to better treatments for the millions who have eczema—a disorder marked by dry red rashes in the creases of elbows, behind knees, and on the back of necks—as well as an array of other allergic reactions. By understanding eczema in a new way, as the product of a delicate interaction between the immune system and the legion of bacteria that live on the skin, one group of scientists hopes to better understand what triggers it and why the number of diagnosed eczema cases in developed countries has dramatically increased over the past few decades.
These researchers, led by Heidi Kong, a dermatologist at the Center for Cancer Research at the National Cancer Institute, and Julie Segre, a geneticist at the NIH, are just one part of the five-year, $173 million Human Microbiome Project (HMP), an effort to characterize the thousands of species of microbes that live on or in us. So far, Jake has made half a dozen trips to Bethesda, sixty miles each way, to donate a few skin cells to the project.
Jake has been struggling with eczema since he was a few months old. The rash never stops itching, and when he scratches, it bleeds and scabs and gets even itchier. His clothes stick to the sores. He has tried many treatments, including petroleum jelly, topical steroids, antibiotics, and also dairy-free, gluten-free, and probiotic diets. None of them has worked very well. When he was younger, he went to school with bandages on the tips of his fingers and slept
with socks over his hands. In bed, he still sometimes lies on his back with both legs sticking straight up so they’re easier to scratch. “I’ve never really gotten a full night’s sleep,” he says.
As many as 30 percent of all children develop eczema, and no one knows what mix of genetic and environmental factors sets it off. The disease runs in families, yet Jake’s twin sister, Becca, has perfect skin. For about 60 percent of children with the disease, it goes away by early adolescence. The others frequently deal with outbreaks for life.
Whether the rash disappears or not, nearly one third of children with eczema go on, like Jake, to develop asthma and hay fever. Asthma and hay fever also involve inflammation, but very little is known about what quirk of the immune system links them all together. “We’ve been to pediatricians, allergists, dermatologists for years,” says Jake’s mother, Debbie, “and nobody can figure him out.”
The average human body is made up of trillions of cells. The average human body also houses about 10 times that number of bacterial cells. Scientists have been curious about our bacterial cohabitants since 1683, when Anton van Leeuwenhoek, using a microscope he had built himself, examined his own dental plaque only to discover “little living animalcules, very prettily a-moving.” But it has only been within the past few decades that scientists have begun to understand just how many varieties of bacteria live in or on our bodies. And now they increasingly suspect that many diseases are caused not by individual bacteria but by the delicate interplay between multiple bacterial species and the human host.
In the Human Microbiome Project, researchers plan to characterize the vast numbers of bacteria, fungi, protozoa, and viruses in our body by sequencing their genes. That won’t be easy. In the past, researchers had to grow each species outside the body before they could identify it, a process that required intense research to determine optimum growing conditions. Only the hardiest and most numerous bacterial species—for example, Staphylococcus aureus and Streptococcus pyogenes, which can cause life-threatening infections—have been thoroughly studied in the laboratory. Now advances in DNA sequencing—the very same that made it possible for the Human Genome Project to decode the 3 billion base pairs of our own genome quickly—have provided the technology to make a comprehensive Human Microbiome Project possible.
“What we want to understand first,” says HMP coordinator Lita Proctor, “is what’s considered the norm. What does a typical healthy human have?” HMP researchers are building a reference database of the genetic fingerprints of about three thousand different bacterial species. Scientists are also thoroughly characterizing the makeup of microbial communities found at half a dozen body sites—including the gut, the mouth, the skin, and the groin—of three hundred normal people. The next step is to compare those results with what researchers find in patients with specific medical conditions, such as eczema, Crohn’s disease, and ulcerative colitis.
The skin samples from Jake and other children with eczema will help Segre and Kong determine whether changing profiles of skin flora, and their interaction with the human immune system, are involved in the rising rates of the disease. Some 34.1 million Americans suffer from asthma, and up to 50 million have seasonal allergies.
“In the last three decades, all of these allergic disorders—asthma, eczema, hay fever—they’ve all tripled,” Segre says. In that short a time frame, the culprit can’t be simply changes in our own genome. “So it must be something about the gene-environment interaction. And I now believe that that’s modulated by the body’s bacteria.”
The first part of the exam is like any other doctor’s visit, Jake says. Sitting on a stool next to him, Kong asks a series of questions. Which medications are you currently taking? Does your school use antibacterial soaps? How bad are your allergies this month? On a diagram of a body, she notes all the spots where Jake’s rash has cropped up that day. Then she pulls on a pair of blue examination gloves and turns to a tray containing a row of sterile swabs and scalpels. The swabbing comes first. Jake stretches out his right arm, palm up, and Kong firmly rubs a wet foam swab in a circular motion in the crook of his elbow; the sterile water solution stings when it hits his open sores. Kong drops the tip of the swab into a plastic tube filled with the same liquid and places the tube in a bucket of dry ice. Then comes the scalpel. Kong moistens the blade and gently scrapes some skin from a spot next to the area she swabbed. She wipes the flakes from the blade with another swab and drops the tip into another plastic tube. Kong repeats the procedure on each elbow, each inner forearm, the back of each knee, and finally in one of his nostrils. Once the sampling is over, she and her colleagues take pictures of Jake’s rash. Then they check his vital signs.
