Microbial metabolites modulate immune cell responses in GVHD. SCFAs derived from fiber and secondary bile acids protect epithelial cells from damage, leading to suppression of immune cell activation. AhR ligands derived from dietary tryptophan can also suppress immune cell activation through reduction of intestinal epithelial damage in GVHD. TMAO is produced by hepatic processing by flavin monooxygenases of TMA following bacterial metabolism of choline and other dietary components. TMAO augmented alloreactive T-cell proliferation via M1 polarization of bone marrow–derived macrophages.