Genomics of bacterial pathobionts and commensals of the human respiratory tract

   Institute of Microbiology and Infection

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  Dr David Cleary  Applications accepted all year round  Self-Funded PhD Students Only

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 carriage, and 4) identify putative interactions both within and between species/strains that may be exploited as potential therapeutic interventions. 


Person Specification (if applicable)

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. 


Biological Sciences (4) Medicine (26)

Funding Notes

Self-funding only


Cleary DW, Morris DE, Anderson RA, Jones J, Alattraqchi AG, et al, The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia. NPJ Biofilms and Microbiomes 2021 7 (1) 1-11
Cleary DW, Devine VT, Morris DE, Osman KL, Gladstone RA, Bentley SD, Faust SN and Clarke SC. Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae. Microbial Genomics 2018, 4
Cleary DW and Clarke SC. The Nasopharyngeal Microbiome. Emerging Topics in Life Sciences 2017 1(4): 297-312

Where will I study?

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