Morteza Nikoubazl/Reuters

Imagine a posh store displaying expensive samples that sell for more than $1,000 an ounce. The donor ate an unprocessed, non-GMO, plant-based diet, with no hormones or antibiotics, ever. The label says it’s from a rare and difficult-to-access source in the Himalayas. The samples are rigorously tested on site to assure purity and quality, and then flown back to the U.S. in a pressure-controlled, refrigerated jet. The lighting in the store is flattering, the sales staff impeccably dressed, and the marble floors so clean you could eat off of them.

Luxury boutiques selling high-octane human stool unadulterated by the perils of Western society may only be fantasy for now, but probably not for long. They’re coming, and here’s why.

There are more than a billion bacteria in each drop of fluid in your colon, an environment we call the microbiome. It's a mixture so distinctive from person to person that your individual constellation of bacteria is a better identifier than your own DNA. Stool consists of about 70 percent bacteria, and which particular species are present in yours can dictate a lot more than just your bathroom habits.

Autoimmune diseases like Crohn's, ulcerative colitis, multiple sclerosis, lupus, and rheumatoid arthritis are common in more developed countries and rare in less developed ones. The "hygiene hypothesis" explains this uneven distribution by suggesting that in affluent societies, less childhood exposure to a variety of gut bacteria actually increases susceptibility to disease by suppressing the natural development of the immune system. (It seems our love affair with antibiotics and hand sanitizer is not all good).

What we eat also correlates strongly with the development of autoimmune diseases, since our diet greatly determines what kinds of bacteria are present in our gut. Italian researchers found that breast-fed children in Florence and Burkina Faso had similar microbes in infancy, but once they started eating the local fare their gut bacteria diverged dramatically. Florentine children consuming a typical Western diet high in sugar, fat, and meat had less bacterial diversity and more species associated with allergy, inflammation, and obesity. The children in Burkina Faso eating an unprocessed, high-fiber plant-based diet had more diverse species and more types associated with leanness. They also had larger numbers of bacteria that produce beneficial compounds called short-chain fatty acids, which may be important in suppressing disease.

Given what we know about the importance of a well-stocked and diverse microbiome, a daily probiotic—essentially a cocktail of beneficial bacteria—may seem like an excellent idea. The problem is, though we've identified several hundred bacterial species in the gut, we've only been able to reliably culture and grow a tiny percentage of them. Also, there are likely thousands more whose acquaintance we haven't yet made, but whose presence is essential for good gut health and proper immune function. Given these limitations, the benefits of taking a daily probiotic seem unrealistically optimistic for someone trying to overcome autoimmune disease or other serious illnesses.

One such serious illness is Clostridium difficile. When someone with depleted gut bacteria encounters C. diff, it proliferates in the large intestine, releasing toxins that cause severe diarrhea, cramping, bloating, and even death. C. diff infection affects approximately a quarter-million people in the U.S. annually and leads to about 14,000 deaths, mostly because of the widespread use of antibiotics—the main risk factor for acquiring the infection.

The growing number of C. diff infections resistant to standard treatment has led to a novel form of therapy known as fecal microbiota transplant (FMT). This technique involves transferring stool from healthy donors into the digestive tract of the person infected with C. diff. The stool may be introduced in a number of ways: via a tube inserted through the nose that delivers it to the intestines, as a rectal enema, or placed in the colon during a colonoscopy. Researchers at the University of Calgary recently created a more palatable way to deliver the transplant: vitamin sized poo-filled pills that release their contents in the colon. Their data shows virtually 100 percent success in clearing recurrent C. diff infections, and a January 2013 study in the New England Journal of Medicine concurred, showing that fecal transplants were far more effective in clearing up recurrent C. diff infection than standard antibiotic therapy.

FMT may seem like a drastic way to rehab your microbiome, but there’s lots of precedence for going straight to the source when it comes to acquiring gut bacteria. Coprophagia, or eating stool, is widely prevalent among certain animals. Baby elephants, pandas, koalas, and hippos eat the feces of their mother or other adults in their herd in order to acquire vital gut bacteria required for digestion. Consumption of fresh camel feces has been observed among certain tribes, including the Bedouins, as a highly effective treatment for infectious diarrhea. And in medieval times it was not uncommon for physicians to taste their patient’s stool to aid in diagnosis (a practice I'm in no hurry to resurrect).

These days coprophagia is most commonly associated with dementia and mental illness, and clearly there is significant risk from eating stool, including the acquisition of hepatitis, bacterial infections, and parasites. But could FMT become the new super-probiotic? The remedy not just for intestinal infections like C. diff, but also for chronic autoimmune diseases and other ailments that may be associated with depleted gut bacteria.

Several studies have looked at the usefulness of FMT in Crohn’s disease and ulcerative colitis, as well as obesity, since gut bacteria differ dramatically between overweight and lean people. A few of the patients in my practice are covert practitioners of FMT. One self-administers weekly enemas of her husband’s stool to keep her severe Crohn’s disease in remission—a last-ditch effort that proved enormously successful after several potent drug regimens failed. (Other than for refractory C. diff and clinical trials, FMT is not routinely available in most doctors’ offices).

There are still lots of unanswered questions when it comes to FMT, including whether through the rectum or mouth is the best way to administer the stool, who should donate (most studies have used first-degree family members but they may not always be the healthiest or best choice), long term effectiveness of stool transplants and safety concerns. But the successes of the early studies are encouraging for those with refractory digestive conditions and for those of us who treat them.

Hippocrates said all disease begins in the gutIt may be that some important remedies are to be found there, too. I believe the “haute manure” store is on the horizon, as we attempt to get back to a dirtier, healthier way of life.