Advanced Spatial and Species Level Imaging of the Human Microbiome

The skin is the human body’s largest organ, colonised by a diverse community of microorganisms, which play an integral role in the maturation and homeostatic regulation of skin cells and host immune networks, with systemic implications to health and disease. Although advances in DNA sequencing and computational approaches have provided important insights into the taxonomic composition and functional behaviour of such microbiomes, these approaches fail to provide information about the spatial organisation of the resident microorganisms. Indeed, there is almost no understanding of where different microrganisms are located in relation to one another, in relation to anatomical sites or allied bodily secretions and micro-environmental conditions. The aim of this project is to capitalise on recent advances in the use of combinatorial labelling and advanced confocal multispectral imaging to help facilitate a step-change in our understanding of the spatial and functional organisation of microbiota in skin/axillary environments. This is an area of growing scientific and industrial importance and insights from this project will be used to inform novel promicrobial and antimicrobial therapeutic approaches for the treatment of a range of human skin disorders and conditions.

This PhD is a multidisciplinary project between the University of Liverpool (UoL), the Forsyth Institute at Harvard Medical School, and Unilever. At the University of Liverpool, the student will be embedded within active research groups conducting advanced cell imaging (https://cci.liv.ac.uk/), microbiology and surface characterisation research (https://biofilms.ac.uk/) highly relevant to the student’s project. Within the groups, several lab members are working on related projects, and adjacent collaborating labs have additional expertise, giving the student access to a large set of other experimentalists to gain advice and intellectual input. The student will receive formal training in cell imaging by dedicated staff in the Centre for Cell Imaging (directed by Dr Bennett, Institute of Integrative Biology), surface characterisation techniques (with Prof Raval, Dept of Chemistry) and microbiology (with Dr Horsburgh, Institute of Integrative Biology). Secondment to the Borisy lab in Boston will provide a unique opportunity to learn CLASI-FISH labelling techniques in the lab which pioneered these techniques. The student will be expected to regularly interact with the supervisors to enable rapid progress and to ensure a broad training in the relevant inter-disciplinary approaches.

The student will also benefit from unique training opportunities at Unilever in the use and development of single and multi-species models, world leading expertise in oral and axillary microbiomics and unique experience in business relevant microbiome function and a unique opportunity to leverage genomic and bioinformatic capability and microbiological analytical and screening capabilities at offered by the MIFOMIC and MIF facilities located at the University of Liverpool. The approaches proposed are state-of-the art (including multi-species models, synthetic substrates, next generation imaging), and the academic and industrial infrastructure and support is exceptionally strong, which will ensure good career development opportunities for the student.

In addition to scientific training, the student will be exposed to the industrial process at Unilever giving them additional insight into Project Management, Corporate Strategy, Regulatory Approaches, Intellectually Property and Product Marketing. The student will cohort with the Liverpool-Newcastle-Durham BBSRC Doctoral Training Programme (DTP) students and will access the full range of established training opportunities including workshops and conferences afforded by the DTP.

The studentship is intended to start between Oct 2018-Sept 2019 and is for UK home students only. Candidates will need to hold, or expect to hold, a first class (or high II.1) degree in microbiology, molecular biology/biochemistry or equivalent, and have demonstrated strong abilities of self management, writing scientific reports, and working in a laboratory environment. For more details please contact Dr Daimark Bennett (UoL; [Email Address Removed]) or Dr Michael Hoptroff (Unilever; [Email Address Removed]).