The composition of the gut microbiome is impacted by a complex array of factors, from nutrient composition and availability, to physical factors like temperature, pH and flow rate, as well as interactions among the members of the microbial community. Many of these factors are affected by the host, raising the question of how host genetic variation impacts microbiome composition. Human studies confirm a role for host genetics, but opinions vary on just how important is host genetic variation in determining gut microbiome composition. The mouse model, by allowing far better control of genetics, nutrition, and other environmental factors, has provided an excellent opportunity to extend this work, and the Diversity Outbred (DO) mice in particular present a chance for mapping host genetic variants that influence specific attributes of microbiome composition. Here we apply 16s sequencing to fecal samples of 247 DO mice and perform QTL mapping on microbial abundances. In addition to finding a number of novel associations, the concordance with heritabilities and associations with both human and mouse studies was striking, including the phylum Tenericutes, family Ruminococcaceae, as well as Staphylococcus and Turicibacter.

High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition