Recent studies in both mice and humans have demonstrated that the intestinal microbiota can affect hematopoiesis. Here, we performed experiments in preclinical mouse models for syngeneic and allogeneic HCT. To study the metabolic effects of intestinal flora depletion on post-transplant hematopoiesis in humans, we performed HCT experiments using a metabolic chamber and bomb calorimetry of feces. Taken together, we show that the intestinal microbiota supports post-transplant hematopoietic reconstitution in HCT recipients through its role in dietary energy uptake.