Jake doesn’t know much about what happens to his skin cells once they disappear into the lab. For the most part, he comes to the clinic, which he found because he was enrolled in an NIH study on asthma, for Kong’s helpful advice about his eczema. (She recommended that he take diluted bleach baths during bad flares, which has given him some relief.) But he says he’s proud to be part of the effort to understand this disease, in case his future children end up with the same troubles.
Jake’s skin samples, like those from the more than twenty other children participating in the study, wind up in a nearby laboratory complex, where they are stored in a large freezer set at –112 degrees F. The inside of the door is lined with thick white snow. Clay Deming, a biologist at the lab, explained to me how he prepares each sample. He selects a tube and defrosts it; adds lysozyme, an enzyme that breaks down bacterial cell walls; and shakes the concoction using a vortex mixer. This releases DNA from the bacterial cells so that it floats freely in the liquid. He then pours the solution over a gel filter designed so that just bacterial DNA fragments will stick to it.
With the DNA fragments thus separated, Deming can use a technique called polymerase chain reaction to make millions of copies of one particular bacterial gene: 16S. All bacteria carry the gene, but its DNA sequence varies from species to species. After amplifying the DNA fragments, Deming is left with a new set of tubes, each holding the 16S pieces harvested from a particular area of the participant’s skin.
He puts the tubes on ice in order to FedEx them to a building five miles north, the NIH Intramural Sequencing Center. There, machines read the precise sequence of 1,500-odd letters in each 16S fragment, giving the chemical signature of each species. Finally, technicians upload the sequence data to an internal network, ready to be mined by Segre and Kong.
The skin is an ecosystem. Like any other ecosystem, it harbors permanent residents and also migrant species that flock to a few hot spots during certain seasons. Those fluctuations powerfully influence how the skin works. Staphylococcus epidermidis, for example, may help educate the skin’s immune system, training it to recognize particular molecules so that it can better respond to an attack by harmful species. S. epidermidis churns out proteins that prevent unwanted invaders from adhering to skin. So it makes sense that disrupting these complex microbial interactions could lead to skin problems.
With the eczema study, Segre says she hopes to find patterns in the microbiome that could predict the onset of an eczema flare in a particular child or even help doctors choose a far more effective treatment; for some patients, bleach baths might help, whereas for others, a round of anti-inflammatory steroids might be the best choice.
Kong and Segre are not the only scientists looking into the connection between the microbiome and inflammatory skin conditions. Martin Blaser, a microbiologist and physician at New York University, thinks the microbiome also plays a role in psoriasis. Some twenty-five years ago, Blaser’s father had told him that his psoriasis—scaly red-and-white patches on the skin—seemed to get better after he started taking allopurinol, a medicine that treats gout. Blaser, who has mild psoriasis himself, took notice. He knew that because allopurinol interferes with the synthesis of DNA, it kills bacteria or makes it very difficult for those bacteria to grow.
His father’s experience spu
rred Blaser to look deeper into the connection between allopurinol and microbes. He discovered that a few decades earlier, researchers had run clinical trials on allopurinol as a treatment for psoriasis. The results were inconclusive, but Blaser thought that the medicine might work on a particular subgroup of psoriasis patients.
In 2002, he finally secured funding to study the microbiomes of psoriasis patients. For the project, Blaser performed a general census of bacteria living on the inner forearms of six healthy people. Later his group did the same analysis on skin from six people with psoriasis, and they found some striking differences. The six psoriasis patients had considerably more bacteria from the Firmicutes phylum than people without psoriasis. What’s more, the most common class of bacteria in healthy skin, Actinobacteria, was significantly underrepresented in the lesions.
“Those results, which were important at the time, now are kind of laughable because they’re on such a small scale,” Blaser says. Now, with funding from the Human Microbiome Project, his team is looking in much greater detail at how the overall microbial numbers, as well as changes in the species distribution, vary in patients with psoriasis.
In May 2009, Kong, Segre, and their colleagues published the first comprehensive catalog of skin microbes, based on samples taken from twenty different body parts—from the oily crease outside the nose to the moist spots between the fingers—of ten healthy people. By sequencing hundreds of the 16S genes in each sample, the researchers found that our epidermal ecosystem is much more diverse than anybody had thought, with discrete bacterial populations ranging in size from fifteen species behind the ear to forty-four on the forearm. The team also looked at whether the microbiome is consistent across individuals; that is, do some individuals always have a certain set of bacterial species, no matter what part of the body those bacteria live in? The researchers learned that, no, the bacteria are finely tailored to specific locations on the body rather than to individual humans. For example, the bacterial communities under your arm are more similar to those under someone else’s arm than to those behind your knee.
