Category Archives: Fecal Microbiota Transplant (FMT)

Study Investigators Find Combination of Vancomycin and FMT Superior In Treating Recurrent C.difficile Infection (rCDI)

The combination of vancomycin and fecal microbiota transplantation was found to be superior to fidaxomicin or vancomycin in the treatment of patients with recurrent Clostridium difficile infection (rCDI), according to a study published in Gastroenterology.

This randomized, single-center trial was designed to compare the efficacy of fecal microbiota transplantation with that of fidaxomicin and vancomycin.

Sixty-four adults with recurrent CDI seen at a gastroenterology clinic in Denmark between April 5, 2016 and June 10, 2018 were randomly assigned to a group receiving fecal microbiota transplantation applied by colonoscopy or nasojejunal tube after 4 to 10 days of 125 mg vancomycin 4 times daily (n=24), or 10 days of 200 mg fidaxomicin 2 times daily (n=24), or 10 days of 125 mg vancomycin 4 times daily (n=16).

Patients experiencing a CDI recurrence after this course of treatment, and those who could not be randomly assigned were provided rescue fecal microbiota transplantation. The primary study outcome was combined clinical resolution and negative polymerase chain reaction test for C difficile toxin at 8 weeks post-treatment, and secondary end points included week 8 clinical resolution.

The combination of negative C difficile test results and clinical resolution was observed in 71% of the 24 participants who received fecal microbiota transplantation (95% CI, 49-87%; n=17), 33% of the 24 participants who received fidaxomicin (95% CI, 16-55%; n=8), and 19% of the 16 participants (95% CI, 5-46%; n=3) who received vancomycin (fecal microbiota transplantation vs fidaxomicinP=.009; fecal microbiota transplantation vs vancomycin, P=.001; fidaxomicin vs vancomycin, P=.31). Clinical resolution was observed in 92% of participants who received fecal microbiota transplantation (n=22; P=.0002), 42% of participants who were treated with fidaxomicin (n=10; <.0001), and 19% of participants who were treated with vancomycin (n=3; P=.13). No significant differences in results were seen between patients receiving initial fecal microbiota transplantation therapy and those who received rescue treatment with such a transplant.

Of note, adverse events (transient abdominal pain, constipation, bloating and diarrhea) were observed in 10 of the participants who received a fecal microbiota transplant, 1 of which was classified as severe.

Researchers noted limitation of a lack of patients with C difficile ribotype 027, such that results may not be generalizable to settings with a high ribotype 027 frequency. Study interventions were also unblinded, introducing the possibility of observer bias, although the C difficile toxin test was applied to all patients at all time points in an effort to obtain objective outcome measures.

Study investigators concluded, “[fecal microbiota transplantation] was superior to both fidaxomicin and vancomycin monotherapies for [recurrent] CDI, with regard to both combined clinical and microbiological resolution and clinical resolution alone.”


Hvas CL, Jørgensen SMD, Jørgensen SP, et al. Fecal microbiota transplantation is superior to fidaxomicin for treatment of recurrent Clostridium difficile infection [published online January 2, 2019]. Gastroenterology. doi: 10.1053/j.gastro.2018.12.019

U.S. Food and Drug Administration (FDA) Grants Breakthrough Therapy Designation to Finch Therapeutics Investigational Drug CP101 for Treatment of Recurrent Clostridium difficile Infection (rCDI)

Finch Therapeutics Group, Inc., a clinical-stage microbiome therapeutics company, announced that the U.S. Food and Drug Administration (FDA) has granted Breakthrough Therapy Designation to investigational drug CP101 for the treatment of patients with recurrent Clostridium difficile (C. difficile) infection. Breakthrough Therapy Designation is intended to expedite the development and review of investigational therapeutics for serious or life-threatening conditions where preliminary clinical evidence indicates that the product may demonstrate a substantial improvement over existing therapies on one or more clinically significant endpoints.

Finch’s lead therapeutic candidate CP101 is designed to prevent recurrent C. difficile, a bacterial infection affecting over 500,000 patients each year and leading to an estimated 29,000 annual deaths. Recurrent C. difficile has been named an urgent public health threat by the Centers for Disease Control (CDC) and, with a high percentage of patients failing standard-of-care antibiotic treatment, presents a clear and urgent unmet medical need.

“We are thrilled that CP101 has been designated as a Breakthrough Therapy for recurrent C. difficile,” said Mark Smith, CEO of Finch. “CP101 is designed to break the cycles of infection by restoring the balance of the gut microbiome, an approach supported by numerous clinical studies and Finch’s extensive experience providing microbial treatments to patients suffering from C. difficile. This designation will accelerate our efforts to provide an effective therapy for patients living with this devastating infection, and we look forward to working closely with the FDA to advance that mission.”

