FMT Research

The Problem With Labeling Gut Troubles ‘Dysbiosis’


“… In their 2017 paper, Hooks and coauthor Maureen O’Malley analyzed more than 500 journal articles about the microbiome that used the word dysbiosis. They found that more than half of the papers defined dysbiosis as an imbalance. Other common definitions were either a general change, or a change in a specific bacterial type.

“I came to think ‘dysbiosis’ is a placeholder,” Hooks says. “But unfortunately it is also a lazy choice.”

Shanahan and a coauthor made a similar argument in a 2019 paper. So did the Massachusetts Institute of Technology’s Scott Olesen and Eric Alm in 2016, calling the idea of balance in the microbiome “a holdover from prescientific thought,” akin to balancing the humors. Olesen is now the scientific director at OpenBiome, a nonprofit stool bank that collects and processes donor feces for use by doctors and researchers. He says he and Alm felt frustrated by how other researchers were talking about dysbiosis.

“It’s not a thing,” Olesen says.”

Read more here.

The Death of a Patient and the Future of Fecal Transplants


“Last month the Food and Drug Administration sent out an emergency alert: Two people who had undergone fecal transplants developed multi-drug-resistant infections from bacteria in the stool they were given, and one died.

The death and illness may be the first serious adverse events associated with the poopy procedure, out of tens of thou sands of times it's believed to have been performed in the US. If those numbers are accurate, that’s an awfully good safety record. But it’s hard to know for sure, because roughly a decade since the procedure became mainstream, it still occupies a legal gray area, and thus whatever data is being collected isn’t comprehensive or public. …

“The material in these cases did not come from OpenBiome,” says Majdi Osman, a physician and the clinical program director at the stool bank, which screens for health risks so thoroughly that it boasts of excluding more than 97 percent of potential donors.

It seems likely the first effect of the patient’s death will be new requirements for thorough donor screening at any place performing transplants. That isn’t yet universal because the relevant professional societies, which typically write such detailed standards, haven’t tackled fecal transplants so far. But in a follow-up to the announcement of the death, the FDA said it will require the places performing poop trans­plants not only to check donations for pathogens, but to question donors about their daily-life risks of exposure to bad bugs.”

The Power of Poop: Fecal Transplants


“If the idea of fecal transplants seems momentarily disquieting, consider that they achieve a 90 percent cure rate for the devastating intestinal infection known as C. diff when antibiotics fail to clear it. Fecal transplants are also being studied as treatment for colitis, Crohn’s disease, and other inflammatory gastrointestinal disorders, and research into their value for urinary tract infections and even Parkinson’s disease is underway. By transferring stool in sterile conditions from a donor to the intestines of someone who is ailing, fecal transplants are designed to introduce a healthy mix of gut bacteria into the body and restore bacterial balance. What’s that good for?”

Watch the panel discussion here.

Doctors Are Now Transplanting Poop — & It's Saving Lives


“Fecal microbiota transplantation (FMT) is the transfer of feces from a healthy donor into the colon of someone who's sick, explains Scott Olesen, PhD, scientific director at OpenBiome, a nonprofit stool bank that conducts research and works with clinicians to facilitate FMT. Specifically, we know that FMT can be helpful in treating C.Diff, a serious and sometimes fatal gut infection caused by bacteria. The belief is that FMT can help "re-shape the environment of the gut," he says. In clinical trials, FMT has been shown to resolve 80-90% of recurrent C.Diff, and that's major.”

3Q: Eric Alm on the mysteries of the microbiome


Clostridium difficile infection is the most common hospital acquired gut infection, and our interest in the disease came after reading a scientific paper that showed fecal transplants work were effective even in cases where standard antibiotic therapy had failed. Patients, however, could not get access to treatment at that time, because doctors didn’t have access to the material for fecal transplants. We knew how to do it in the lab, and in 2013, my graduate student Mark Smith started a non-profit stool bank called OpenBiome, and we treated our first patient later that year. We’ve treated about 40,000 people so far. We’re partnering with over 1,000 hospital networks across the U.S. to make sure everyone has safe access to this medical procedure.”

Fecal matter pills used to treat peanut allergies in Boston study (VIDEO)


“There's evidence that when someone has a food allergy, gut bacteria send the wrong message about what the body should tolerate. 

‘We looked at babies who were allergic and babies who were not allergic and we analyzed their microbiota and we found significant differences between the babies that were allergic and the babies that were not allergic,’ said Dr. Rachid.

The thought is by transplanting another person's healthy gut bacteria into someone with an allergy, the microbiome can be repaired and send healthy signals to the immune system to tolerate allergens like peanuts.” 

