Project No. 2449

STANDARD PROJECT

Primary Supervisor

Dr Nela Nikolic- University of Southampton

Co-Supervisor(s)

Dr Anastasios Tsaousis – University of Kent

Dr Sandra Wilks – University of Southampton

Prof Xunli Zhang – University of Southampton

Summary

Human-caused changes, such as antibiotic overuse and misuse, climate change and pollution are increasingly affecting the microbial life on Earth.

How do bacteria respond so effectively to the myriad of environmental insults they face? This project will investigate the flexibility of these resilient bacteria that is encoded in their ‘accessory’ genome, which can add novel (often unknown) functions to their core genome. Accessory genes are not present in all members of the same species, which drives the genetic diversity necessary for the species to adapt to new conditions. Specifically, this project aims at elucidating roles of the bacterial accessory genome during colonization of a new host.

The PhD student will have the opportunity to employ microbiology, molecular biology, host-pathogen biology and single-cell techniques (Nikolic and Wilks groups) alongside engineering (Zhang group) and bioinformatics (Tsaousis group), to address three main goals. First, the student will investigate functional (e.g. biofilm formation) and structural (e.g. genome stability) roles of accessory genes in a set of Escherichia coli strains with annotated genomes, e.g. a zoonotic strain that is a foodborne pathogen, strains involved in urinary tract infection which exhibit increasing prevalence of antimicrobial resistance, a commensal strain that is part of the human gut microbiota. Second, the student will study host-bacteria interactions by employing larvae of the wax moth Galleria mellonella as the host model system. And third, the student will develop novel devices and macroscopic technology setups to follow host colonization in real time.

This project will utilize interdisciplinary approaches and develop new technologies to address how accessory genes supercharge a bacterial species to invade new hosts. Findings will help advance our understanding of the bacterial life and pathogen evolution; for instance, how a friendly bacterium, commensal to animal gut, can take up genetic material from another pathogen species, and transform itself to a human pathogen via this accessory material. Ultimately, the project will tackle a fundamental question of what determines where bacterial species can live, to be able to predict their responses to anthropogenic changes.

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