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  (MRC DTP CASE) Determination of the role of viruses in the microbiome of biofilms formed in the ear of patients with otitis media

   Faculty of Biology, Medicine and Health

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  Prof P Vallely, Prof P Klapper, Prof Simon Lovell, Mrs Jaya Nichani  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

Otitis media (OM) is a very common infection of the middle ear characterised by redness, swelling and build-up of fluid behind the eardrum. It can occur at any age but is most often found in infants aged 6 – 24 months. Episodes can be recurrent and become chronic, leading to long term conductive hearing loss affecting the child’s speech and development.

The bacterial organisms associated with OM are well characterised, with three major pathogens consistently implicated: Streptococcus pneumoniae, Haemophilus pneumoniae and Moraxella catarrhalis. These organisms may colonise the middle ear in the form of a biofilm which is a complex, surface-attached community of bacterial cells which form into an organised structure allowing the organisms to survive longer by evading the immune system and resisting treatments such as antibiotics. OM is typically initiated by a viral infection, and viruses are found in the middle ear in cases of OM. In recent studies viruses have also been shown to be able to form biofilms, either alone or together with bacteria. But this phenomenon has not been investigated for biofilms in OM. In this project we propose to test clinical samples taken from the middle ear of children with OM and use metagenomics and next generation sequencing to identify the bacterial and viral species that are present in the samples. We will then use this information to work with our industrial collaborators who are experts in biofilms to develop an in vitro model to test the dynamics of viral/bacterial interaction in the biofilm and evaluate possible ways to disrupt the biofilm and offer novel ways to treat OM.


Applicants must have obtained or be about to obtain a First or Upper Second class UK honours degree, or the equivalent qualifications gained outside the UK, in a relevant discipline.

Before you Apply

Applicants must make direct contact with preferred supervisors before applying. It is your responsibility to make arrangements to meet with potential supervisors, prior to submitting a formal online application.

How to Apply

To be considered for this project you MUST submit a formal online application form - full details on how to apply can be found on the MRC DTP website

Your application form must be accompanied by a number of supporting documents by the advertised deadlines. Without all the required documents submitted at the time of application, your application will not be processed and we cannot accept responsibility for late or missed deadlines. Incomplete applications will not be considered. If you have any queries regarding making an application please contact our admissions team.

Equality, Diversity and Inclusion

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website

Biological Sciences (4) Medicine (26)

Funding Notes

This is a 4 year CASE studentship in partnership with 5D Health Protection Group. This scheme is open to UK applicants only. Therefore, full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.


European Congenital Cytomegalovirus Initiative (PK mid-author, PV penultimate author): Consensus recommendation for prenatal, neonatal and postnatal management of congenital cytomegalovirus infection from the European Congenital Infection initiative (ECCI). The Lancet Regional Health – Europe - InPress
Faqih L, Vallely P, Klapper P. Genetic stability of SIV Gag/Tat gene inserted into Del-II in modified vaccinia virus ankara after serial passage of recombinant vector in pCEFs cells. J.Virol.Methods (2023)
Sallah S, Sergouniotis PI, Hardcastle C, Ramsden S, Lotery AJ, Lench N, Lovell SC, Black GCM, Assessing the pathogenicity of In-Frame CACNA 1F Indel variants using structural modelling. Journal of Molecular Diagnostics 24(12) (2022)
López-Labrador FX, Brown JR, Fischer N, Harvala H,…Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC; ESCV Network on Next-Generation Sequencing. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. Journal of Clinical Virology. (2021)
Heward E, Saeed H, Bate S, Rajai A, Molloy J, Isba R, Ashcroft DM, Hay AD, Nichani JR, Bruce IA. Risk factors associated with the development of chronic suppurative otitis media in children: Systematic review and meta-analysis. Clin Otolaryngol. 2024 Jan;49(1):62-73. doi: 10.1111/coa.14102. Epub 2023 Oct 4. PMID: 37794685.