Finch is actively enrolling patients with recurrent C. difficile in PRISM3, a randomized, placebo-controlled Phase II clinical study to assess the safety and efficacy of CP101. The study drug is an oral capsule that is administered in a single dose. For more information about this trial, please visit

CP101 is not approved in any country.The FDA’s Breakthrough Therapy Designation does not constitute or guarantee a future approval and does not alter the standards for approval.

About Finch Therapeutics Group, Inc.Finch Therapeutics Group, Inc. (Finch) is developing novel microbial therapies to serve patients with serious unmet medical needs. Built on 30 years of translational research at OpenBiome, MIT, University of Minnesota and the Center for Digestive Diseases, Finch uses  Human-First Discovery  to develop therapies from microbes that have demonstrated clinically significant impacts on patient outcomes. Finch is unique in having both a donor-derived  Full-Spectrum Microbiota  ( FSM ) product platform and a  Rationally Selected Microbiota  ( RSM ) product platform based on microbes grown in pure culture. Finch’s lead program, CP101, is an investigational  FSM  product for prevention of recurrent  C. difficile  infections. Finch’s  RSM  platform employs machine-learning algorithms to mine Finch’s unique clinical datasets, reverse engineering successful clinical experience to identify the key microbes driving patient outcomes. Finch has a strategic partnership with Takeda to develop FIN-524, an investigational  RSM  product for inflammatory bowel disease. Finch is using a rich foundation of clinical data to advance its pipeline, leveraging proof-of-principle results to evaluate target indications and inform the design of this new therapeutic class.

Full-Spectrum Microbiota, FSM, Rationally-Selected Microbiota, RSM, and Human-First Discovery are trademarks of Finch Therapeutics Group, Inc.

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Recurrent Clostridium difficile associated diarrhea (rCDAD) Research Study Begins Enrollment

A research consortium across multiple institutions has begun enrolling patients in a clinical trial examining whether fecal microbiota transplantation by enema is safe and effective in preventing recurrent Clostridium difficile-associated disease, according to a press release.

The researchers hope to enroll 162 volunteers aged 18 years or older who have had two or more episodes of C. difficile-associated disease (CDAD) within the past 6 months, according to the release.

Trial sites include Emory University, Duke University Medical Center and Vanderbilt University Medical Center.

Each site is a member of the Vaccine and Treatment Evaluation Unit, which is a network funded by the National Institute of Allergy and Infectious Diseases (NIAID).

The researchers hope to enroll 162 volunteers aged 18 years or older who have had two or more episodes of C. difficile-associated disease (CDAD) within the past 6 months, according to the release.

Clostridium difficile-associated disease, a significant problem in health care facilities, causes an estimated 15,000 deaths in the United States each year,” Anthony S. Fauci, MD, NIAID director, said in the release. “This randomized, controlled trial aims to provide critical data on the efficacy and long-term safety of using fecal microbiota transplants by enema to cure C. diff infections.”

Volunteers will be enrolled in the trial after completing a standard course of antibiotics for a recurrent CDAD episode, presuming their diarrhea symptoms cease on treatment.

Participants will then be randomly assigned to either a group (n = 108) that will take an anti-diarrheal medication and receive a stool transplant (FMT) delivered by retention enema, or a group (n = 54) that will take an anti-diarrheal medication and receive a placebo solution delivered by retention enema.

The placebo is a saline solution that has been colored to mimic an active stool transplant product, to ensure that the study is partially blinded.

Researchers will collect stool and blood samples from participating at designated intervals for a year from the date of effective treatment for CDAD, or from the date of their last treatment if it was unsuccessful, according to the release.

Investigators will evaluate the stool samples for gut microbial diversity and infectious pathogens changes and will examine the blood samples for metabolic syndrome markers.

All participants will be monitored for adverse side effects for 3 years following the completion of recurrent CDAD treatment.


Researchers Examine Changes to the Microbiota Composition and Metabolic Profiles of Patients with Recurrent Clostridium difficile Infection (rCDI) Following Treatment with Faecal Microbiota Transplant (FMT)


This study aimed to examine changes to the microbiota composition and metabolic profiles of seven patients with recurrent Clostridium difficile infection (rCDI), following treatment with faecal microbiota transplant (FMT).



This study aimed to examine changes to the microbiota composition and metabolic profiles of seven patients with recurrent Clostridium difficile infection (rCDI), following treatment with faecal microbiota transplant (FMT).


16S rDNA sequencing and 1H NMR were performed on faecal samples from the patients (pre-, post-FMT, and follow-up) and the associated donor samples. Sparse partial-least-square analysis was used to identify correlations between the two datasets.


