Results from auto-FMT pilot

Our team at Memorial Sloan Kettering has been investigating the intestinal microbiota of patients receiving bone marrow transplantations for more than eight years now. We have found through several studies that these patients lose important healthy bacteria from their microbiota and that these losses are mostly caused by the antibiotics given as prophylaxis or to treat infections. We also found that the drastic changes in the microbiota composition, especially the intestinal dominations by bacteria such as Enterococcus, increase the risk of transplant-related complications and lowered patient survival. Here we tested whether autologous microbiota transplant (auto-FMT) could reconstitute lost bacteria. In this randomized study led by Ying Taur and Eric Pamer we could see that auto-FMT indeed reconstituted important microbial groups to patients.

The success of auto-FMT varied from patient to patient, though. In the best case a patient recovered practically 100% but in the worst case, recovery was 50%. The effect of auto-FMT was statistically significantly overall, but understanding why its success can vary between patients (which could be due to factors like the actual composition of the transplant, the state of the microbiota before the transplant or even personal factors like host genetics or the underlying disease) is an important direction for future research, and for future microbiota therapies.

As the pilot study continues we should be able to determine whether auto-FMT also improves clinical outcomes for this patients. This is a question left unanswered in our report but which will be addressed in the near future.


Timeline for a study patient undergoing allo-HSCT and randomized to receive auto-FMT.  Allo-HSCT was initiated with pretransplant conditioning [chemotherapy and total body irradiation (TBI)], followed by allogeneic hematopoietic stem cell infusion (day 0). Various antibiotics were given throughout this period for prophylactic and treatment purposes. After stem cell engraftment, randomization assigned this patient to the treatment arm and the patient received an auto-FMT on day 49 using the patient’s initial pretreatment feces, which had been collected and stored before allo-HSCT (initial feces collected at day −21). The intestinal microbiota was restored to that before the transplant.

Read the paper: Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Taur et alScience Translational Medicine [PDF]

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