Avian gut microbiome reflects spatial genetic structure in a small island population

Comparative studies are important to provide knowledge on host-microbe relationships in the wild. However, only a few combined microbiome with genetic investigation in natural populations. We investigated a non-model species, the red-legged partridge (Alectoris rufa), whose poor flight ability was deemed as key to assess if microbiome mirrors genetics at a small spatial scale in wild birds. We focused on a small Italian population consisting of two demes resident on the opposite sides of Elba Island (West and East). In previous studies, although genetically diverging, these subpopulations turned out to hold a comparable level of diversity. We used fecal pellets as proxy for the gut microbiome and set up a sampling protocol mitigating any possible relevant environmental variation among the study sites (e.g., habitat, season, age of faeces). We found significant differences between the two subpopulations in terms of microbial composition and diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher degree of diversity in western than in eastern A. rufa, a result that could also have been affected by a much lower intensity of past restocking in the former than in the latter region of Elba. Overall, the microbiome assembly steadily reflects host genetic spatial structure across the island, even though its diversity does not mirror their similarity in genetic variability. Our results represent the very first investigation on Alectoris microbiome and provide weight for a more informed adaptive management of the Elban partridge population.