Autologous FMT (AGFR) – bank your own stool at Taymount.

Patients who normally attend Taymount Clinic for FMT are coming for a number of reasons but are all generally suffering from health conditions or a collection of symptoms that are having a negative effect on their quality of life.

Maybe they have taken too many antibiotics over the years and this has depleted their gut flora, or maybe they have developed an illness that either stems from, or has contributed to, a dysbiotic microbiome. Either way, their gut bacteria are not flourishing, and they are seeking to re-establish a diverse bacterial colony via the use of healthy donors’ stool.

So far, this should all be familiar to most of our readers.

But what about those who are lucky enough to already have a healthy gut, yet are faced with a procedure or event that could potentially damage their microbiome? What if they had the option of harvesting their own healthy gut bacteria, storing it away for safe keeping, and then re-administering it at later date when they need it?

Having an FMT using your own stool is known as Autologous Gut Flora Restoration (AGFR). Studies have shown that this form of FMT is a safe and effective way to replenish the gut microflora after it has been impaired by antibiotics or other events that may have had a negative impact.

One study looked at a group of cancer patients who were due to receive an intense course of antibiotics whilst undergoing allogenic hematopoietic stem cell transplantation. Those patients who received post treatment, autologous FMT, had a boost in their microbial diversity and their original microbial composition was re-established. (Suez. 2018)

Another study compared the use of multi-strain probiotics versus autologous FMT for restoring the mucosal microbiome after antibiotic use. Surprisingly, they found that the probiotics actually hindered the return to a normal microbiome, whereas autologous FMT “induced a rapid and near-complete recovery within days of administration.” (Taur et al. 2018)

In a prospective trial carried out by Mohty et al (2017), researchers looked at Autologous FMT in Acute Myloid Leukemia (AML) patients. Patients banked their stool prior to undergoing intensive antibiotic and chemotherapy treatment. This treatment is known to negatively impact the gut bacteria and this may in turn impact the immune system and have consequences on the outcome for these patients. The trial found that autologous FMT was able to correct dysbiosis and restore a normal microbiota.

Based on the findings of these studies, coupled with our existing knowledge about the fundamental importance of a healthy, diverse microbiome, Taymount would like to offer the option of autologous FMT to any potential candidates.

People who are generally fit and healthy will be able to safeguard their existing microbiome by having their stool processed and stored in a secure and protective facility, with access to later restoration when the need arises.

Circumstances where one might consider banking stool for later use include:

  • Planned use of antibiotics e.g. after an operation or elective caesarean
  • Surgery/other medical or dental procedures that may have a negative impact on the gut bacteria
  • Prior to foreign travel – to restore the microbiome after a case of food poisoning or possible antibiotic intervention.
  • Prolonged fasting/water or juice fasts that might deplete the microbiome.
  • An upcoming period of high stress
  • As an insurance policy for unseen events that might have a deleterious effect bacterial density or diversity
  • Keep reading below for two illustrative case studies.

A male patient (62) suffered Achilles’ tendon damage at the beach whilst on holiday.  He was operated on for repair of the tendon in a lengthy surgery.  The skin was stretched very thin over the ankle sutures with poor localised blood supply and infection set in very soon after surgery (Staphylococcus Aureas).  Antibiotics were given as a normal response to this infection but during the course of the antibiotics the patient became very agitated and irritable and his character changed quite considerably.  Luckily, the patient had previously deposited faecal material with the Taymount clinic and a small number of implants were prepared and stored with his ID in the clinic freezer. The half-life of the antibiotics was established, and it was determined that the second day after the course finished, it was safe to go ahead and do gut flora restoration (FMT).

On the day of the chosen restoration, the patient self-administered one of his own implants at 5pm.  He reported that by 7pm he felt very much better; this was not obvious to those around him at that time, but certainly by the next morning, he awoke “as himself”, his old amiable character had returned, and he was back to his usual behaviour and emotions.  It only took one implant to restore his old gut flora’s status quo and leave him feeling like normal once again.  The other of his implants remain in the Ultra Low laboratory freezer and at temperatures of -80°C, they will be good for several years in case they are needed.

A young mother-to-be (29) was planning a natural birth for her first baby and had organised a home delivery with carefully chosen midwives to attend her.  All through the pregnancy she had carefully nurtured her gut microbiome to maximise the precious microbial gift to her new-born during delivery.  She ate well and with huge diversity and believed that her gut flora was in the best of conditions.  The labour started normally at home and she was confident that her birth plan would give her infant the best start in life that she could offer.  Unfortunately, the baby was lying in a difficult position and her head was not engaged in exactly the right trajectory.  Labour was long and difficult and by supreme effort on the part of the mother, the baby was delivered normally but causing a 2nd degree tear in the delicate membranes of her vagina and vulva.  The attending midwives stitched her a little over-enthusiastically and within a few hours it was obvious that surgery was needed to rectify the tear and the stitches.

Upon admission to hospital the young mother was kept nil-by-mouth whist surgery was organised and was told she would have IV antibiotics to ward off possible infection from the surgical procedures.  This would have put antibiotics in the colostrum and early breast milk that the infant was taking and would have knocked back the delicate microbiome that the baby was beginning to colonise from her mother.  It looked quite alarming for the family, who prized the health of the microbiome highly.  It was not possible for the mother to produce a stool which could have been banked – she was pretty much empty of food having laboured for the whole of the previous day and been nil-by-mouth for this second day, so there was no stool forthcoming which could have been harvested.

Happily, the surgeon found that only minimal suture correction was needed, and the IV antibiotic was cancelled.  The family heaved a huge sigh of relief – but quickly banked a stool sample at the next opportunity as insurance for the future.

Had the mother banked stool and had implants frozen for her (AGFR), she could have approached the surgery and antibiotics with confidence knowing that she could restore her gut flora with a single implant following the surgery and IV drugs.

The moral to this story is that when planning a birth, AGFR would be a good precaution to take just in case the birth does not go according to plan.  A lot of them don’t, but AGFR would give you the peace of mind that whatever drugs are required, for whatever reason, the collateral damage could be reversed with AGFR.

Please contact the clinic for further information.


  1. Suez, J. et al. (2018). Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell, 174(6), pp.1406-1423.e16.
  2. Mohty, M. et al. (2017). Prevention of Dysbiosis Complications with Autologous Fecal Microbiota Transplantation (auto-FMT) in Acute Myeloid Leukemia (AML) Patients Undergoing Intensive Treatment (ODYSSEE study): First Results of a Prospective Multicenter Trial. Blood, 130, pp.2624.
  3. Taur, Y et al. (2018). Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Science Translational Medicine, Sep 26;10(460).