PhD Studentship: Nutrition of the Respiratory Microbiome

The lower respiratory tract has a microbiome. It is sparser than the gut microbiome and much less well characterised, but similarly varies in health and disease, has stable composition and has direct interactions with the immune system. In this project we aim to discover how this microbiome functions and particularly how it obtains nutrition focusing on respiratory mucin as carbon source and the nutritional links between different members in this ecosystem. The project aims are to

• Characterise the mucin degrading and binding capabilities of the Respiratory Microbiome Group culture collection
• Build a model consortium that represents the healthy respiratory tract using high throughput screening of artificial communities
• Subject this model to challenges such as pathogen invasion, drug interactions and nutrient availability

This will allow us to build a picture of how the respiratory microbiome functions in health, identify how it responds to changes in its environment and how to predict these responses. It will also allow us to identify keystone species that are central to the function of this ecosystem and start to give us the tools to alter the respiratory microbiome to promote health and combat disease.

Techniques will include culture, growth and genome sequencing of novel respiratory tract isolates. Bioinformatic analysis of polysaccharide degradation and binding potential. TLC and HPLC for mucin degradation characterisation. High throughput community assembly using OnChip droplet flow cytometry and cell sorting.

The Crouch Lab works on understanding glycobiology at the human/host interface with a focus on functional understanding of the enzymes and organisms involved in relevant glycan and polysaccharide degradation. This collaboration with the Respiratory Microbiome Group who mostly use DNA sequencing and culture methods to understand the respiratory microbiome in humans brings together a unique combination of expertise opening up new areas of research for both groups and the wider microbiome field.

The work is a collaboration, bringing together expertise in microbial ecology and in glycobiology at the interface of the host and microbiome. The PGR will benefit from working across both groups who are co-located in the same lab space. 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 Lucy Crouch. 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.

Advert information