Job offer in england Exploring the Evolutionary and Genetic Basis for Bacterial Species at University of Exeter

University of Exeter – College of Life and Environmental Sciences

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence. The partnership has a strong track record in advancing knowledge through high quality research and teaching in partnership with industry and government.

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP). Up to 4 fully-funded studentships are being offered to start in September 2018 at the University of Exeter.

Academic Supervisors

Main supervisor: Dr Ben Raymond
Co-supervisor: Prof Sam Sheppard
Co-supervisor: Dr Michiel Vos
Collaborator: Dr Leyla Slamti

Project description

Understanding the forces that shape bacterial genetic variation is a fundamental problem in microbiology. Many bacterial species have been shown to exhibit extensive variation in gene repertoires, where a set of core genes shared by all strains are supplemented with a set of accessory genes that are only present in a subset of strains. The ability to exploit particular niches is thought to depend on the acquisition of a range of accessory genes, typically acquired via horizontal gene transfer (Vos et al. 2015). However, genetic variation in core genes shared between different strains is often associated with ecological niche (Raymond et al 2010, Zheng et al 2017) (Figure 1), suggesting that variation in core genes may be ecologically significant. This project will explore the extent to which core genetic variation arises from neutral genetic drift process and from positive selection in distinct habitats, a question with broad importance for understanding bacterial biology and evolution. For instance, many isolates of economic and therapeutic importance are closely related to isolates capable of causing disease. In both these cases, humans consume large doses of viable microbes in food or as therapeutic agents.

Understanding the potential of beneficial bacteria to cause harm or acquire harmful genes is particularly important for assessing the safety of these uses. If core genetic variation limits virulence or niche shifts then the risk of these applications will be substantially reduced. Bacillus thuringiensis, in particular, has an excellent safety record and is the most widely applied microbial insecticide, facilitating environmentally friendly mosquito control and pest management. Nevertheless, disagreements regarding its ecological niche, and it taxonomic status relative to Bacillus cereus, a causative agent of diarrhoea, have threatened its continued use in the European Union. In this project, the student will (1) carry out genome sequencing and phenotypic characterization of isolates from natural populations (2) apply experimental evolution and re-sequencing approaches to look for convergent adaptive mutations in novel niches (3) use CRISPR-Cas9 genome editing to introduce putative adaptive alleles into different genetic backgrounds. This project will be lead by Dr Ben Raymond & Dr Michiel Vos at the University of Exeter and co-supervised by Prof Sam Sheppard at the University of Bath. Dr Raymond has worked on Bacillus thuringiensis and its relatives for more than 15 years. Michiel Vos has a longstanding interest in bacterial recombination and genome evolution. Prof Sam Sheppard leads a population genomics group at the University of Bath.

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