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Allogeneic hematopoietic stem cell transplantation (allo-SCT) offers cure for a variety of conditions, in particular but not limited to hematologic malignancies. However, it can be associated with life-threatening complications, including graft-versus-host disease (GVHD) and infections, that are factors limiting its widespread use. Technical advances in the field of microbiome research have allowed for a better understanding of the microbial flora of the human intestine and dissection of their interactions with the host immune system i