The authors identify AgcT as the glycosyltransferase required for synthesis of Bacteroides fragilis-derived α-galactosylceramides (BfaGCs), metabolites known to regulate natural killer T cells, and its structural homologue BgsB that synthesizes α-glycosyl diacylglycerols (aGDGs). They establish a functional link between the production of BfaGCs or aGDGs and the activity and development of natural killer T cells.