Dr. Mazmanian and other researchers now must manage a tricky balancing act. On one hand, their experiments have proven remarkably encouraging; on the other, scientists don’t want to encourage the notion that microbiome-based cures for diseases like Parkinson’s are around the corner.

That’s not easy when people can buy probiotics without a prescription, and when some companies are willing to use preliminary research to peddle microbes to treat conditions like depression.

“The science can get mixed up with what the pseudoscientists are doing,” said Dr. Hsiao.

Dr. Costa-Mattioli hopes that L. reuteri some day will help some people with autism, but he warns parents against treating their children with store-bought probiotics. Some strains of L. reuteri alter the behavior of mice, he’s found, and others don’t.

Dr. Costa-Mattioli and his colleagues are still searching for the most effective strain and figuring out the right dose to try on people. “You want to go into a clinical trial with the best weapon, and I’m not sure we have it,” he said.

Katarzyna B. Hooks, a computational biologist at the University of Bordeaux in France, warned that studies like Dr. Costa-Mattioli’s are still unusual. Most of these findings come from research with fecal transplants or germ-free mice — experiments in which it’s especially hard to pinpoint the causes of changes in behavior.

“We have the edges of the puzzle, and we’re now trying to figure out what’s in the picture itself,” she said.