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Bacteriophage role in the establishment of preterm infants’ gut microbiota (Ref: SF20/APP/SMITH3)

Faculty of Health and Life Sciences

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Dr Darren Smith Applications accepted all year round Self-Funded PhD Students Only

About the Project

Survival of very preterm infants has increased over the last 20 years, but late onset sepsis (LOS) and necrotising enterocolitis (NEC) remain a major cause of death and ongoing developmental problems in this population. Breast milk from mothers of preterm infants is nutritionally and biologically distinct from term breast milk. The bacterial communities within breast milk have been mapped previously but there has been less focus on breast milk associated viruses or bacteriophages and how this differs over time. Therefore, little is known about the ‘phageome’ in preterm breast milk and the role it plays in the establishment of the gut microbiota or protection from opportunistic bacteria and infection. It has been demonstrated that specific phages delivered to the gut bind to mucosal surfaces increasing their chance of successfully infecting surrounding or new bacteria entering the system. We have significant untargeted metagenome data of breast milk viruses, and this study will begin to mine these data using comparative genomic approaches to determine key phage similarities. These may offer genetic markers of function or selection that may aid their role in the establishment of a healthy gut in preterm and term infants. There will be opportunity to test these phenotypes identified from genomic and other -omic derived data in lab-based culture and model systems of the gut mucosa.

You will use the latest in omics technologies and learn bioinformatic skills supported by an experienced team in collaboration with the Greath Northern Childrens Hospital, Newcastle. 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

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 Address Removed])

Funding Notes

This project will be self funded – fee bands are available at . A relevant fee band will be discussed at interview based on project running costs


Young GR, van der Gast CJ, Smith DL, Berrington JE,. Embleton ND, Lanyon CV (2019). Acquisition and development of the extremely preterm infant microbiota across multiple anatomical sites. Journal of Pediatric Gastroenterology and Nutrition. November 9, 2019 - Volume Publish Ahead of Print - Issue - p
doi: 10.1097/MPG.0000000000002549

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.

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

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