Pseudomonas aeruginosa is a key opportunistic respiratory pathogen in patients with cystic fibrosis and non-cystic fibrosis bronchiectasis. The genomes of these pathogens are enriched with mobile genetic elements including diverse temperate phages. The role of these prophage that can be mobilised to infect other Pseudomonads in chronic lung infections is poorly understood although research has illustrated that multiple can induce from the same bacterial host. Temperate bacteriophages genomes have conserved order of genes as it is required for their life cycle including infection, proliferation and release. Importantly for this study they also carry genes of accessory function, sometimes known as cargo genes that can offer positive selection for the bacteriophage or lysogen in that environment. A high proportion of phage genes outside of those annotated have no assigned function but these genes are conserved across phages in this environment. This may mean that they are important in this environment.
We have surveyed the genomes of over 1500 P.aeruginosa for phage regions, from both cross-sectional and longitudinal studies of chronic lung infection compared to environmental samples and have discovered the key groups of phages that are lung related. We have isolated phages from each of these key taxonomic groups and are now looking to further research into their role in colonisation and infection in the lung environment.
You will use the latest in omics technologies and learn bioinformatic skills supported by an experienced team. You will learn lab-based methods in handling bacteriophages, their infection and how to characterise and curate bacteriophage genomes. You will learn how to data mine these bacteriophage genomes for specific function and to use molecular methods to determine if these traits are unequivocally functional.
Eligibility and How to Apply:
Please note eligibility requirement:
• Academic excellence of the proposed student i.e. 2:1 (or equivalent GPA from non-UK universities [preference for 1st class honours]); or a Masters (preference for Merit or above); or APEL evidence of substantial practitioner achievement.
• Appropriate IELTS score, if required.
• Applicants cannot apply for this funding if currently engaged in Doctoral study at Northumbria or elsewhere.
For further details of how to apply, entry requirements and the application form, see https://www.northumbria.ac.uk/research/postgraduate-research-degrees/how-to-apply/
Please note: Applications should include a covering letter that includes a short summary (500 words max.) of a relevant piece of research that you have previously completed and the reasons you consider yourself suited to the project. Applications that do not include the advert reference (e.g. SF20/…) will not be considered.
Deadline for applications: 1st July for October start, or 1st December for March start
Start Date: October or March
Northumbria University takes pride in, and values, the quality and diversity of our staff. We welcome applications from all members of the community. The University holds an Athena SWAN Bronze award in recognition of our commitment to improving employment practices for the advancement of gender equality.
Informal enquiries to Dr Darren Smith ([email protected]
Tariq MA, Everest FLC, Cowley LA, Wright R, Holt GS, Ingram H, Duignan LAM, Nelson A, Lanyon CV, Perry A, Perry JD, Bourke S, Brockhurst MA, Bridge SH, De Soyza A, Smith DL. 2019. Temperate bacteriophages from chronic Pseudomonas aeruginosa lung infections show disease-specific changes in host range and modulate antimicrobial susceptibility. mSystems 4:e00191-18. https://doi.org/10.1128/mSystems.00191-18.
Holt, G. S, Lodge, J, McCarthy, A. J, Graham, A.K, Young, G, Bridge, S. H, Brown, A. K, Veses-Garcia, M, Lanyon, C.V, Sails, A, Allison, H. E. and Smith, D. L. (2017) Shigatoxin encoding Bacteriophage φ24 B modulates bacterial metabolism to raise antimicrobial tolerance Nature Scientific Reports 7, 40424; doi: 10.1038/srep40424 (2017).
Tariq, M. A., Everest, F. L. C., Cowley, L. A., De Soyza, A., Holt, G. S., Bridge, S. H., Perry, A., Perry, J. D., Bourke, S. J., Cummings, S. P., Lanyon, C. V., Barr, J, J, Smith, D. L. (2015). A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients. Frontiers in Microbiology, 6. doi:10.3389/fmicb.2015.00097