PhD Studentship: Defining Interactions Between Vaccine Targetable Airway Pathobionts

The upper and lower respiratory tract harbours a microbiome that includes potential pathogens that can become disease causing when the immune homeostasis is challenged. Diverse species of Haemophilus, Neisseria are always present in the respiratory tract and often at the same time. Most understanding of these important potential pathogens comes from studying them in disease and in isolation, but most of the time these organisms are apparently harmless and also never present alone.

In this project we aim to

• Develop innovative methods to examine pathobiont interactions in physiologically relevant models including mixed-species biofilms, OnChip micro-communities and in co-culture with host epithelial cells.
• Investigate pathobiont-pathobiont, and host-pathobiont interactions using transcriptomic and mass spec approaches.
• Refine interaction models between key pathobionts in the context of known species heterogeneity using the extensive isolate collections of the Cox and Cleary groups.

Overall we aim to resolve the function and interaction of these understudied ubiquitous pathobionts. Dr Cox and Dr Cleary have complementary expertise in the lower and upper respiratory tract microbiomes respectively. They take different approaches to answer similar questions, with Cleary more focused on bacterial genomics and Cox on microbial communities. Both use culture and sequencing approaches and working together in this first collaboration broadens the approaches that can be applied in this studentship.

Techniques will include bacterial genome sequencing and bioinformatic analysis. Co-culture model development. OnChip flow-cytometry and cell sorting. Transcriptomics and metabolomics. Both PIs have strong clinical links and collaborations with more established groups to support the training and experience for their PGRs including joint lab meetings and journal clubs. We are based in the Department of Microbes, Infection and Microbiomes and part of the Institute of Microbiology and Infection at the University of Birmingham, UK, one of the largest collections of Microbiology researchers in the world.

The project will be supervised by Dr Michael Cox (m.j.cox@bham.ac.uk) and Dr David Cleary. For more information, please see: https://warwick.ac.uk/fac/cross_fac/mibtp/

Funding notes:

The project is offered through the Midlands Integrative Biosciences Training Partnership (MIBTP) which is funded by a BBSRC Doctoral Landscape Award. Applications should be made through the MIBTP website, though interested candidates are strongly advised to get in touch with the supervisors first.

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