It’s often been observed that the human body is something of a wonderland for bacteria — vast colonies of which live on your skin, in your mouth, and inside your intestinal tract, which is home to one of the densest bacterial populations on Earth. It’s the latter which has been the focus of an ongoing and intensifying battle in guts across America; in this age of antibiotics, strains of dangerously immune “superbugs” are proliferating, and when they find their way inside a host, they can be tough to get rid of. What results is tantamount to a war inside you — between the “good” bacteria and the “bad” — inside a vast-but-tiny universe that doctors are only beginning to understand.

His name is Dr. Johannes Aas, and he’s a gastroenterologist. Not long ago, a patient of his was battling a nasty infection that wouldn’t go away, caused by a potent and largely antibiotics-immune bacterium called C. difficile. It’s inside many of us, but is usually kept in check by the population of beneficial intestinal bacterium, or flora, which digest our food and provide nutrients to the body. But if the balance of this ongoing battle is tipped — say, by a dose of antibiotics which kills the beneficial flora but not the C. difficile — then the bad guys can take over, producing a toxin that causes serious diarrhea and over time can destroy the colon lining. In other words: bad news.

From Physorg.com:

Patients like this used to be rare. But C. difficile is one of a growing number of microorganisms that have become resistant to antibiotics, while at the same time becoming more common and virulent. According to the U.S. Centers for Disease Control and Prevention, hospitalizations from C. difficile infections increased by 23 percent each year between 2000 and 2005. Death rates tripled between 1999 and 2004.

Dr. Aas’ patient was facing serious side effects, and even death. Desperate, Aas scoured medical literature, and finally hit upon an old Norwegian folk remedy — the poo cure. Definitely low tech, and a bit nasty-sounding, it involves injecting a bit of stool into a patient, in the hopes that someone else’s flora can replace their own, and tilt the battle of the bacteria back toward the side of good.

Here’s how the procedure, and the recovery, went down:

On a crisp fall day, she sat in the exam room with an opaque tube running through her nose, down her throat and into her stomach.

“We just need that little brown bag,” said Dr. Timothy Rubin, a gastroenterologist who works with Aas. He meant the stool sample from Jolliffe’s husband, which was being processed in the lab. It was mixed with water and filtered to take out the organic matter, leaving a dark brown liquid that contained billions of bacteria.

When the little bag arrived with the sample inside, Rubin used a large syringe to inject the liquid through the tube and into Jolliffe’s stomach. It was over in less than a minute.

“All I felt was cold,” she said.

Rubin says that when Aas first told him about the procedure he thought it was unusual, yes, but also brilliant. “He kept it simple, inexpensive and available to anyone,” he said.

Dr. Khoruts, another gastroenterologist, recently did his first stool transplant. The patient was an older woman whose C. difficile infection was so bad that she had to live in a diaper. Instead of a nose tube, he gave her a liquid stool enema. Within days, she was better.

“It was striking,” he said. Now, he and microbial ecologist Mike Sadowsky at the university are starting a similar research project to identify the crucial bacteria.

The funny thing is, scientists only understand why the poo cure works in the most rudimentary way; little is known about the universe of bacteria in our guts, though new research is underway, including a project nicknamed the “bacteria genome project,” which hopes to identify all the microscopic combatants inside us.