Exactly how the microbes interact with the illness—whether as a trigger or as a shield—remains mostly a mystery. But Mazmanian and his colleagues have identified one possible link: a chemical called 4-ethylphenylsulphate, or 4EPS, which seems to be produced by gut bacteria. They’ve found that mice with symptoms of autism have blood levels of 4EPS more than 40 times higher than other mice. The link between 4EPS levels and the brain isn’t clear, but when the animals were injected with the compound, they developed autism-like symptoms.

Mazmanian, who in 2012 was awarded a MacArthur grant for his microbiome work, sees this as a “potential breakthrough” in understanding how microbes contribute to autism and other neurodevelopmental disorders. He says the results so far suggest that adjusting gut bacteria could be a viable treatment for the disease, at least in some patients. “We may be able to reverse these ailments,” he says. “If you turn off the faucet that produces this compound, then the symptoms disappear. That’s what we see in the mouse model.”

Scientists have also gathered evidence that gut bacteria can influence anxiety and depression. Stephen Collins, a gastroenterology researcher at McMaster University in Hamilton, Ontario, has found that strains of two bacteria, lactobacillus and bifidobacterium, reduce anxiety-like behavior in mice (scientists don’t call it “anxiety” because you can’t ask a mouse how it’s feeling). Humans also carry strains of these bacteria in their guts. In one study, he and his colleague collected gut bacteria from a strain of mice prone to anxious behavior, and then transplanted these microbes into another strain inclined to be calm. The result: The tranquil animals appeared to become anxious.

Overall, both of these microbes seem to be major players in the gut-brain axis. John Cryan, a neuroscientist at the University College of Cork in Ireland, has examined the effects of both of them on depression in animals. In a 2010 paper published in Neuroscience, he gave mice either bifidobacterium or the antidepressant Lexapro; he then subjected them to a series of stressful situations, including a test which measured how long they continued to swim in a tank of water with no way out. (They were pulled out after a short period of time, before they drowned.) The microbe and the drug were both effective at increasing the animals’ perseverance, and reducing levels of hormones linked to stress. Another experiment, this time using lactobacillus, had similar results. Cryan is launching a study with humans (using measurements other than the forced swim test to gauge subjects’ response).

So far, most microbiome-based brain research has been in mice. But there have already been a few studies involving humans. Last year, for example, Collins transferred gut bacteria from anxious humans into “germ-free” mice—animals that had been raised (very carefully) so their guts contained no bacteria at all. After the transplant, these animals also behaved more anxiously.