Abstract
Host-microbe interactions are shaped by both host and environmental factors. However, little is known about how host-microbe interactions vary across populations within a species. Here, we characterized the gut microbiota of 191 wild threespine stickleback fish ( Gasterosteus aculeatus ) from six populations from Alaskan lakes spanning a gradient of surface area. We tested how environmental context (lake size and ecotype) and host traits (sex, body mass, gravidity, Schistocephalus solidus ( S. solidus ) infection, and fibrosis) influence stickleback gut microbial composition using 16S rRNA gene sequencing. We found that the lake surface area strongly predicted fish gut microbial alpha diversity. Fish from intermediate-sized lakes harbored significantly more diverse microbiota than those from small and large lakes, independent of ecotype. Body mass was associated with gut microbial diversity. Model-predicted marginal effects from the mass and lake surface area interaction analysis showed that the association between fish mass and microbial alpha diversity was strongly negative in the smallest lakes, weakest in intermediate-sized lakes, and strongly positive in the largest lakes. In addition, sex and S. solidus infection were significantly associated with gut microbiota alpha and beta diversity, whereas fibrosis and gravidity showed minimal effects. Differential abundance analysis revealed lake size-dependent associations between body mass and individual taxa. Together, these results demonstrate that both habitat context and host variation interactively shape stickleback gut microbial communities in the wild. Integrating lake-level and individual-level analyses reveals how ecological setting modulates host-microbe associations, offering insights into the role of the gut microbiota in host adaptation and population divergence.