By the time a child crawls, he is blanketed by an enormous cloud of microorganisms. Illustration by Nishant Choksi

Helicobacter pylori may be the most successful pathogen in human history. While not as deadly as the bacteria that cause tuberculosis, cholera, and the plague, it infects more people than all the others combined. H. pylori, which migrated out of Africa along with our ancestors, has been intertwined with our species for at least two hundred thousand years. Although the bacterium occupies half the stomachs on earth, its role in our lives was never clear. Then, in 1982, to the astonishment of the medical world, two scientists, Barry Marshall and J. Robin Warren, discovered that H. pylori is the principal cause of gastritis and peptic ulcers; it has since been associated with an increased risk of stomach cancer as well. Until that discovery, for which the men shared a Nobel Prize, in 2005, stress, not an infection, was assumed to be the major cause of peptic ulcers.

H. pylori is shaped like a corkscrew and is three microns long. (A grain of sand is about three hundred microns.) It is also one of the rare microbes that live comfortably in the brutally acidic surroundings of the stomach. Doctors realized that antibiotics could rid the body of the bacterium and cure the disease; treating ulcers this way has been so successful that there have been periodic discussions of trying to eradicate H. pylori altogether. The consensus was clear; as one prominent gastroenterologist wrote in 1997, “The only good Helicobacter pylori is a dead Helicobacter pylori.” Eradication proved complicated and expensive, however, and the effort never gained momentum. Yet few scientists questioned the goal. “Helicobacter was a cause of cancer and of ulcers,’’ Martin J. Blaser, the chairman of the Department of Medicine and a professor of microbiology at the New York University School of Medicine, told me recently. “It was bad for us. So the idea was to get it out of our bodies, as fast as we can. I don’t know of anyone who said, Gee, we better think about the consequences.”

No one was more eager to rout the organism from the human gut than Blaser, who has devoted most of his working life to the study of H. pylori. His laboratory at N.Y.U. developed the first standard blood tests to identify the microbe, and most of them are commonly in use today. But Blaser, a restless intellect who, in addition to his medical duties, helped start the Bellevue Literary Review, wondered how an organism as old as humans could survive if it caused nothing but harm. “That isn’t how evolution works,” he said. “H. pylori is an ancestral component of humanity.” By the nineteen-nineties, Blaser had begun to look more closely at the bacterium’s molecular behavior, and in 1998 he published a paper in the British Medical Journal suggesting, contrary to prevailing views, that it might not be so dangerous after all. The following year, he started the Foundation for Bacteriology, to help focus attention on the critical, and usually positive, role that these organisms play in human evolution.

“We have a certain narrative,’’ he said, sitting in his laboratory. A Tennessee license plate—“HPYLORI”—rested on his desk and a detailed map of the bacterium’s genome was hanging on a wall. Blaser, wearing a crisp blue sports coat, and with well-tended gray hair, projects an air of genial confidence; he seems more like the chief executive of a conglomerate than like the bench scientist he has been for decades. “Germs make us sick,” he said. “But everyone focusses on the harm. And it’s not that simple, because without most of these organisms we could never survive.’’

Since 1953, when James Watson and Francis Crick described the structure of DNA, we have looked upon genes as our biological destiny. The double helix provided a blueprint for life, and the process of making a human, while staggeringly complex, was also straightforward: genes manufacture proteins, which, in turn, build the various parts we need. When DNA is damaged or genes interact poorly with one another, the eventual result is disease. To understand how and when our genes malfunction, then, would be to understand how to prevent, treat, and cure everything from cancer to the common cold. That search became the central task of molecular biology. In the past decade, however, aided by the rapidly escalating power of computer processing and by the same revolution in DNA-sequencing technology that made it possible to map our genome, another truth has emerged: while our health is certainly influenced by genes, it may be affected even more powerfully by bacteria.

We inherit every one of our genes, but we leave the womb without a single microbe. As we pass through our mother’s birth canal, we begin to attract entire colonies of bacteria. By the time a child can crawl, he has been blanketed by an enormous, unseen cloud of microorganisms—a hundred trillion or more. They are bacteria, mostly, but also viruses and fungi (including a variety of yeasts), and they come at us from all directions: other people, food, furniture, clothing, cars, buildings, trees, pets, even the air we breathe. They congregate in our digestive systems and our mouths, fill the space between our teeth, cover our skin, and line our throats. We are inhabited by as many as ten thousand bacterial species; these cells outnumber those which we consider our own by ten to one, and weigh, all told, about three pounds—the same as our brain. Together, they are referred to as our microbiome—and they play such a crucial role in our lives that scientists like Blaser have begun to reconsider what it means to be human.

“I love genetics,” Blaser said. “But the model that places our genes at the root of all human development is wrong. By itself, it simply cannot explain how rapidly the incidence of many diseases has risen.” He stressed that genes matter immensely, but that one must take into account more than just the twenty-three thousand genes we inherit from our parents. The passengers in our microbiome contain at least four million genes, and they work constantly on our behalf: they manufacture vitamins and patrol our guts to prevent infections; they help to form and bolster our immune systems, and digest food. Recent research suggests that bacteria may even alter our brain chemistry, thus affecting our moods and behavior.

The process of learning about our microbiome is in its early days, but even the most tentative results have begun to transform our understanding of human health_._ Recently, a group at the University of Maryland School of Medicine identified twenty-six bacterial species that reside in the guts of members of the Old Order Amish sect—a closed population, with a nearly identical gene pool—that seem to account for common metabolic abnormalities such as high blood pressure and insulin resistance. Similar research has suggested that the destruction of bacteria may contribute to Crohn’s disease, obesity, asthma, and many other chronic illnesses. “The prospects here are endless,’’ Blaser said. “We need to be careful with the science and not oversell it. But I have been a practicing physician and medical researcher for more than thirty years, and this is the most exciting and important work of my lifetime.”