PhD Theses.Microbes are ubiquitous, and are often found in close associations with a host, where they affect its physiology, immune functions and even behaviours. In this thesis, I explored host-microbe interactions in wild vertebrate species to disentangle the role of genetic and environmental determinisms of those interactions. In Chapter Two, together with my collaborators, I brought evidence for the evolution of local adaptation of three-spined stickleback (Gasterosteus aculeatus) gut microbiomes through population-specific microbiomes, caused by localised environmental pressures and/or genetic determinism. In Chapter Three, I established the baseline relationship between parasites and stickleback diet, as both can impact host-microbe interactions. I confirmed that feeding ecology is not independent of host-parasite interactions and both parasite resistance and feeding ecology evolve under local adaptation. Chapter Four highlighted how the host’s microbiome is influenced by genotype-by-environment interactions, with changes in the microbiome correlating with interactions between host evolutionary lineage, local environment, and seasonal variation. Interestingly, microbial diversity decreased with increased parasite infections, suggesting intricate host-parasite-microbe interactions. Additionally, I found evidence that a host’s microbiome is linked to feeding ecology, but the direction of this relationship was context-dependent. Finally, in Chapter Five, I tested the generality of the conclusions obtained in the fish system by changing host species to the philopatric and locally-adapted loggerhead sea turtle (Caretta caretta) nesting at the Cabo Verde Archipelago. I found population-specific cloacal microbiomes among closely related nesting groups and as well as host-parasite-microbe interactions. Overall, this thesis focused on teasing apart the diverse determinisms of wild host-microbe interactions. It relied on a series of field experiments and sampling of wild individuals and ultimately shows how fundamental the role of the host microbiome is for species evolution
