The composite human microbiome of Western populations has probably changed over the past century,brought on by new environmental triggers that often have a negative impact on human health.Here we show that consumption of a diet high in saturated (milk derived) fat, but not polyunsaturated (safflower oil) fat, changes the conditions for microbial assemblage and promotes the expansion of a low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia.