The researchers initially hypothesized that transplantation would be helped by first clearing out the recipient’s gut microbes with antibiotics, according to Manichanh. But they discovered that the antibiotics were so powerful that they interfered with the establishment of the new microbial colonies. The rats that didn’t get antibiotics showed more changes in their flora than the ones that did.

George M. Weinstock, a professor of genetics at Washington University in St. Louis and associate director of the school’s Genome Center, says it’s too soon to tell whether similar transplantation will work in people, and if so, for which diseases. While anecdotal experiments have shown that changing someone’s microbiome can be a treatment for disease, definitive experiments are lacking, he says.

David A. Relman, a professor of medicine and of microbiology and immunology at Stanford University, says it also remains to be seen whether the transplantation can be standardized to produce reliable and reproducible results. Getting someone else’s gut microbes could conceivably have a positive effect on disorders that involve bacterial overgrowth, but could also have potentially dangerous effects. This new study followed the rats for three months and found that the new colonies of microbes were stable. But future studies will have to follow the transplant recipients over a longer term, Relman says.

The next step in their research, Manichanh says, is to see if a microbiome transplant can affect the course of a sick animal’s disease. She and her team first plan to look at irritable bowel syndrome. They are already working to catalog the microbiotic diversity of people with the disorder, and hope to associate specific strains of bacteria with the disease.