In a small group of patients, autologous fecal microbiota transplantation (auto-FMT) was shown to replenish a patient’s gut microbiota after microbiota-depleting antibiotic treatment during allogeneic hematopoietic stem cell transplantation (allo-HSCT) (ClinicalTrials.Org Identifier: NCT02269150).1 Antibiotics are typically given during allo-HSCT to deplete the gut microbiota, but doing so also puts the patient at risk for later infection. The study findings were published online September 26, 2018, in Science Translational Medicine.

The study is based on an analysis of 25 patients enrolled in an ongoing randomized, open-label, phase 2 clinical trial at Memorial Sloan Kettering Cancer Center. The trial is designed to evaluate auto-FMT as a treatment for patients whom have undergone allo-HSCT. At the time of analysis, 14 patients had received auto-FMT treatment and 11 patients in the control group had not. Stool samples were collected at various time points to evaluate the changes in microbial diversity and composition.

The patients who received auto-FMT regained microbial diversity and composition to the state it was before antibiotic treatment and allo-HSCT. The patients who served as controls, however, did not regain gut microbial composition to the state it was before treatment with antibiotics and allo-HSCT. These outcome differences were present despite both groups starting with high microbial diversity before allo-HSCT and showing comparable reductions in gut microbiota composition after allo-HSCT.

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“These results demonstrate the potential for fecal sample banking and posttreatment remediation of a patient’s gut microbiota after microbiota-depleting antibiotic treatment during allo-HSCT,” the study authors wrote.

The trial investigators are continuing to monitor existing and newly recruited patients to determine whether auto-FMT improves clinical outcomes.


  1. Taur Y, Coyte K, Schluter J, et al. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant [published online September 26, 2018]. Sci Transl Med. doi: 10.1126/scitranslmed.aap9489