Category Archives: Fecal Microbiota Transplant (FMT)

On June 13th the U.S. Food and Drug Administration Warned of Infections From Fecal Microbiota Transplantation (FMT) Linked to a Patient’s Death

Dr. Peter Marks, director the Center for Biologics Evaluation and Research at the U.S. Food and Drug Administration stated, “While we support this area of scientific discovery, it’s important to note that fecal microbiota for transplantation does not come without risk,”

Two patients contracted severe infections, and one of them died, from fecal transplants that contained drug-resistant bacteria.

The agency said two patients received donated stool that had not been screened for drug-resistant germs, leading it to halt clinical trials until researchers prove proper testing procedures are in place.

After reports of serious, antibiotic-resistant infections linked to the procedures, the FDA wants “to alert all health care professionals who administer FMT [fecal microbiota transplant] about this potential serious risk so they can inform their patients.” said Dr. Peter Marks, director the Center for Biologics Evaluation and Research at the U.S. Food and Drug Administration.

Other samples from the same donor were tested after the patients got sick. The samples were found to harbor the same dangerous germs found in the patients, known as multi-drug-resistant organisms (MDRO). They were E. coli bacteria that produced an enzyme called extended-spectrum beta-lactamase, which makes them resistant to multiple antibiotics. The stool had not been tested for the germs before being given to the patients.

The F.D.A. on Thursday issued a warning to researchers that stool from donors in studies of fecal transplantation should be screened for drug-resistant microbes, and not used if those were present. It is also warning patients that the procedure can be risky, is not approved by the agency and should be used only as a last resort when C. difficile does not respond to standard treatments.

Dr. Marks said the agency was trying to strike a balance between giving patients who need the treatment access to it while also establishing safeguards to protect them from infection. In a statement, he said, “While we support this area of scientific discovery, it’s important to note that fecal microbiota for transplantation does not come without risk.”

Researchers are also looking into the use of fecal transplants to treat chronic gastrointestinal illnesses such as ulcerative colitis or irritable bowel syndrome.

The patients received treatment as part of a clinical trial, and the researchers conducting the trial reported the cases as adverse events to the F.D.A., which they are required to do. But the rules governing this kind of experiment prohibit the F.D.A. from revealing details about the treatment or who provided it.

 

SOURCE:  https://www.nytimes.com/2019/06/13/health/fecal-transplant-fda.html

FDA Safety Alert Regarding Use of Fecal Microbiota for Transplantation and Risk of Serious Adverse Reactions d/t Multi-drug Resistant Organisms

Important Safety Alert Regarding Use of Fecal Microbiota for Transplantation and Risk of Serious Adverse Reactions Due to Transmission of Multi-Drug Resistant Organisms

The Food and Drug Administration (FDA) is informing health care providers and patients of the potential risk of serious or life-threatening infections with the use of fecal microbiota for transplantation (FMT).  The agency is now aware of bacterial infections caused by multi-drug resistant organisms (MDROs) that have occurred due to transmission of a MDRO from use of investigational FMT.

Summary of the Issue

  • Two immunocompromised adults who received investigational FMT developed invasive infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E.coli). One of the individuals died.
  • FMT used in these two individuals were prepared from stool obtained from the same donor.
  • The donor stool and resulting FMT used in these two individuals were not tested for ESBL-producing gram-negative organisms prior to use. After these adverse events occurred, stored preparations of FMT from this stool donor were tested and found to be positive for ESBL-producing E. coli identical to the organisms isolated from the two patients.

Information for Health Care Providers and Patients

In July 2013, FDA issued guidance stating that it intends to exercise enforcement discretion under limited conditions regarding the IND requirements for the use of FMT to treat Clostridium difficile (C. difficile) infection in patients who have not responded to standard therapies. The guidance states that FDA intends to exercise enforcement discretion provided that the treating physician obtains adequate consent for the use of FMT from the patient or his or her legally authorized representative. The consent should include, at a minimum, a statement that the use of FMT to treat C. difficile is investigational and a discussion of its potential risks. FDA is informing members of the medical and scientific communities and other interested persons of the potential risk of transmission of MDROs by FMT and the resultant serious adverse reactions that may occur.

Patients considering FMT to treat C. difficile infection should speak to their health care provider to understand the potential risks associated with the product’s use.

Additional Protections for Investigational Use of FMT

  • Because of these serious adverse reactions that occurred with investigational FMT, FDA has determined that the following protections are needed for any investigational use of FMT:
    • Donor screening with questions that specifically address risk factors for colonization with MDROs, and exclusion of individuals at higher risk of colonization with MDROs.
    • MDRO testing of donor stool and exclusion of stool that tests positive for MDRO. FDA scientists have determined the specific MDRO testing and frequency that should be implemented.

Reporting Adverse Event

FDA encourages all health care providers administering FMT products to report suspected adverse events to the FDA at 1-800-FDA-1088 or http://www.fda.gov/medwatch.

June 13, 2019


C Diff Foundation Welcomes Dr. Sahil Khanna, M.B.B.S.

We are pleased to welcome Dr. Sahil Khanna
as a Member of the C Diff Foundation and Medical Advisory Board.

Dr. Sahil Khanna is an Associate Professor of Medicine in the Division of Gastroenterology and Hepatology at Mayo Clinic, Rochester, MN. He is directing the Comprehensive Gastroenterology Interest group,
C. difficile Clinic, Fecal Microbiota Transplantation program and
C. difficile related Clinical Trials at Mayo Clinic, Rochester, MN.

He completed Medical School at the All India Institute of Medical Sciences, New Delhi; followed by Post Doctoral Research at University of California San Diego, CA; residency in Internal Medicine and Fellowship in Gastroenterology and Hepatology at Mayo Clinic, Rochester, MN before joining the Faculty. He also completed Masters in Clinical and Translational Sciences during his fellowship. His research and clinical interests include Epidemiology, Outcomes and Emerging Therapeutics for Clostridium difficile infection, an arena in which he has had numerous publications and presentations.

Dr. Khanna has over 100 peer-reviewed publications and serves as reviewer and on the editorial board of several journals. He has won numerous awards including the Miles and Shirley Fiterman Award, Mayo Brothers Distinguished Fellowship Award, Donald C. Balfour Mayo Clinic Alumni Association Research Award, Hartz Foundation Young Investigators’ Scholarship and the Most Distinguished Resident Physician Award from the American Association of Physicians of Indian Origin.

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.”

Reference

https://www.infectiousdiseaseadvisor.com/respiratory/new-powder-formulation-tuberculosis-vaccine-candidate-is-in-human-trial/article/829508/

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 www.prism3trial.com.

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.

View source version on businesswire.com:https://www.businesswire.com/news/home/20190208005039/en/

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.

Source:  https://www.healio.com/gastroenterology/infection/news/online/%7B1402ede4-5de1-40a3-b23f-a0070e01ad7a%7D/trial-testing-fmt-for-recurrent-diarrheal-disease-begins

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)

Objectives

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).

Summary

Objectives

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).

Methods

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.

Results

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.

Conclusions

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.

Introduction

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

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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