Mus musculus Raw sequence reads. Mus musculus

Understanding the factors that shape diversity in host-associated bacterial communities within host species is critical for understanding meta-organism evolution and maintenance. However, to which degree host genetics plays a role in shaping the microbial community composition is still unknown. Here, we document a major role for host genetics in determining gut microbiome composition between wild derived incipient species of the wild Mus musculus. We find that many bacterial taxa have substantial heritability estimates and these estimates correlate with their respective estimated cospeciation rate. We identified 443 loci contribution to variation in 123 taxa and identify promising candidate genes and pathways. We show significant overlap with previous gut microbiome QTL studies performed in reconstituted lab mice, as well as pathways involved in human diseases. Taken together, these results suggest a clear role for host genetics in shaping the microbial community as new species form.