Influence of urbanisation on the gut microbiota of avian hosts and implications for host fitness

The gut microbiota plays a fundamental role for host health and fitness. The gut microbiota is known to be shaped by host traits and environmental factors. One of the dominant causes of contemporary environmental change is the increase in human activity, with urbanisation representing one of the most radical forms of land use alterations in terrestrial ecosystems. These anthropogenic alterations are likely to alter host-associated microbiomes and the interactions between host and microbiota, resulting in adverse effects on hosts. The main aim of this thesis was to investigate the effect of anthropogenic alterations, on the characteristics of the gut microbiota of two passerine hosts, and to further examine the role of specific factors, notably diet and the rearing environment in shaping the gut microbiota. By studying gut microbiota of free-ranging house sparrows and great tits in habitats with different levels of urbanisation I found that microbial diversity was reduced with urbanisation in house sparrows, but no effect was found in great tits. Urbanisation was also associated with modifications in taxonomic composition and community structure, and changes in functional composition. By exposing wild house sparrows from urban and rural populations to contrasting diets in an experimental set-up, with experimental diets based on a rural vs urban diet, I observed gut microbiota modifications with alterations of both α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. The influence of the nesting environment on the gut microbiota was investigated by performing a partial cross-fostering experiment in great tits halfway during nestling development. Results showed a significant decrease in microbial diversity between 8 and 15 days after hatching, as well as changes in community composition. In addition, fostered nestlings became more similar to their nest mates, providing evidence that the rearing environment plays a role in shaping the nestlings’ microbiota. Finally, gut microbiota characteristics were found to be related to host condition in both species with an effect of the microbial diversity, taxonomic and functional composition on the body mass and mass gain of the host. To conclude, this thesis reports new insights on the effect of urbanisation on gut microbiota characteristics and provides experimental evidence for major factors that may induce microbiota changes, notably diet and rearing environment. It also highlights the potential impact of the gut microbiota and its disturbance on the performance of hosts living in cities.

Publication year:2020

Keywords:Doctoral thesis

Accessibility:Open