Diet is one of the factors that shape the gut microbiome; however, little is known about the influence of diet on the microbiome in other tissues or organs. Shively et al. used a non-human primate model to investigate whether diet can modify the breast tissue-specific microbiota. Animals fed a Mediterranean diet had higher levels of Lactobacillus populations in their mammary gland tissues, whereas consumption of a Western diet led to increased levels of bacteria in the Ruminococcus, Lachnospiraceae, Oscillospira and Coprococcus genera. These results highlight both differences and similarities of the diet-mediated modulation of the microbiota in the gut and mammary gland tissues. A Mediterranean diet also led to increased levels of bile acid metabolites and bacterial-modified bioactive compounds, which may affect inflammation in the breast and modulate breast cancer risk. Thus, diet influences microbiome populations not only in the intestinal tract but also at distal sites.