The patients’ microbiota post-FMT tended to shift towards the donor microbiota, specifically through proportional increases of Bacteroides, Blautia, and Ruminococcus, and proportional decreases of Enterococcus, Escherichia, and Klebsiella. However, although cured of infection, one patient, who suffers from chronic alcohol abuse, retained the compositional characteristics of the pre-FMT microbiota. Following FMT, increased levels of short-chain fatty acids, particularly butyrate and acetate, were observed in all patients. Sparse partial-least-square analysis confirmed a positive correlation between butyrate and Bacteroides, Blautia, and Ruminococcus, with a negative correlation between butyrate and Klebsiella and Enterococcus.


Clear differences were observed in the microbiota composition and metabolic profiles between donors and rCDI patients, which were largely resolved in patients following FMT. Increased levels of butyrate appear to be a factor associated with resolution of rCDI.


Although Clostridium difficile is present in the intestines of ∼3–5% of healthy adults,1 the occurrence of C. difficile infection (CDI) in healthy individuals is relatively uncommon due to the protective effect of the gut microbiota. The incidents and severity of CDI has risen significantly over the last decade, and it is now recognised as the main causative agent of healthcare-associated infectious diarrhoea in hospitals worldwide.2 The standard treatment for CDI is the administration of metronidazole for mild to moderate infections, and oral vancomycin or fidaxomicin for severe infections and relapses. The ability of C. difficile to form spores, coupled with the increase in antibiotic-resistant strains, can lead to persistence of infection, relapses, and the administration of more antibiotics, which further depletes the commensal bacteria. This creates an environment that is more favourable to C. difficile, thus setting up a cycle of relapse and re-infection. It is estimated that 20-30% of patients who develop a first episode of CDI go on to have at least one relapse, and of these, a further 60% develop further episodes of relapses.3 This increases the need for further antibiotics, the risk of antibiotic-resistance in the gut commensal flora, and costs to the health service, with each episode of CDI estimated to cost approximately £7000 in 2010.4

Faecal microbiota transplants (FMT) represents an effective alternative to antibiotics to treat recurrent CDI (rCDI), with a primary cure rate as high as 91%.5 The central tenet behind FMT is that the introduction of a healthy bacterial community into the intestines produces an environment that is less favourable to C. difficile by increasing colonisation resistance and reinstating a protective effect. The advantages of this treatment are that it is quick, cost-effective, and could help to eradicate antibiotic resistant strains of C. difficile.

It is known that a dysbiotic gut microbiota increases the risk of developing CDI, however whether there is a common element within this community composition that could help to determine if a patient is at greater risk of rCDI is as yet unknown. The reduction in diversity within the dysbiotic gut microbiota would also suggest a reduction in metabolic potential through the loss of gene diversity. The functional redundancy6 within the gut microbiota suggests, that metabolic function is more relevant than which species are present or absent. Whilst a number of studies have looked at the changes in microbiota composition due to FMT,7, 8, 9, 10 we know little about the changes to the metabolic capacities of the altered microbiota. The aim of this study was to assess FMT-induced changes in both the microbial community structure and metabolite profiles of the gut microbiomes of seven patients with rCDI, as well as those of their associated FMT donors.

Patients and methods


Patients were selected as candidates for the FMT procedure if they had at least two confirmed recurrences of CDI. C. difficile testing was based on a two stage algorithm in line with Public Health England recommendations.11 This involves screening faecal samples by glutamate dehydrogenase enzyme immunoassay (Techlab, USA), followed by C. difficile toxin testing by enzyme immunoassay (Techlab, USA). Glutamate dehydrogenase positive, toxin negative samples were further tested for the presence of toxigenic genes by PCR. FMT exclusion criteria included immunocompromised patients, those aged less than 16, and those with severe comorbidities which would make the patient unfit for endoscopy. FMT was introduced into clinical care at Norfolk and Norwich University Hospital following approval by the New Therapies committee, and was performed in accordance with the Helsinki Declaration of 1975. Patients were consented for the study by a clinician following a detailed discussion of the procedure with the patient or their next of kin. All patient data is fully anonymised.

Donor screening

The faecal donors used for the cohort of patients who underwent FMT in this study were both healthy Caucasian males with a BMI between 24 and 27 kg/m2, aged 36 (D05) and 30 (D03) years of age, respectively. Potential donors were asked to complete a questionnaire adapted from van Nood et al.12 regarding their medical history and lifestyle habits to identify risk factors for potentially transmittable diseases. Eligible candidates provided blood and stool samples for laboratory screening tests. Blood samples were screened for hepatitis A, B, C, and E antibodies, HIV 1 & 2, human T-lymphotropic virus 1 & 2, Epstein-Barr virus, Cytomegalovirus, syphilis, Entamoeba histolytica, Strongyloides stercoralis, and Treponema pallidum. Stool samples were tested for the presence of C. difficile or its toxins, Helicobacter pylori antigen, Norovirus, methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum β-lactamase-producing organisms, carbapenemase-producing Enterobacteriaceae, Escherichia coli O157, Salmonella spp., Shigella spp., and Campylobacter species. In addition, microscopy was used to investigate for ova, cysts, and parasites. Prior to the donation of stool samples for each FMT procedure, donors were asked to refrain from eating peanuts and shellfish, and to complete a short screening questionnaire to confirm no changes to health or lifestyle since the last donor screening that may put the patient at risk.

Faecal suspension preparation

Donor faeces were collected in a sterile container on the day of the procedure, and transferred to a sterilised class II safety cabinet (Walker Ltd, UK). A maximum of 80 g of donor stool was homogenised with sterile saline (0.9%), to a ratio of 5 ml saline per gram of stool, in a strainer bag (BA6141/STR; Seward Limited, UK) using a Stomacher® 400 Circulator (Seward Limited, UK) set to 230 RPM for a duration of 1 min. The filtered faecal preparation was drawn up into labelled sterile 60 ml syringes using nasojejunal tubing connected to the Luer lock. The syringes were secured with sterile Luer lock caps and transported immediately to the hospital. Aliquots of the donor faecal sample were immediately stored at −20 °C until analysis.

Faecal suspension infusion

Patients were prescribed oral vancomycin 500 mg four times daily for 4 days, with the last dose received the night before the procedure. Also, on the day before the FMT procedure, a bowel lavage is performed using 4 l of macrogol solution (Klean-Prep, Norgine). Patients were taken to the endoscopy unit for insertion of nasojejunal tube the night before the procedure. Our FMT protocol was adapted from that of van Nood et al.12 On the day of FMT infusion, the patient’s headrest was elevated to 45°, patency of the nasojejunal tube was checked by flushing with water, and 420 ml of faecal suspension was delivered slowly by the patient’s bedside in the isolation room via a nasojejunal tube using the prefilled syringes. This was performed at a rate of ∼20 ml per minute with a break of 5-10 minutes applied halfway through the procedure. Post-infusion instructions were to monitor observations, and record bowel motions. Patients could take on fluids one hour after the procedure, and were observed overnight before discharge the next day at the earliest. Although there are no agreed durations of follow-up post-FMT,13 van Nood et al.12 used two endpoints to measure cure, namely no relapse after 5 weeks, and no relapse after 10 weeks. Resolution was defined as type 4 or less on the Bristol stool chart or stool normal for the patient e.g. in case of percutaneous endoscopic gastrostomy feeding. We followed patients up by telephone or in person if they were re-admitted into the hospital for an unrelated illness. Post-FMT samples were collected after a minimum of 10 days post-FMT, and postal kits were provided to patients who were willing to donate a ‘follow-up’ sample up to 2 weeks later.

Sample analysis

Faecal microbiota analysis

Faecal samples were collected from recipients within 9 days prior to FMT, however the pre-FMT sample for patient R13 was not collected within this timeframe, and a previously frozen sample obtained whilst the patient was suffering from the same episode of CDI was used. Further samples were collected for all recipients following the procedure (‘post-FMT’ range: 11–141 days; ‘follow-up’ range: 4–14 days after post-FMT sample), and stored at −20 °C until analysis. The DNA was extracted using the FastDNA SPIN Kit for Soil (MP Biomedicals, UK) with a bead-beating step.14 DNA yield was quantified using the Qubit fluorometer prior to the samples being sent to the Earlham Institute (UK), where the V4 hypervariable region of the 16S rRNA genes were amplified using the 515F and 806R primers with built-in degeneracy.15 The amplicons were sequenced using paired-end Illumina sequencing (2 × 250 bp) on the MiSeq platform (Illumina, USA). Sequencing data, for the 21 samples that had an appropriate level of sequencing depth, were analysed using the Quantitative Insights Into Microbial Ecology (QIIME) 1.9 software and RDP classifier 16S rRNA gene sequence database.16,17 The trimmed reads were filtered for chimeric sequences using ChimeraSlayer, bacterial taxonomy assignment with a confidence value threshold of 50% was performed with the RDP classifier (version 2.10), and trimmed reads clustered into operational taxonomic units at 97% identity level. Alpha diversity and rarefaction plots were computed using the Chao1 index. Weighted and unweighted UniFrac distances were used to generate beta diversity principal coordinates analysis plots, which were visualised using the Emperor tool.

