Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study

Jakob Wirbel; Wael Saber; Michael J. Martens; Jonathan U. Peled; Tessa M. Andermann; Teng Fei; Erin F. Brooks; Boryana Doyle; Nathan B. Pincus; Robert R. Jenq; Merav Bar; Javier Bolaños‐Meade; Brandi Bratrude; Saurabh Chhabra; Sung Won Choi; William Clark; Suman R. Das; Hany Elmariah; Mahasweta Gooptu; Shernan G. Holtan; Richard John Jones; Levine Jp; Brent R. Logan; Monzr M. Al Malki; Hemant S. Murthy; Armin Rashidi; Andrew R. Rezvani; Marcie Riches; Lyndsey Runaas; Karamjeet Sandhu

doi:10.64898/2026.02.19.706769

MicrobiologybioRxivFeb 20, 2026

Preprint

Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study

Jakob Wirbel iD, Wael Saber iD, Michael J. Martens iD, Jonathan U. Peled iD, Tessa M. Andermann iD, Teng Fei iD, Erin F. Brooks iD, Boryana Doyle iD, Nathan B. Pincus iD, Robert R. Jenq iD, Merav Bar iD, Javier Bolaños‐Meade iD, Brandi Bratrude iD, Saurabh Chhabra iD, Sung Won Choi iD, William Clark, Suman R. Das iD, Hany Elmariah iD, Mahasweta Gooptu iD, Shernan G. Holtan iD, Richard John Jones iD, Levine Jp, Brent R. Logan iD, Monzr M. Al Malki iD, Hemant S. Murthy iD, , Ami Siddharth Bhatt iD

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Abstract

Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment for many hematological malignancies, but graft-versus-host disease (GVHD) is a common complication. Low gut microbiome diversity is associated with higher GVHD risk and shorter survival in multiple studies. Recently, the BMT CTN 1703 clinical trial demonstrated superiority of a GVHD-prophylaxis regimen including post-transplant cyclophosphamide (PTCy) compared to the standard prophylaxis (tacrolimus and methotrexate, Tac/MTX) in terms of GVHD-free, relapse-free survival at one year among reduced intensity conditioning allo-HCT recipients. However, the effect of PTCy on the gut microbiome and its association with clinical outcome have not been described. Here, we report on a companion randomized clinical controlled trial (BMT CTN 1801), which collected 2575 longitudinal stool samples from 304 study participants. Samples were obtained up to weekly up to day 84 post allo-HCT and at less frequent intervals thereafter, up to 2 years. Microbiome diversity and absolute microbial load were lower in the PTCy group compared to the Tac/MTX group on days 14-28 post-HCT. However, diversity at the timepoint closest to neutrophil engraftment was not significantly associated with non-relapse mortality after one year or other clinical outcomes, contrary to expectations from previous studies. Microbial domination events, when a single species exceeds 30% relative abundance, were comparable across treatment arms and reflected both pathogen blooms as well as less severe disruptions of the microbial community. Clostridium scindens and secondary bile acid metabolism pathways were less prevalent in the PTCy arm than in the Tac/MTX arm post-HCT, yet presence of secondary bile acid metabolism pathways was associated with a lower risk of chronic GVHD. Given that PTCy was associated with a greater disruption of the microbiome as measured by diversity, absolute microbial abundance, and bile acid metabolism capability, but better clinical outcomes overall, these data suggest that the importance of the microbiome in modulating the host immune systems after allo-HCT is specific to different types of GVHD prophylaxis.