“It’s become more and more clear that these microbes can affect the immune system, even in diseases that are not in the gut,” says Veena Taneja, an immunologist at the Mayo Clinic in Rochester, Minnesota, who has found clear differences in the bacterial populations of mice bred to be genetically prone to rheumatoid arthritis. In those more susceptible to the disease, a species of bacteria from the Clostridium family dominates. In mice without arthritis, other strains flourish, and the Clostridium strains are scarce.

“This is frontier stuff,” says Scher, the director of the NYU’s Microbiome Center for Rheumatology and Autoimmunity. “This is a shift in paradigm. By including the microbiome, we’ve added a new player to the game.”

Scientists are especially intrigued by how these bacteria influence the immune system. In recent decades, the incidence of many autoimmune diseases has been increasing; many microbiome researchers argue that at least some of this rise is due to changes in our bacterial ecosystem. Altered diet, the explosion of antibiotic use, and decreasing contact with the microbe-packed natural world of animals and plants have all combined to transform the bacteria that call humans home. “Our microbiome has changed significantly over the past century, and especially over the past 50 years,” says NYU microbiologist Martin Blaser, who puts much of the blame on widespread use of antibiotics. “We’re losing microbes with each generation; they are going extinct. These changes have consequences.”

Blaser points to his own research on a species of bacteria called Helicobacter pylori (so named because it looks something like a helicopter). He sampled the gut bacteria of a group of U.S. children, and found that Helicobacter pylori existed in only 6 percent of them. By comparison, other research has shown that the strain is common in the vast majority of people from many parts of the world, especially in developing countries. The decline of Helicobacter pylori in the West, which is likely related to the spread of antibiotics as well as improved sanitation, may have medical consequences: Some research indicates that the bacteria may reduce the risk of asthma, perhaps by curtailing the body’s immune response to airborne stimuli. Blaser suspects that asthma is one of the illnesses affected by our changing microbiome: Rates in the U.S. have been climbing for three decades, and grew by more than 28 percent between 2001 and 2011.

Blaser argues that H. pylori and other gut microbes are so deeply involved in our bodily operations that they shouldn’t really be considered aliens. “They are part of who we are,” he says. “These organisms are part of our developmental choreography; they have an enormous amount to do with how our immune system develops.”

In fact, these bacteria have a powerful vested interest in controlling how our bodies respond to interlopers. Blaser and others say that it appears that many of the bugs that live inside us have thrived by modulating the immune system to avoid being recognized—and attacked—as invaders; in essence, these organisms train immune cells not to be trigger-happy. A microbiome with the wrong sorts of bugs, or the wrong ratio of bugs—a situation known as dysbiosis—may unbalance this immune system, causing immune cells to assault not only bacteria, but also the body itself.