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Influence of anthropogenic alterations on the gastrointestinal microbiota of avian hosts and implications for host fitness

Key-words: gut microbiota, anthropogenic habitat alterations, House sparrow, Great tits, next-generation sequencing.

All animals host a huge variety of microorganisms inside their gut, forming complex and dynamic communities known as the gastrointestinal microbiota. This gut microbiota performs a number of essential functions for its host, such as a central role in digestion, immunity and protection against pathogens of the host. The composition and the diversity of the gut microbiota are expected to be shaped not only by the characteristics of the host, such as genotype, age or sex but also by that of the environment in which the host lives. However, little is known on the effects of anthropogenic habitat alterations on the gut microbiota of natural populations and how this may in turn affect host fitness and host population dynamics.

In order to address this question, the aim of my PhD is to study the gut microbiota of two passerine birds species inhabiting contrasting habitats along an urbanisation gradient , the house sparrow (Passer domesticus) and the great tits (Parus major). Two main approaches will be used: a wide-scale microbiota sampling program throughout Flanders and in a number of contrasting environments and short-term experiments carried out in aviaries.

Gut bacterial communities will be characterised using a combin ation of next-generation sequencing techniques (Illumina Miseq) and community-fingerprinting techniques (ARISA).

My PhD project is divided in 4 main aims:

  • to determine whether environmental factors and genetic structure of sparrow populations explain variation in gut microbiota composition by sampling urban and rural populations throughout Flanders (region of Gent, Antwerp and Leuven);
  • to investigate the role of diet in gut microbiota composition by experimental feeding experiments using contrasting diets (aviary experiment);
  • to test the role of group living in shaping microbiota composition by manipulating group size and monitoring behavioural interactions between individuals (aviary experiment);
  • to investigate the acquisition and establishment of the gut microbiota in chicks through parental effects and the nesting environment in great tits (field study).

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