Gasterosteus aculeatus Raw sequence reads. Gasterosteus aculeatus

Individual plant and animal hosts vary substantially in the microbial (e.g. bacterial) assemblages that inhabit their body sites, but understanding the role of host genetic background in this variation has been a challenge. We co-reared threespine stickleback fish without restrictions, throughout development, and measured their gut microbiomes as juveniles. Because we used several genetically distinct stickleback lines, and hybrids between the lines, we were able to test for associations between genetic and microbiome similarity. We found a clear, positive relationship between genetic and microbiome dissimilarity, and found that the strength of this relationship varied along the genome, an analysis made possible by genotyping the fish at thousands of genetic markers.