Faecal metabolite analysis

A known mass (∼ 100 mg) of thawed faecal samples were added to sterile tubes. The faecal waters were generated by adding the phosphate buffer (prepared in D2O) to 8.3% w/v. Homogenised faecal waters were centrifuged at 16,200 x g at room temperature for 5 min. The supernatants were filter sterilised (0.2 µm) and placed in a 5 mm NMR tube. The 1H NMR spectra were recorded at 600 MHz on a Bruker Avance spectrometer (Bruker BioSpin GmbH, Germany) running Topspin 2.0 software and fitted with a cryoprobe and a 60-slot autosampler. Each 1H NMR spectrum was acquired with 1280 scans, a spectral width of 12,300 Hz, and an acquisition time of 2.67 s. The “noesypr1d” pre-saturation sequence was used to suppress the residual water signal with a low-power selective irradiation at the water frequency during the recycle delay and a mixing time of 10 ms. Spectra were transformed with a 0.3 Hz line broadening, and were manually phased, baseline corrected, and referenced by setting the TSP methyl signal to 0 ppm. The metabolites were quantified using the software Chenomx® NMR Suite 7.0TM.

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What Is Poop? A Serious Question For the FDA In Order To Regulate Fecal Microbiota Transplants

When severe, chronic diarrhea strikes, sometimes the only cure is … more feces. It might seem bizarre, but a transplant of healthy human stool and its bacterial ecosystem can mean freedom from a painful, life-threatening illness.

The transplants — called fecal microbiota transplants, or FMTs — are becoming more and more popular. So popular that the stool bank OpenBiome has supplied more than 30,000 stool samples to clinicians and scientists since 2012. Right now, though, the government isn’t quite sure how to regulate fecal transplants. That uncertainty comes from what seems like a simple question: What is poop? Is it a drug? Is it a bodily tissue? Is it a little of both? Then, is the transplant itself a procedure? That’s a whole other regulatory category.

Out of concern that regulations would cut out desperate patients or send companies running to more profitable enterprises, FMTs aren’t actually regulated at all. That leads to the potential for unscreened and potentially dangerous fecal samples to flood the market. A group of doctors and scientists from the University of Maryland School of Medicine in Baltimore have tried to cut through the confusion with a three-track policy plan that would help keep poop transplants clean (as clean as fecal matter gets, anyway), while still allowing patients to get transplants when they need them. The scientists also hope to encourage companies to develop potentially lucrative products for future FMTs — including options that are almost feces-free.

A fecal transplant involves taking a mixture of a donor’s poop and saline (sometimes mixed with the help of a kitchen blender) and inserting it into a patient’s large intestine or far down the gut with a nasogastric tube. Companies are working on alternatives to that procedure, such as pills that deliver the same benefits with less of an “ick” factor.

Currently, FMTs have the most potential for treating Clostridium difficile infections. C. diff is a bacterium normally found in our guts and feces. But unchecked, it can take over the large intestine. The result is inflammation and chronic severe diarrhea that can last weeks or months. There are more than 450,000 estimated cases in the United States each year, and more than 29,000 deaths. Doctors can prescribe antibiotics to kick the bugs out, but in 20 percent of patients, the infection comes back again. And again.

For those patients, FMTs can be a miracle. They resolve symptoms in 85 percent of patients with recurrent C. diff infections, compared with the roughly 20 to 30 percent success rates of antibiotics.

Unfortunately, FMTs also come with a dose of danger. Feces is a mixture of our undigested waste, the beneficial microbes needed to keep our guts healthy and whatever bacteria, fungi and viruses we’ve picked up in our busy lives. So donors need to be screened for pathogens that might make a sick recipient sicker. And the poop needs to be handled carefully to avoid contamination or infection in the people who handle and receive it.

Gastroenterologist Erik von Rosenvinge of the University of Maryland School of Medicine in Baltimore has performed more than 40 FMTs. “When I first started doing these in 2013, I was having the patients identify a friend or family member, and they would bring in the stool and I would process it myself,” he says. After the first few donations, von Rosenvinge switched to using stool from the OpenBiome stool bank. It saves money and time.

For each donation, the stool bank or hospital will test the feces for pathogens. But who sets the standard to ensure that people getting treated for C. diff are receiving “clean” stool, either from their friends or from a stool bank?

Well, right now, no one.

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Poop: Drug or tissue?

The first problem is to figure out what an FMT actually is, at least, in terms of how the government should regulate one. Feces is like a drug, in that the microbes in it can change how the body functions. But because of those very microbes, feces is also a living thing that differs from person to person. In fact, in some ways, poop is like biological tissue, in that it comes from the human body.

But then, the FMT itself is something like a procedure — there’s a method involved in getting one. But that procedure is also delivering a drug. Or is it transplanting a tissue? Here we go again.

“The FDA has been reticent to create a new regulatory product category,” says Jacques Ravel, who studies the microbiome and women’s health at the University of Maryland School of Medicine.  “They’ve been trying to fit the stool into one of the regulated product categories, and there’s limitations every time you do, there’s pros and cons.”

In 2013, the FDA declared that FMTs counted as a drug (technically a “live biotherapeutic product”) in terms of how they would be regulated, which, von Rosenvinge notes, “means all of us are pharmaceutical factories,” pooping out “drugs” once a day on average.

But FMTs don’t have FDA approval yet, so as a drug, an FMT is considered “investigational.” Giving one to a patient would require an investigational new drug application, or IND. Those are associated with clinical trials, meaning someone who needed an FMT would probably have to get into a clinical trial to get treatment.  “At that point [in 2013], I’d only done a handful, and I had to stop because I didn’t have an IND,” von Rosenvinge recalls.

The FDA’s goal was to make sure that FMTs were safe for people. But the requirements meant that most doctors could not give FMTs. At a public workshop about FMTs in 2013, scientists and physicians spoke out against the requirements. In response, the FDA noted that it would practice “enforcement discretion.” That’s government-speak for politely looking the other way while doctors treated C. diff patients outside of clinical trials.

Unfortunately, looking the other way means that FMTs — whether prepared from a donor by a doctor or purchased from a stool bank — are still completely unregulated. As FMTs gain popularity for C. diff, von Rosenvinge notes, that could lead to problems. “You don’t want someone grabbing poop out of the local [port-a-potty] and selling it. That would be horrible,” he says. “If someone’s going to be using stool to put into a human, you want to have assurances that it was properly handled, that the donor was properly screened, that we’re doing everything within reason to minimize risk of causing problems.”

The stool banks themselves aren’t pleased with the arrangement, either. “We’re all operating on a bit of uncertainty,” says Carolyn Edelstein, the CEO of OpenBiome. Right now, OpenBiome screens all of their samples by their own standards, because the government hasn’t given them any. Everyone knows that “looking the other way” could end at any time, a move that the FDA proposed in March 2016. Then, INDs would be required again, and patients could be out of luck.

Balancing regulation and access

To patients, access — cheap access — is paramount. “The big challenge at the end of the day is access to treatment, and the fact that FMT is really cheap as its performed right now,” says Ravel. “Right now there’s no true alternative, even those coming down the pipe may be able to cure [C. diff], but they’re not going to be cheap.”

But to doctors, scientists and government, access needs to be balanced with safety. “People are doing this at home, and I think that raises issues about the safety of donations,” notes Diane Hoffman, who studies health law at the University of Maryland. “Do [patients] understand the potential for contamination and disease transmission?”

The right balance might also help promote the development of new drugs for treating C. diff — ones that extract the most useful bacteria, for example, and don’t involve an enema.

To this end, Hoffman, von Rosenvinge, Ravel and colleagues worked with a large working group of scientists, lawyers, industry partners and patient advocates to come up with recommendations for regulating FMTs, which they outlined in December in Science. The result is a slim, three-track system.

Individual FMTs for C. diff done by doctors with donors who are friends or family of the patients would be classified under “practice of medicine.”  This is an exception that allows doctors to use their expertise and judgment when treating patients, as long as the treatments they’re using are legally available. No FDA approval or IND required. “We’re trusting the doctor to do what’s in the best interests of the patient,” Hoffman explains.

Stool banks, on the other hand, would be regulated like tissue banks. They’d have to comply with good manufacturing and safety practices and screen and test their donors. The banks would also have to track the patients who receive donations, and submit their long-term data to a national registry. The banks would be free to sell FMT samples, but only to treat C. diff. Any other use that the FMT hasn’t been approved for would still require a clinical trial.

The third track would be for “stool-based products.” These would be pills or delivery systems that offer, say, combinations of microbes, rather than the current practice of basically “polishing a turd,” notes von Rosenvinge. These would be regulated as biological products or drugs.

In practice, this would mean stool banks and stool transplants would be regulated more like cell and tissue banks and transplants. “Stool-based products” on the other hand, would be regulated more like drugs. No matter what, patients would have to be informed of all the risks associated with an FMT.

A continuum

According to some scientists, medical professionals and industry partners, regulation for fecal transplants could be divided along the lines of who is providing the product and what the product is. “Stool-derived” products would be regulated more like biological drugs, with stool itself regulated more like a body tissue.

