Back then, such samples normally went to a laboratory to be grown in a petri dish for analysis, a good way to study those microbes that happen to be at home in a petri dish. Relman had the bold idea of adding DNA sequencing as a way of seeing every living thing. In the years since, the cost of sequencing has plunged and taking swab samples from various neighborhoods of the body for DNA analysis has become the standard practice of microbiome research.
In the laboratory, each Q-tip sample ends up in one of 96 little wells on a plastic collection plate smaller than a paperback book. A technologist then puts the plate on a sort of paint shaker, with a pebble and some detergent in each well to break open the cell walls, the first step in extracting the DNA. The resulting liquid gets drawn up by a pipetter—imagine a device with eight tiny turkey basters in a row—and transferred to wells in a series of eight more collection plates, each step taking the sample closer to pure DNA. The finished product then goes to the sequencer, a countertop device that looks about as impressive as an automated teller machine married to a bar refrigerator. But what it tells us about our own bodies is astonishing.
It’s not just that there are more than 1,000 possible microbial species in your mouth. The census, as it currently stands, also counts 150 behind your ear, 440 on the insides of your forearm and any of several thousand in your intestines. In fact, microbes inhabit almost every corner of the body, from belly button to birth canal, all told more than 10,000 species. Looked at in terms of the microbes they host, your mouth and your gut are more different than a hot spring and an ice cap, according to Rob Knight, a microbial ecologist at the University of Colorado. Even your left and right hands may have only 17 percent of their bacterial species in common, according to a 2010 study.
But the real news is that the microbial community makes a significant difference in how we live and even how we think and feel. Recent studies have linked changes in the microbiome to some of the most pressing medical problems of our time, including obesity, allergies, diabetes, bowel disorders and even psychiatric problems like autism, schizophrenia and depression. Just within the past year, for instance, researchers have found that:
•Infants exposed to antibiotics in the first six months of life are 22 percent more likely to be overweight as toddlers than unexposed infants, perhaps because antibiotics knock down essential microbes.
•A lack of normal gut microbes early in life disturbs the central nervous system in rodents, and may permanently alter serotonin levels in the adult brain. Scientists suspect that the same could hold for humans.
•Just giving enough food to starving children may not permanently fix their malnutrition unless they also have the “right” digestive micro-organisms, according to a study of kids in Malawi.
Researchers generally can’t say for sure if changes in the microbiome cause certain conditions, or merely occur as a consequence of those conditions. Even so, the intriguing correlations have stirred up intense scientific interest, particularly with the publication last June of the first results from the Human Microbiome Project, a $173 million effort by the National Institutes of Health. The aim of that project was to establish a normal profile of microbial life in 300 healthy individuals. For the medical community, it was like discovering a new organ within the human body—or more than that, a whole new operating system. Suddenly doctors had “another lever,” as an article in the American Journal of Epidemiology put it this January, “to pry open the proverbial black box” of human health and sickness.
The public has also embraced the microbiome, beginning a few years ago when researchers at Washington University noticed a curious fact about obesity: Fat mice have more of a bacterial group called Firmicutes in their guts and thin mice have more Bacteroidetes. Feed the mice the same diet, and the ones with more Firmicutes extract more calories and lay on more fat. When the same differences showed up in humans, it seemed to explain the common complaint of many overweight people that they get fat just smelling food their skinny friends gorge on with impunity.
Such studies have stirred up remarkable enthusiasm in a subject matter most people would once have dismissed as yucky, gross or worse. It’s as if people suddenly loved Gulliver’s Travels for the passage where Jonathan Swift depicts a scientifically inclined student trying to return human excrement to the foods from which it originated.
This past winter, two rival efforts invited microbiome enthusiasts to submit their own fecal, oral, genital or skin samples for microbial analysis, and each raised more than $300,000 from crowd-funded donations typically under $100 apiece. The first effort, managed by Rob Knight’s Colorado lab and called American Gut, emphasized participation by top scientists in the field. Prevention magazine ranked the project’s $99 “map of your very own gut bacteria ecosystem” among its top 10 foodie gifts for the holidays. (For romantics, the $189 “Microbes for Two” package included analysis of a stool sample for both you and your partner. Or your dog.)