Earlier this summer, scientists reported the success of an unusual medical transplant; a woman with a life-threatening Clostridium difficile infection was treated, and apparently cured, with an injection of some of her healthy husband's gut bacteria. Researchers are now exploring the effects of this type of transplant in greater detail. They hope to eventually treat a wide range of ailments--from bowel diseases to obesity, diabetes to depression--by manipulating the bacteria that live in the human gut.

The microbes that inhabit our digestive tract, skin, mouth, and other body parts--known collectively as the human microbiome--play a key role in human health, influencing metabolism, immune function, and more. (Each of us contains roughly 10 times as many microbial cells as human ones.) Scientists are exploring a number of ways to manipulate one's microbes, including eating foods such as yogurt that contain healthy bacteria. But transplanting entire microbial populations may provide a more powerful way to overhaul our intestinal ecosystems. Eating more yogurt, for instance, hasn't helped people with C. difficile infections, says Rob Knight, associate professor of chemistry and biochemistry at the University of Colorado at Boulder.

Knight and collaborators from Barcelona, Spain, are studying microbe transplants in rodents with the hope of more effectively applying the approach to people. In a paper published last week in the journal Genome Research, the researchers demonstrated that they could successfully transplant the entire microbial community of one healthy rat's digestive system into another's. After three months, the recipient's microbiome more closely resembled the donor's, though the two microbiomes were not identical.

They also reported that antibiotics, which they had hoped would make the colonization easier, actually impeded growth. Animals treated with the drugs prior to the transplant ended up with a less diverse microbiome, which also had less resemblance to the donor's. Though the finding needs to be confirmed in people, it suggests that antibiotics might be counterproductive in the transplantation process, says Knight.

Unlike with traditional transplants of organs or tissue, the rats showed no evidence of rejection. "We didn't notice anything. They were not sick--not even diarrhea," says Chaysavanh Manichanh, a researcher in the Digestive System Research Unit at the University Hospital Vall d'Hebron Research Institute in Barcelona and the paper's first author.

Jo Handelsman, a professor in Yale University's department of molecular, cell, and developmental biology, says the idea of transplanting an entire microbiome is very provocative, because we don't yet understand which microbes are important and which aren't.

"Sometimes when we try to define every gene and every organism that needs to be there, we miss things. That's the attraction of taking a real community and transferring the whole thing," she says. Eventually, we will have a better handle on which microbes are most important, and on what we can eat--or avoid eating--to foster the growth and stability of "good" microbe communities, she says.