D.E. Hoffmann et al/Gut Microbes 2017 (CC BY-NC-ND 4.0)

“I think the stand-out, excellent point of this proposed regulatory scheme is that stool banks need to be regulated, and there need to be rigorous data collection of outcomes,” says Kelly Hills, a bioethicist with Rogue Bioethics. “Track everything. The whole enchilada. We have historical precedents [such as in vitro fertilization] where we didn’t track outcomes, and 20 or 40 years down the line we’ve been kicking ourselves. It’d be nice to learn from our mistakes!”

This is especially important because while FMTs have very clear benefits for C. diff in the short term, no one really knows what the long-term effects will be. “We don’t have a lot of [long-term data] right now,” Hills notes. “We know that when you change someone’s gut microbiome you actually change a lot in their life. We have the anecdotal stories of people losing lots of weight, for example, or people’s dietary desires changing.” But the plural of anecdote isn’t data. A registry might help scientists keep track of exactly what transplants people received and their long-term effects.

But “practice of medicine” might give too much leeway to doctors to try FMT for things that they probably shouldn’t, worries Leigh Turner, a bioethicist at the University of Minnesota in Minneapolis. “‘Practice of medicine’ isn’t a curb on advertising or promotional claims,” he notes.

The group behind the policy proposal was careful not to stand in the way of further drug development. That third track was designed with the hope of promoting stool-based products, so that companies might be encouraged to pursue more of them. But if FMTs aren’t broken, why would companies — let alone patients — want to take the risks to fix them? With FMTs freely available, it might be hard to recruit patients to potential clinical trials for new drugs. “If you have a cheap solution that works and you have a patient with C. diff, that patient will not want to enter a trial with a placebo arm,” notes Ravel. After all, what if they got the placebo? They want a cure, not a game of roulette.

The policy brief isn’t policy, and the FDA hasn’t made a final call. But looking the other way isn’t going to cut it in the long term. FMTs are only used for recurrent C. diff infections right now. But scientists are interested in them for many other things. “You can get into weird science fiction areas. Would athletes start doing FMTs to try and improve their Tour de France time? Could you lose weight?” notes Hills. Some of these could be lucrative options for companies. And because FMTs are so easy to perform, people are already making headlines with the do-it-yourself route.

No matter what, a lack of regulation isn’t a long-term strategy. People are going to find other uses for feces, and the FDA will need to be prepared when they do.

Researchers Utilize Deep Metagenomic Sequencing to Profile FMT ‘s Retracting the Gut Microbiome Features That Coincided With Successful Fecal Transplant Engraftment

A team led by investigators at the Broad Institute have started untangling the bacterial strains that influence successful fecal microbiota transplantation (FMT) engraftment in individuals treated for recurrent Clostridium difficile infection.

As they reported in Cell Host & Microbe today, researchers from the Broad Institute, Massachusetts Institute of Technology, Massachusetts General Hospital, and elsewhere used deep metagenomic sequencing to profile FMT in four FMT donors and 19 recipients with C. difficile infections, retracing the gut microbiome features that coincided with successful fecal transplant engraftment.

The initial gut microbial communities in both the donors and the recipients seemed to influence this process, the team noted, particularly bacterial abundance and strain phylogeny. The final gut microbe composition differed between donors and post-FMT recipients, though, with specific strains that originated in the host either taking hold or falling by the wayside in recipients in an “all-or-nothing” manner.

“This paper provides a context for understanding how to make these live biological therapeutics as an alternative to transferring raw fecal matter,” co-senior author Eric Alm, co-director of MIT’s Center for Microbiome Informatics and Therapeutics, said in a statement.

“We describe a model focused on three elements, including bacterial engraftment, growth, and mechanism of action, that need to be considered when developing these live therapies targeting the gut microorganisms, or microbiome,” added Alm, who is also affiliated with the Broad Institute and Finch Therapeutics.

Along with its use for treating recurrent C. difficile infection, the team noted that FMT has been proposed in other conditions such as inflammatory bowel disease and metabolic syndrome. Even so, there is a ways to go in understanding the factors influencing bacterial engraftment and effectiveness in the recipient gut — information needed to move the approach from a shotgun approach using fecal donor material to microbe-based treatments based on purified collections of specific bacteria.

“Although the success of FMT requires donor bacteria to engraft in the patient’s gut, the forces governing engraftment in humans are unknown,” the authors wrote.

To follow this process, the researchers used the Illumina GAIIx instrument to do deep metagenomic sequencing on seven stool samples from four healthy donors and 67 samples collected over time from 19 individuals treated for C. difficile infection with FMT.

