École doctorale : University of Antwerp, Faculty of Sciences, Department of Biology, Evolutionary Ecology Group – Ghent University, Faculty of Sciences, Department of Biology, Terrestrial Ecology Unit (Belgium)
Équipe de recherche : UMR EDB
Date de soutenance : le 29/06/2020
Direction : Joël White (ENSFEA), Matthysen Erik (Université d’Anvers, Belgique) et Lens Luc (Université de Gand – Belgique)
Titre : Influence of urbanisation on the gut microbiota of avian hosts and implications for host fitness.
Résumé : The gut microbiota plays a fundamental role for host health and fitness, as it mediates processes such as digestion and nutrient synthesis, immunomodulation and pathogen defense. It also more widely influences life-history traits or even host behavior. 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 environmental changes, with a specific interest in anthropogenic alteration, 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 the level of urbanisation affected both diversity and composition of the gut microbiota. Microbial diversity was reduced with urbanisation in house sparrows, but no effect was found in great tits. Gut microbiota of urban house sparrows were also characterized by a lower relative abundance of Enterococcaceae and Staphylococcaceae and a higher abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts.
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 diet-induced 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. Additionally, diet-induced shifts resembled initial differences between free-ranging urban and rural birds highlighting the contribution of the diet in explaining the differences in the gut microbiota along the urbanization gradient.
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. I found that microbial diversity was positively correlated with body mass or body mass gain in great tit nestlings and in captive house sparrows. Moreover, I also found some associations between functional and taxonomic composition of microbiota and body condition in free-living sparrows.
To conclude, this thesis reports new insights on the effect of urbanisation on gut microbiota characteristics and how this could affect the host. In addition it 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.
Mots-clés : (non disponible)
