Alterations to the gut microbiota of a wild juvenile passerine in an urban mosaic

Urbanisation is a major anthropogenic perturbation that progressively alters multiple environmental parameters, thereby presenting novel evolutionary challenges to wild populations. Symbiotic microorganisms residing in the gastrointestinal tracts (gut) of vertebrates have well-established mutual connections with the physiology of their hosts and respond quickly to environmental alterations. However, the impacts of anthropogenic changes and urbanisation on gut microbiota remain poorly understood, especially in early host development. To address this knowledge gap, we investigated the gut microbiota in juvenile great tits (Parus major) in an urban mosaic. First, we compared the microbiota of nestlings reared in artificial nest boxes or natural cavities. Next, we analysed microbiota variations employing two distinct urbanisation frameworks, (i) the classical urban/rural dichotomy and (ii) gradual changes in the amount of impervious surface area (ISA) in the urban space and identified the environmental variables that predicted the changes in the microbial communities. Alpha diversity was influenced by cavity type and by the amount of impervious surface surrounding the breeding location. Alpha diversity was also positively correlated with the tree cover density. Beta diversity differed between urban and rural sites, and these alterations covaried with sound pollution, the distance to the city centre and the distance to the closest road. Overall, the microbial communities reflect and are possibly influenced by the heterogeneous environmental modifications that are typical of the urban space. Strikingly, the choice of framework used to define the urban space can influence the outcomes of studies investigating animal-microbe symbiosis. Our results open new perspectives from which the potential function of microbial symbionts in the adaptation of their hosts to anthropogenic stress can be investigated.