With the help of statistical modeling and a new computational method dubbed Strain Finder, the team looked at the bacterial species that successfully engrafted in FMT recipients and followed strain genotypes over time. It also mapped the metagenomes to Human Microbiome Project reference genomes to take a look at bacterial taxa abundance.

Prior to treatment, for example, FMT recipients had lower-than-usual gut microbiome diversity. And while gut microbial community patterns shifted in recipients after FMT, the resulting gut microbiomes continued to differ from the original donor microbiomes, the researchers reported.

Even so, their analytical methods made it possible predict post-FMR metagenomic operational taxa unit abundance and incidence.

With nearly 1,100 bacterial strains in the 79 samples considered, the team traced transmission of certain strains from FMT donors to recipients, noting that bacterial strains tended to engraft in an “all-or-nothing” manner, “whereby no strains or complete sets of strains colonize the patients.”

“We find that engraftment can be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient,” Alm and co-authors wrote. “Furthermore, donor strains within a species engraft in an all-or-nothing manner and previously undetected strains frequently colonize patients receiving FMT.”

Such patterns were supported by the researchers’ follow-up analyses on 16S ribosomal RNA sequence data for stool samples from 10 more FMT donors and 18 recipients, as well as an analysis of metagenomic sequence data for samples from five individuals treated with FMT for metabolic syndrome.

“Together,” they authors said, “these findings suggest that the principles of engraftment we discovered for recurrent C. difficile infection may generalize to other disease indications, including metabolic syndrome.”


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The American Gastroenterological Association (AGA) Fecal Microbiota Transplantation (FMT) National Registry Enrolls First Patient

Largest planned fecal microbiota transplantation (FMT) study enrolls first patient

The FMT National Registry also announces collaborations with American Gut and OpenBiome

The first participant has enrolled in the American Gastroenterological Association (AGA) Fecal Microbiota Transplantation (FMT) National Registry, which is planned to be the largest FMT study ever.

The AGA FMT National Registry — funded by the National Institutes of Health (NIH) and administered by the AGA Center for Gut Microbiome Research and Educationwill track 4,000 patients for 10 years after their FMT procedure, providing a wealth of data about the procedure’s effectiveness and both short- and long-term effects of FMT.

Fecal microbiota transplant is a medical procedure in which the stool from a healthy person is prepared and then put into the intestine of a sick patient. FMT is most commonly used to treat Clostridium difficile (C. diff) infection, if antibiotics have not been able to get rid of the infection.

“Today is an important milestone for the AGA FMT National Registry. What’s ahead is a significant repository of data for investigators working to advance FMT research, better information for physicians on when and how to use FMT, and reassurance for patients that we now understand the risks and benefits of this procedure,” said Gary D. Wu, MD, a principal investigator for the registry and founding chair of the AGA Center for Gut Microbiome Research and Education scientific advisory board. “We look forward to embarking on this comprehensive data collection project and are eager to share our findings with the public.”

First Patient Enrolled

The first patient enrolled in the FMT National Registry received a fecal transplant through the Gastroenterology Center of Connecticut/Medical Research Center of Connecticut by Paul Feuerstadt, MD, assistant clinical professor of medicine at Yale School of Medicine, New Haven, CT. The patient being treated had experienced multiple recurrences of C. difficile infection. As part of the registry,

Dr. Feuerstadt will follow up with the patient four times over the next two years and report back on the patient’s health post-FMT. The patient will also provide yearly reports for up to 10 years.

How Patients Can Take Part in the FMT National Registry

AGA expects 75 sites to be included in this registry. Visit ClinicalTrials.Gov <> on a regular basis to track new sites added to the registry. Patients should reach out to their health care provider to discuss participation in the registry.

Patients should first review AGA’s patient information on fecal microbiota transplantation (FMT) <>.

UC San Diego to Build FMT National Registry Biobank

AGA is collaborating with the American Gut Project — an academic effort run by the laboratory of Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at the University of California, San Diego — to build a biobank of stool samples from participants in the FMT National Registry. American Gut will receive stool samples from registry participants before and after their FMT. The microbiota will be sequenced in each sample, and remaining material will be frozen to be made available for future research. Eventually, this information could help doctors screen and select the best donor samples for individual patients.

OpenBiome Joins as a Registry Collaborator

AGA is also collaborating with OpenBiome, a public stool bank and nonprofit research organization that provides clinicians with rigorously screened, ready-to-use stool preparations for fecal transplant procedures. As the only public stool bank in the country, OpenBiome serves as the source of stool preparations for nearly 1,000 clinical partners performing FMT across the United States. For patients enrolled in the registry who receive OpenBiome FMT material, OpenBiome will provide screening information and samples to support the registry’s research analyses.

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