Bacterial pathobiont and commensal colonisation in the human respiratory tract

About the Project

Bacterial colonisation of the human upper respiratory tract (URT) is a pre-requisite for multiple diseases including pneumonia, otitis media, sinusitis, exacerbations of chronic obstructive pulmonary disease (COPD), and, less commonly, diseases resulting from bacteraemia such as meningitis. These diseases are responsible for millions of deaths worldwide with a significant burden from pneumonia and lower respiratory tract infections falling on children <5 years of age.

Common pathobionts responsible for these infections include Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus. In the same airway niche, there are also commensal species (belonging to the genera Corynebacterium and Dolosigranulum) that are thought to play a role in shaping microbial communities in such a way that prevents or reduces pathobiont colonisation and/or invasion. In contrast to the pathobionts, little is known about these commensals, particularly with respect to strain diversity in different human populations.

In our lab we undertake genomic characterisation of both pathobionts and commensals in order to 1) determine strain diversity and epidemiology in different populations and disease backgrounds, 2) elucidate microbial community compositions, 3) examine longitudinal genomic stability during prolonged colonisation, and 4) identify putative interactions both within and between species/strains that may be exploited as potential therapeutic interventions.

The Cleary lab is looking for enthusiastic PhD students interested in airway microbiology/microbiomes and, specifically, the use of genomics to investigate the carriage/disease epidemiology of human pathobionts and commensals. Applicants should have a strong background in microbiology, and ideally some experience in microbial genomics, bioinformatics or computational biology. They should have a commitment to respiratory infectious disease research and hold or realistically expect to obtain at least an Upper Second Class Honours Degree or equivalent in a relevant subject.

Applications should be directed to Dr David Cleary (email d.w.cleary@bham.ac.uk). To apply, please send:

• A detailed CV, including your nationality and country of birth;
• Names and addresses of two referees;
• A covering letter highlighting your research experience/capabilities;
• Copies of your degree certificates with transcripts;
• Evidence of your proficiency in the English language, if applicable.