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Abstract

A growing literature demonstrates the impact of helminths on their host gut microbiome. We
investigated whether the stickleback host microbiome depends on eco-evolutionary variables by
testing the impact of exposure to the cestode parasite Schistocephalus solidus with respect to infection
success, host genotype, parasite genotype, and parasite microbiome composition. We observed
constitutive differences in the microbiome of sticklebacks of different origin, and those differences
increased when sticklebacks exposed to the parasite resisted infection. In contrast, the microbiome of
successfully infected sticklebacks varied with parasite genotype. More specifically, we revealed that
the association between microbiome and immune gene expression increased in infected individuals
and varied with parasite genotype. In addition, we showed that S. solidus hosts a complex endo-
microbiome and that bacterial abundance in the parasite correlates with expression of host immune
genes. Within this comprehensive analysis we demonstrated that (i) parasites contribute to modulating
the host microbiome through both successful and unsuccessful infection, (ii) when infection is
successful, the host microbiome varies with parasite genotype due to genotype-dependent variation in
parasite immunomodulation, and (iii) the parasite-associated microbiome is distinct from its host’s
and impacts the host immune response to infection.