Read More →

People V. Cancer: The Microbiome Connection (VIDEO)


“How does the gut microbiome help with patients’ receptivity to immunotherapy? What key factors influence it and what strategies offer the opportunity to shape it and augment therapeutic response?”

Watch the video below:

A User's Guide to Cheating Death: Germs (VIDEO)


“Are we too clean? Germ theory and hand washing saved millions of lives, but has the pendulum swung too far in the opposite direction? We talk about everything from regular soap versus anti-bacterial, our microbiome and the role of probiotics, the hygiene hypothesis and the rise of auto-immune diseases, and explore both fecal transplants and helminthic therapy.”

Watch the episode here!

(Requires subscription)

What's Living In You? (VIDEO)


“Whether they make you fat, fart, or freak out, microbes play a central role in your life. Right beneath your nose—on your face, in your gut, and everywhere in between—trillions of bacteria, viruses, and fungi are so abundant in your body, they outnumber your human cells. But these aren’t just nasty hitch-hikers. Many are crucial to your survival.”

Watch the full episode here.

Fecal Transplant Increasingly Seen As an Option to Treat a Nasty Superbug


“…while research to date shows fmt to be safe and effective, experts note that studies haven't yet been done to determine what long-term risks of fmt could be. "None of us want to do any harm to the patients, and I think that's the one thing that's just kind of in the back of our minds is we don't have really long-term data," Parian says.

The primary known risk is passing along disease or infection in stool. "The stool can have microscopic amounts of blood in it. So we really treat it like a regular organ transplant," Parian says. "So we test them for really everything that could be passed with the blood as well as within the stool. Of course we make sure to screen all the donors." Or she adds they use stool purchased from a non-profit stool bank called OpenBiome, just outside of Boston, that carefully screens donors, and provides liquefied stool preparations to clinicians and researchers for fmt.”

Read more:

When Poop Becomes Medicine (VIDEO)


"Fecal transplants—where doctors try to cure sick people of various ills by giving them the stools of healthy donors—have been used since at least fourth-century China, according to texts that make reference to 'yellow soup.' The unusual treatment has been rediscovered many times since, but it’s finally starting to enter the medical mainstream. Partly, that’s because of a surge of interest in the microbiome—the trillions of microbes that share our bodies. Partly, it’s because many well-conducted studies have shown that fecal transplants are incredibly effective at treating Clostridium difficile—a nasty, hardy bacterium that causes severe, recurring, and potentially fatal bouts of diarrhea."

See the video here.

Experts call for new approach to regulating fecal transplants


"A paper today in Science calls for a better way to regulate an increasingly popular method of treating recurrent Clostridium difficile infection (CDI).

The method, known as fecal microbiota transplantation (FMT), involves the transfer of stool from a healthy donor—via colonoscopy, nasogastric tube, or enema—into the colon of a patient who has recurrent CDI to re-introduce healthy bacteria into the gut. While still an investigational treatment, FMT has produced strong results in several small clinical trials in recent years, with cure rates as high as 90%.

A growing number of physicians are turning to it as an alternative to antibiotics—which can contribute to re-infection by wiping out the beneficial gut bacteria that keep C difficile bacteria in check—and several medical societies have said it should be a standard of care for patients with multiply recurrent CDI.

But proponents of FMT are concerned that the unsettled regulatory landscape may be preventing the procedure from being more widely accessible."

Gut Feeling


“In a study by Cryan and colleagues, a fecal microbiota transplantation from depressed human patients to GF rats resulted in behavioral and physiological symptoms of depression in the animals. “In effect, we were able to transfer the blues,” says Cryan. “Experiments like this are helping us move away from just describing changes and toward causative effects.”

The animal evidence seems promising, but translating this treatment to humans is still in the very early stages. OpenBiome, a nonprofit stool bank based in Cambridge, Massachusetts, is planning the first trials of fecal microbiota transplants for depressed patients. “We will try to select a donor that would complement the deficiency or replenish those bacterial communities that are depleted in patients with depression,” says Shrish Budree, senior clinical research scientist at OpenBiome (Figure 4, right). “One great aspect of OpenBiome is that we highly characterize all our stool donors,” Burdree notes. “They go through a rigorous clinical and serological screening, and we also genetically sequence all our donors so we know the exact microbial composition of their stool. If we know that certain bacterial communities are abnormal in a recipient, we can select a donor who is enriched in those bacteria.”

7 Startups Making The World A Better Place


"It’s one of the most exciting areas of science right now, the microbiome. Trillions of organisms define your own unique makeup, and a large portion of these microbes is found in the gut, which forms an integral part of your immune system. This area, if tweaked, has the ability to transform your health. The race is now on in biomedicine to help deliver a new wave of treatment based on this area. One of those startups spearheading research and interest in this is OpenBiome, founded by Mark Smith and James Burgess, a startup based out of Massachusetts dedicated to expanding safe access to fecal microbiota transplantation (FMT) through its public stool bank and catalyzing research into the human microbiome."

Forbes 30 Under 30 2017: Science

Mark Smith, 29
Cofounder, OpenBiome

Smith's company, OpenBiome, developed a therapy called fecal microbiota transplantation to treat Clostridium difficile, a common hospital-acquired infection. Like a blood bank for human stool, the nonprofit's work has helped over 18,000 patients. 

Click here for the full profile.


With the rise of antibiotic resistance, the search is on for therapies that can combat bacterial infections without engaging in an evolutionary arms race.

OpenBiome is a nonprofit stool bank that aims to expand safe access to fecal transplantation for patients with recurrent C. difficile and to catalyze research on the microbiome’s role in human health. OpenBiome provides clinicians with rigorously screened, ready-to-use stool preparations and supports researchers with a suite of tools to discover how gut bacteria might treat diseases beyond C. difficile.

Since 2013, OpenBiome has partnered with over 700 healthcare institutions across all 50 states and 6 countries to deliver over 14,000 treatments for recurrent C. difficile. Its portfolio includes 50% of all U.S. trials exploring the use of fecal transplants in new diseases. Watch the TED Talk here.

The Demand for Poop

"Passing a stool-screening test may be the hardest part of the process. “It’s actually more difficult than getting into Harvard,” says Smith. Only about four per cent of people who volunteer to be stool donors pass the three-step screening process, which involves a questionnaire, and stool and blood test, meant to rule out the presence of any known pathogens. (It’s easier to pass the mail-in variety lab test, which collect much less information.)

Despite the rigorous screening process, OpenBiome still manages to collect enough stool to supply 371 clinics and hospitals in 48 states and five countries. The bank collected its first sample in October 2013 and treated six patients by the end of the year. In 2014, they treated 2,000 patients, and by now they’ve provided stool for 5,419 treatments, and counting. “I didn’t really anticipate that it was going to grow as quickly as it has,” says Smith. And while there’s a distinct ick factor tied to his product, Smith says the stuff sells itself. “What’s kind of crazy about this thing is I sent out one email to a group of clinicians who were doing fecal transplants, and since then we’ve just been responding to requests.”"

To Ease Fecal Treatment, Stool Bank Starts Producing Long-Awaited "Poop Pill"

"OpenBiome, the nation’s first stool bank, is beginning large-scale production of a poop pill. This week marks the first time such a pill will be commercially available to hospitals and clinics.

Early tests suggest the pill is highly effective and comparable to traditional, more invasive delivery methods — for instance via colonoscopy, enema or a plastic tube through the nose and into the stomach or intestines.

'Fecal transplants came from what used to be this dark art — where you needed a donor and a blender,” says Mark Smith, research director at OpenBiome and one of its founders. “And now you basically take something out of the freezer and can treat the patient immediately. I’m very, very excited about this.'"


There's a Huge Advancement in Poop Science That Could Save Thousands of Lives


"This latest advancement could change lives. Instead of a colonoscopy, enema or tube up the nose, C. diff can now be treated by swallowing a small capsule. 

Yes, the pills are actually filled with poop. They contain essentially healthy fecal matter covered in an oil layer to protect the capsule, Edelstein said. Like the traditional FMT liquid, the pills are frozen to protect the bacteria.

You need a good sense of humor if you're going to work with poop all day. When Smith tells people about his line of work, "it usually leads to a very long conversation," he said. "It's very fun." People get excited about it — "maybe too excited about it," Smith continued. "People ask, 'What's it like to mail poo to strangers?'"

Save Your Microbiome for a Rainy Day

"Many of these transplants, which now only require swallowing a pill, have been done with OpenBiome’s material. The group serves as a repository and screening facility for willing "poop donors" and has provided safe transplant material to 7,000 patients. Now, it is piloting a new service called PersonalBiome, which will allow people who are vulnerable to C. diff infections to proactively save their own microbiome for a rainy day. Burgess compares it to the way a woman might freeze her eggs, if she’s worried about her future fertility."

Find out about how to participate in OpenBiome's pilot launch of PersonalBiome here