If some twisted genius vaporized all 10 trillion cells in your body — along with the hair, the fingernails, and other tissue they create — it would not leave empty space behind. A body-shaped cloud made of bacteria, viruses, and other former stowaways would hover briefly in the air. The cloud would outline your skin, delineate your lungs, trace your digestive tract. You might be gone for good, but your shadow biosphere would remain.
We got our first glimpse of these tiny tenants — now known collectively as the microbiome — in the late 17th century, when a Dutch lens grinder named Anton van Leeuwenhoek noticed a layer of white scum between his teeth. He mixed some of the gunk with pure rainwater and then placed it under one of his handmade microscopes. “I found, to my great surprise,” he wrote, “that it contained many small animalcules, the motions of which were very pleasing to behold.”
With the advent of fast DNA sequencing, today’s microbiologists can delve deep into this weird inner universe, and they’re just as amazed as Van Leeuwenhoek was. It’s not just the sheer quantity of microbial cells (100 trillion or so for one person alone) but also their diversity: Each of us is home to thousands of species of microbes, and no two people have quite the same mix.
We’re just beginning to learn the effects our microbiome has on us, but it’s clear that they can be profound. Certain species help digest food and synthesize vitamins; others guide the immune system. Medical researchers have linked obesity, heart disease, and anxiety to properties of the microbiome. In many cases, it’s not the individual species that seem to matter but the richness of the ecosystem. Just as the health of a forest depends upon diversity, our own health appears to benefit from the presence of a wide range of uninvited guests, many of which coevolved with us.
See below for a guided tour of your own personal ecosystem. From the top of your head to the depth of your gut, there’s a jungle in — and on — you.
THE FIRST 15 MONTHS: HOW OUR MICROBIOME DEVELOPS AND DIVERSIFIES
We start out sterile in the womb. But every baby gets coated with microbes the moment it passes through the birth canal. (Babies born by cesarean section are colonized by microbes from their mother’s skin.) More germs take up residence inside our bodies in the months that follow, delivered by bacteria-laced milk and fingertips and contact with floors, high chairs, and affectionate pets. This chart shows how microbial diversity in the large intestine grew during the first 15 months of one child’s life.
The brain is walled off from the microbiome by a series of biochemical moats and ramparts known as the blood-brain barrier. But there are indirect ways for microbes to change our minds. Bacteria in the gut release compounds into the bloodstream that pass through the blood-brain barrier; gut microbes can also trigger immunological and hormonal signals that penetrate the barrier. Together, these signals have been shown to influence hunger; one study of mice found that changing the gut bacteria even affected personality.
Microbes will worm their way into any place they can. In July, a team based at the Translational Genomics Research Institute in Flagstaff, Arizona, published an investigation of life inside the ear, based on samples from an 8-year-old boy with a chronic ear infection. The researchers found 11 species of bacteria, many of them new to science. They also were able to trace the origin of the bacteria — not to a playground or a bathroom but to the boy’s own insides. The germs had migrated from his adenoids, possibly by way of the eustachian tube.
Think about a mountain: Climbing from sea level to summit takes you through several ecosystems, each with vegetation and animals adapted to its particular conditions. Our skin, too, has many zones, each fostering a different balance of species. The face alone has several of these microclimates: The forehead and creases along the nose are greasy, for instance, so bacteria there are adapted to feeding on oils; microbes in other areas thrive on sweat, perhaps extracting nitrogen from it.
Our mouths are loaded with more than 500 species of microbes, but they’re not all the same from one person to the next. Scientists analyzed three mouths (see below) and found 818 species in total, a quarter of which were not shared by any of the subjects. Roughly half of the total (387) were shared by all three, leading researchers to conclude that these might represent a “core” microbiome for the oral cavity. What’s clear is that the balance in each person’s mouth helps shut out bugs that cause tooth decay and other maladies.
Ever since Van Leeuwenhoek, scientists who study the microbiome have focused mainly on bacteria. But increasingly, that spotlight is expanding to include viruses. In the throat alone, there are at least 200 million virus particles in each milliliter of mucus. When scientists survey the viruses of the microbiome, 90 percent typically match no known species. And yet these viruses do not make us sick; instead, they infect the bacteria in our microbiome, possibly helping to keep our microbial ecosystem stable.
We all know that cleaning a cut helps avoid infection. So it can be disturbing to find out that the entire surface of our skin is sheathed in microbes. Usually they don’t cause infection — in fact, immune cells, which prowl the sweat glands and hair shafts in search of invaders, give these hangers-on a pass. In turn, these germs help us out: Staphylococcus epidermis, for example, releases toxins that kill pathogens and also sends immune signals that speed healing. Keep washing your hands, for sure, but a whole-body sterilization would do more harm than good.
The more we learn about the microbiome, the more surprising connections we find to our health. Take atherosclerosis, once thought to result entirely from an unhealthy diet. Scientists recently harvested DNA from arterial plaques and discovered bacteria living inside them. Stranger still, many of the plaque-dwelling species are normally found in the mouth or gut. One of the researchers, Ruth Ley of Cornell, thinks that when these bacteria enter blood vessels, they might trigger the immune system to produce inflammation, causing the vessels to swell and form plaques.
Until recently, scientists believed that healthy lungs were sterile. When they tried to culture bacteria from lung fluid, they ended up with nothing. But now that they can use sequencing to fish for microbial genes, they know that lungs host a thriving community of bacteria. Researchers have also found that people who suffer from asthma or other pulmonary diseases have a different balance of species in their lungs, which might account for some of their symptoms — sufferers may, for example, be missing species that would normally tamp down their immune response.
Comparing the bacteria on subjects’ hands, scientists found that on average just 17 percent of the species on the left hand also live on the right.
More than 100 species of microbes live in the stomach, where they graze on the slime lining its walls. The most famous of all stomach-dwellers is Helicobacter pylori, which has been found to cause gastritis and ulcers — a discovery that won a Nobel Prize for two Australian researchers in 2005. But H. pylori’s reputation has improved since then. In the stomachs of children, it sends out signals that help the immune system mature. Youngsters who lose their H. pylori by taking antibiotics are more likely to develop asthma and allergies.
The large intestine is the microbiome megalopolis, with the densest gathering of microbes in the entire body: usually around 200 prevalent species and up to 1,000 less-common ones. As food moves through the stomach and small intestine, our own cells do their best to break it down and pass nutrients into the bloodstream. But much is left undigested by the time it reaches the colon. There, we depend upon microbes to break up starches and other tough molecules; they also dismantle some of the toxins in our food and build essential vitamins.
OBESITY TRANSFORMS THE ECOSYSTEM
Average number of species in a lean person’s gut: 783
Average number of species in an obese person’s gut: 569
We are what we eat, and so are our gut flora. When people switch to a high-calorie diet, their microbiome changes, with rare species becoming common and common species becoming rare. It also becomes less diverse. Scientists have tested the effect of the obese microbiome by rearing mice without any bacteria in them at all, then inoculating some of them with microbes from mice fed a high-calorie, high-fat Western diet and others with bacteria from mice fed a low-calorie diet. The mice that got the high-calorie germs became fat.
Antibiotics = Microbiome Killer
Studies have revealed some alarming costs of taking antibiotics, which don’t discriminate between disease-causing bacteria and our natural microbiome. Graphed below is the diversity of gut bacteria from one important genus (Bacteroides) in a patient who took a weeklong course of clindamycin; different colors represent the different species. For nine months after exposure, the subject’s gut was left with nothing but one type, a clindamycin-resistant strain of Bacteroides thetaiotaomicron. Even two years out, the flora had not regained their former diversity.