Eukaryotic and bacterial gastrointestinal diversity in natural populations of House mouse (Mus musculus)

Parasites and other host-associated eukaryotes are, among a multitude of bacteria, part of the intestinal ecosystem. The role of eukaryotes in the gut ecosystem is, however, less understood than that of bacteria. The composition of the bacterial microbiome contributes e.g. to health in inbred laboratory mice and host genetics in outbred wild or wild-derived mice influences microbiome composition. The global impact of host genetics on gastrointestinal eukaryotes is less well explored.We here used a multi-marker amplicon sequencing approach, to simultaneously study gastrointestinal eukaryotes and bacteria in natural populations from house mice (Mus musculus). We compared gastrointestinal diversity, composition and abundance across a gradient of pure and hybrid genotypes in the European house mouse hybrid zone between the subspecies M. musculus musculus and M. musculus domesticus.