Anyone can publish on Medium per our Policies, but we don’t fact-check every story. For more info about the coronavirus, see

The Power of Poo

Why fecal transplants are now being considered for everything from obesity to autism.

Katherine Wu
Mar 15, 2018 · 7 min read

Think of the worst pill you’ve ever had to take — something big, bitter, and chalky with a terrible aftertaste. Would you rather have to swallow that pill, or a small helping of someone else’s feces?

This unappetizing hypothetical may soon be a medical reality for many. A so-called fecal microbiota transplant is… well, exactly what it sounds like: the therapeutic transfer of a donor’s feces into a recipient in the hopes that the microbes contained within will improve the recipient’s health.

Honed in recent years as an end-of-the-line treatment (no pun intended) for particularly stubborn bacterial infections, fecal transplants have shown amazing success, and are now being considered for everything from obesity to autism. However, most applications are still considered experimental and considerably risky — for the simple fact that there is still much to be learned about the microbes within us.

Save the Poopulation

The gut microbiota, or the community of bacteria, viruses, and other microbes that share the large intestine with our own human cells, has been hailed in recent years for its immense ability to affect nearly every aspect of human health. The friendly bacteria that reside in our colons have been shown to enhance the metabolism of food, provide us with essential nutrients, bolster our immune defenses, protect us against infectious disease, and even contribute to hormonal signaling and brain function. These microbes colonize us at birth and remain with us throughout life, forming a robust and stable population that wards off harm in exchange for simple room and board.

But just as a happy, stable microbiota contributes to good health, perturbations to this community can contribute to disease. Think of a lush and vibrant garden, full of diverse species and colors of flowers and trees with different blooms and fruits. While weeds are a natural and even inevitable part of most gardens, if weeds overgrow, they can overrun the desired flora. These imbalances are paralleled in the gut microbiota, which can be affected by travel, illness, antibiotic use, diet, and more.

The gut microbiota is fairly resilient. Most times, after a temporary disruption has ended, things return to normal. But sometimes even the best of whackers can’t triumph over the weeds, and the gut microbiota remains in flux or dominated by an unhealthy community, wreaking havoc on our health. Lasting imbalances in the gut microbiota have been linked to inflammatory bowel disease, irritable bowel syndrome, obesity, diabetes, multiple sclerosis, autism, colorectal cancer, and more.

Many of these conditions and their causes remain poorly understood. What they have in common, though, is a diseased gut microbiota — an entity so vital for function that, in recent years, it has been referred to as one of the body’s major organs. Scientists have realized that, as with any organ that gets damaged beyond repair, the best option may be a transplant: replacing old and sick with healthy and new. Because bacteria from our guts account for up to 30% of the mass of our stool, feces are actually a very elegant solution. And the best thing about a fecal transplant? The donor is no worse off without it — and would (in most cases) otherwise be flushing the “waste” down a toilet.

The Old Switch-A-Poo

As unsavory as fecal microbiota transplants sound, they’re not as bad as you might first expect. Patients aren’t simply chugging poop smoothies. In fact, you may not even be able to identify a dose of prepared feces by eye (or nose): much of the fecal matter is diluted into a slurry and filtered out beforehand.

The whole process is actually surprisingly simple. Once doctors obtain feces from a donor, they add water, saline, or milk, blend it up, and strain the mixture through a coffee filter. The resulting solution is then passed into the body through either the front door or the back — that is, through a nasogastric tube or through an enema or colonoscopy.

In fact, the idea of ingesting someone else’s feces isn’t even as outlandish as it may seem. Many animals, including dung beetles, mice, and koalas, regularly engage in this practice, formally known as coprophagy, as a way to spread seeds, acquire nutrients, and bolster their own microbiota. Some social insects like termites actually skip the middleman and engage in what’s called proctodeal trophallaxis — that is, communal butt-licking — to obtain these beneficial microbes. As for humans? People have been using feces as a form of medicine as early as the fourth century in China. Records show that aptly-named recipes for “yellow soup” and “golden syrup” were actually slurries of unfiltered feces from humans, used to treat gastrointestinal distress and diarrhea. And recipes sometimes got wild — quite literally: in World War II, German soldiers resorted to ingesting the feces of camels to treat crippling dysentery. By comparison, modern fecal transplants sound like McFlurries.

One Man’s Trash is Another Man’s Treasure

The majority of the clinical applications of fecal transplants have been to treat a bacterium called Clostridium difficile, which causes severe and potentially lethal diarrhea and colon inflammation in nearly half a million people each year. Many cases of C. difficile are caused by antibiotic use, which, when administered to prevent infections, inadvertently wipes out friendly members of the gut microbiota. This can clear the way for “opportunistic” pathogens like C. difficile, which takes advantage of the newly vacated property and spreads rapidly. Although some instances of C. difficile are curable with other powerful antibiotics, 20–35% of cases lead to recurrent infections that are often unresponsive to drug therapy, leading to years of intermittent diarrhea, hospital stays, and hefty health care bills.

Medical resources exhausted, a group of doctors in the 1950s decided to try a more radical idea: silencing the weedy overgrowth of C. difficile by re-planting hardy foliage to compete them away. They reasoned that if the infection was due to a weakened gut microbiota, the smartest thing to do would be simply replace it with a stronger one. And so was introduced the concept of modern fecal microbiota transplants: the restoration of a healthy microbiota and its protective qualities.

Incredibly, the average cure rate of C. difficile patients treated with fecal transplants is about 90%. This speaks to the amazing power of a healthy gut microbiota to outcompete and defend against invaders. Seeing the results with C difficile, doctors were quick to apply this treatment to other diseases. In clinical trials, fecal transplants have a cure rate of up to 60% in cases of ulcerative colitis. And in a handful of studies in patients with irritable bowel syndrome, about 70% of those who received fecal transplants had long-term symptom relief.

More radical possibilities may also be on the horizon. Work in mice has shown that transferring the microbiota from a lean mouse into an obese mouse can help the obese mouse lose weight. And the list goes on — cardiovascular disease, Parkinson’s disease, autism, and even cancer are all conditions in which the gut microbiota undergoes a marked change. It’s unclear whether these diseases cause a change in the gut or vice versa, but in either case, a fecal transplant could potentially be hitting the reset button in many of these patients. Importantly, though, a lot of these studies haven’t yet left the realm of lab rats, and there’s no guarantee that humans will experience the same positive side effects.

Winning at Number Two?

Fecal transplants may sound like quite the miracle treatment. And in some cases, they may be. After all, nowadays, it’s pretty much impossible to find a health condition that isn’t affected in some way by the microbiota.

But let’s return to that ick factor for a second. There are a few more downsides than a literal turn of the stomach. The largest one is that we simply don’t understand enough about the gut microbiota to really know what we’re doing every step of the way. Many of the bacteria we think are in the gut microbiota can’t yet be cultured in a lab, and are thus difficult to study. Even the ones we can manipulate haven’t been fully characterized: we know they’re there, but not what their exact roles are, or how they interact with other species and our bodies. At the end of the day, fecal transplants are a bit of a black box — and what we’re transferring is far more mystery than known fact.

Of course, we can screen for infectious microbes and certain red flags, but plot twists can still occur. For instance, one woman who received a fecal transplant for a chronic C. difficile infection became clinically obese in the months after an (otherwise successful) treatment. Why the weight gain? Doctors think it was because the woman had received the transplant from her overweight daughter. In a sense, her daughter’s microbiota was healthy in one way (i.e., resilient against C. difficile), but unhealthy in another (i.e., predisposed to weight gain). And it was a trade-off that doctors didn’t see coming.

In other cases, fecal transplants have resulted in temporary adverse effects such as diarrhea and cramping. So far, no serious or life-threatening consequences have been reported.

To complicate things further: just as there isn’t one way to live healthfully, there isn’t only one healthy microbiota. In fact, while individuals harbor about 160 individual species in their guts, there are over 1100 prevalent species in the human population. In other words, there are many acceptable substitutions in any given recipe for a “good gut.”

As a result, the FDA has cleared fecal transplants for use in treating only the most extreme C. difficile infections. But in an attempt to capitalize on the increasing number of potential fecal transplant applications, some companies have opened stool banks to stockpile safe, pre-screened fecal samples for treating C. difficile (and possibly other diseases) in the future. Despite this forward thinking, and the many success stories passed around on the Internet, we’re far from poop pills going mainstream. At the end of the day, only time will tell whether fecal transplants are truly flush with success.

I Contain Multitudes is a multi-part video series dedicated to exploring the wonderful, hidden world of the microbiome.

I Contain Multitudes

HHMI is a science philanthropy whose mission is to advance…

Katherine Wu

Written by

I’m a scientist, writer, and science writer, not necessarily in that order. I study how bacteria deal with stress so I can someday learn to do the same.

I Contain Multitudes

HHMI is a science philanthropy whose mission is to advance biomedical research and science education for the benefit of humanity. Tangled Bank Studios was established as an extension of HHMI's longstanding science education mission.

Katherine Wu

Written by

I’m a scientist, writer, and science writer, not necessarily in that order. I study how bacteria deal with stress so I can someday learn to do the same.

I Contain Multitudes

HHMI is a science philanthropy whose mission is to advance biomedical research and science education for the benefit of humanity. Tangled Bank Studios was established as an extension of HHMI's longstanding science education mission.

Welcome to a place where words matter. On Medium, smart voices and original ideas take center stage - with no ads in sight. Watch
Follow all the topics you care about, and we’ll deliver the best stories for you to your homepage and inbox. Explore
Get unlimited access to the best stories on Medium — and support writers while you’re at it. Just $5/month. Upgrade

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store