The unassuming one-storey office building on the periphery of the Wellswood neighbourhood in Tampa, Florida – a discreet concrete box with windows constructed from privacy glass blocks – houses two gastroenterologist practices. One of them, RDS Infusions, is among the few places in the entire Southeastern USA where people with C. diff. can go for treatment. The process begins at an endoscopy centre less than a mile away, where donor poo is inserted into sedated patients: up one end through a colonoscope and down the other through an endoscope that extends past the throat and stomach to the jejunum – the midsection of the small intestine.

The three- or five-day process ends back here in the office, on a bed that slopes downward toward the head, allowing gravity to help patients retain their follow-up faecal enemas. In one of the rooms, a small laminated poster depicts a rainbow arcing through a cloudbank and a single word repeated eight times in progressively bigger letters: “BREATHE”.

Among the 60 or so C. diff. patients that have followed his directives, R David Shepard, a gastroenterologist in Tampa, says he hasn’t had a failure yet. Until the FDA forced him to put his ulcerative colitis programme on hold, he had achieved a success rate of about 70 per cent for that condition, he says. Marion’s daughter was the first.

Dressed casually in a light blue short-sleeve button-up shirt with black slacks, Shepard is cautious and unfailingly polite. He is soft-spoken with a subtle Southern accent and a steady gaze. At a table in a small kitchen behind the practice’s warren of rooms and narrow hallways, he describes his foray into a therapeutic field that he initially dismissed. Talk to half a dozen doctors, in fact, and you’ll begin to hear some common themes.

The first fleeting reference, whether in medical school or from a patient, is quickly brushed off.

“The thought of it was basically one of disgust and ‘Oh, I’ll never do that. You’ve got to be kidding’,” Shepard says.

Elaine Petrof, an infectious-disease specialist at Queen’s University and Kingston General Hospital in Ontario, says doctors in her specialty are often conditioned to associate infections with germs that must be eliminated. “Just conceptually speaking, pouring sewage into people doesn’t seem like a good idea, right?” she says. “I confess that I fell into that category until I saw what this can actually do for people’s lives and actually turn them around.”

The technique lingered on the margins of accepted medical practice for years because there simply wasn’t a great need for it, says Alexander Khoruts, a gastroenterologist and immunologist at the University of Minnesota in Minneapolis. That changed within the last decade, when C. diff. became an epidemic and a more virulent strain emerged from Quebec. Doctors now routinely encounter patients whose infections have stopped responding to all antibiotics.

A motivated, well-educated patient or family begs them to reconsider.

Most doctors still refuse to offer the procedure. “Five years ago or a little more, that was the end of the conversation,” Shepard says. But the internet has changed everything. Now, he says, patients search until they find somebody who will do it.

They can also be persuasive. For Petrof, the turning point came in 2009. After a woman’s recurrent C. diff. infection stopped responding to antibiotics, she began bouncing in and out of the intensive care unit. Every day, the patient’s relatives asked Petrof to consider a faecal transplant. “I thought, ‘This is crazy’,” she recalls.

Then they brought her a bucket of poo.

The doctor finally yields.

“What completely floored me was the fact that within less than 72 hours, this patient, who had been having over a dozen bowel movements a day, basically completely turned around and at the end of the week walked out of the hospital,” Petrof says.

The therapy, using any of a range of methods, continues to work better than predicted.

“What is currently done is kind of medieval, and that’s how I started,” Khoruts says. “You plop a turd in the blender and draw it up in a syringe. Voila! There’s your transplant.” Some providers may send it up the colon, some down to the stomach or beyond, some – like Shepard – from both ends.

Although most providers haven’t published their overall success rates, their self-reported results are surprisingly similar, and consistent with what published reports there are. Khoruts says he has achieved a success rate of about 90 per cent after one infusion, 99 per cent after two. “In medicine, it’s pretty startling to have therapy that’s that effective for the most refractory patients with that condition,” he says. Colleen Kelly, a gastroenterologist with the Women’s Medicine Collaborative in Providence, Rhode Island, has performed the procedure on 130 patients with recurrent C. diff., with a success rate of about 95 per cent. Most of the transplants have taken after just one attempt.

For a relatively simple bacterial infection, Petrof says, the potential remedy may be fairly straightforward. “With recurrent C. diff. what you’ve done is you’ve basically torched the forest,” she says. Nearly everything has been killed off by the antibiotics, leaving very low bacterial diversity. “So the C. diff. can just take root and grow.” Adding back almost any other flora – the equivalent of planting seedlings in the dirt – could help the ecosystem keep interloping pathogens at bay.

For more complicated conditions, though, a simple faecal transplant may not be enough, at least with donors from the Western world. One hypothesis suggests that people in lower-income countries might harbour more diverse bacterial populations in their guts than those who have grown up in a more sterile, antibiotic-rich environment. And in fact, a 2012 study found that residents of Venezuela’s Amazonas State and rural Malawi had markedly more diverse gut microbiomes than people living in three US metropolitan areas. Scientists have already raised the idea that a rise in allergies and autoimmunity in industrialised nations may derive from a kind of collective defect of reduced microbial diversity.

“We cannot find people who’ve never been on antibiotics,” Khoruts says of his donors. For complex autoimmune diseases such as ulcerative colitis, faecal transplants may offer only a partial solution. And with some data suggesting that susceptibility may be linked in part to past antibiotic exposure, perhaps no Western donor can provide the microbes needed to fully reseed the gut.

What then? Khoruts says it may be necessary to seek out ancestral microbial communities – the ones all humans hosted before the advent of the antibiotic era – within people in Africa or the Amazon. “It’s just a disappearing resource,” he says.

Thomas Borody, founder and Director of the Centre for Digestive Diseases in Sydney and a pioneer in the faecal transplant field, finds some merit in the notion that we should seek out a more natural human microbiome. Any donor-screening process, though, would have to account for endemic parasites and pathogens. And researchers, he says, still know very little about the components of this complex and variable organ that may derive its power not only from bacteria but also from fungi and viruses such as bacteria-infecting bacteriophages. “The shortest way of saying it is, ‘We don’t know shit, man’.”