While scientists remain uncertain about the specific causes of rheumatoid arthritis, an emerging body of research has led many to suspect that the microbiome—the bacteria that live in the gastrointestinal tract—may be to blame.

Rheumatoid arthritis occurs when the body attacks its own joints: several recent studies have found additional correlations between gut microbes and other diseases in which the body’s immune system goes ‘awry,’ and begins to attack its own tissue.

In 2013, Jose Scher, a rheumatologist at New York University, published a study that found people with rheumatoid arthritis were far more likely to have a bug called Prevotella copri in their intestines than people without the disease. Another study two years later indicated that aptients with psoriac arthritis, another type of autoimmune joint disease, had significantly lower levels of other types of intestinal bacteria.

Scher’s work is part of a growing effort by researchers across the globe to understand the ways in which the microbiome affects overall health. The gut contains up to one thousand different species of bacteria, which collectively weight between one and three pounds. This mass contains trillions of cells, more than the number of cells that make up our bodies. Throughout the past several years, scientists have compiled a growing collection of evidence that confirms links between these bugs and overall wellness.

These microbes can directly affect the immune system, even with diseases not located in the gut. An immunologist at the Mayo Clinic, Veena Taneja, has found striking differences in the bacterial populations of mice bred to be genetically prone to rheumatoid arthritis. Scher, director of NYU’s Microbiome Center for Rheuamtology and Autoimmunity, believes this is “frontier stuff…a shift in paradigm. By including the microbiome, we’ve added a new player to the game.”

Other research has focused on the influence of these bacteria on the immune system, as recent decades have seen a spike in the incidence of many autoimmune diseases. Several researchers state that this rise is, at least partially, due to changes in our bacterial ecosystem: altered diet, the proliferation of antibiotic use, and decreasing contact with the ‘microbe-packed natural world of animal plants’ have transformed the bacteria. NYU microbiologist Martin Blaser argues that because we lose microbes with each generation, “They are going extinct. These changes have consequences.”

Blaser’s own research has pinpointed the gut bacteria of U.S. children, finding that a specific species of bacteria thought to reduce the risk of asthma was very low. The decline of this bacteria in the West, as opposed to its appearance in the vast majority of the developing world, could have medical consequences. Blaser suspects that asthma is one of the primary illnesses affected by the changing microbiome; rates have escalated in the U.S. for the past three decades, growing over 28 percent between 2001 and 2011.

Dozens of researchers are looking into a range of potential strategies to use bacteria as medicine for immune disorders. Scher believes that eventually, it will be possible to treat arthritis, and other immune disorders, by adjusting the microbiome. At the Mayo Clinic, Taneja has found that a species of bacteria can prevent or halt the mouse versions of both rheumatoid arthritis, and multiple sclerosis—an autoimmune disease of the brain and nerves. Harvard University microbiologist Dennis Kasper, who discovered a targeted compound in the gut that protects mice from certain autoimmune diseases, including MS, is optimistic: “In 10 or 15 years, I think the microbiome will be a key therapeutic option for some of these diseases. There will be challenges, but I don’t see why it can’t happen. This isn’t science fiction.”