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Eco-evolutionary dynamics of the gut microbiota


About This PhD Project

Project Description

The intestinal microbiota is composed of multiple species of microorganisms that have important functions for the health of the human host. These microbial communities result from complex relationships between its single components (such as competition or collaboration), and the interactions of microbial species with the host. Disruption of the natural microbial flora is linked to infection, autoimmune diseases and cancer, yet detailed knowledge about these inter-species dynamics, their evolution and response to external factors remains scarce.

In this project, you will investigate the eco-evolutionary dynamics between major species and strains of the human gut microbiota by combining experimental evolution and bioinformatic analyses. The main research objectives are: (1) To characterize the types of relationships established between gut microbial species; (2) to identify genetic changes (mutations and gene flows between species) that may help us to understand adaptive evolution within the human gut; and (3) to investigate how abiotic factors (culture media, diet carbohydrates, oxygen, antibiotics,…) affect these interspecies relationships and evolutionary processes. A good comprehension of these processes will be of high value for the rational design of probiotics and for the treatment of gut-associated infectious diseases.

Applied techniques:
- Preparation of gut microbiota co-cultures in the anaerobic and fermentation platforms.
- Experimental evolution and in vitro competition experiments of multiple species and strains.
- Automatic extraction of (meta)genomic DNA for high-throughput sequencing.
- Bioinformatic and statistical analyses of metagenomic data and single bacterial genomes.

The Raes Lab:
Our lab combines large-scale, next-generation sequencing with novel computational approaches to investigate the functioning and variability of the healthy human microbiome at the systems level and study its alteration in disease. We hold a growing culture collection of thousands of bacteria isolated from the gut, in addition to cross-sectional and temporal microbiome information coupled with rich metadata for thousands of individuals living in Flanders.

How to apply:
For more information and informal enquiries, contact with Dr Rodrigo Bacigalupe () or Prof Jeroen Raes ().

To apply for this PhD project, please send a brief motivational letter, a copy of your CV and details of two referees to and . Please quote the project title in the subject of the email.

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