The Bloomsbury Colleges | PhD Studentships | Studentships 2019 | “Omics” based characterisation of host genetics and gut microbiome composition in relation to pathogen abundance in chickens
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“Omics” based characterisation of host genetics and gut microbiome composition in relation to pathogen abundance in chickens

Principal supervisor: Dr Androniki Psifidi

Co-supervisors: Professor Fiona Tomley, Professor Damer Blake

Award includes tuition fees and a stipend of £16,777 including London Weighting (at 2018/19 rates, so slightly higher for 2019 entry)

100% FTE for 3 years, from September 2019.

Project Description:

Pathogenic microbes limit economic production of poultry, compromise animal welfare and pose a risk to human health. Vaccines are available for some pathogens but are expensive, with limited availability in many countries. A complementary strategy to control disease is to enhance inherent resistance traits of chickens by selective breeding strategies1,3,4.

Enteric-microbiome composition varies widely between individuals and is associated with differences in health and productivity. Recently we discovered that gut-microbiome composition is a heritable complex-trait in chickens2,3, and we identified SNP-markers associated with this trait2,3. These preliminary results support the potential of selective breeding to promote protective gut microbiota and reduce dependence on antibiotic-mediated pathogen control.

Globally, the highest growth in demand for poultry products is in South Asia, particularly India. As poultry production systems evolve there is an opportunity to explore the microbiological and genetic basis of traits which can be used to define “good health”. This project is aimed at investigating microbiome composition, pathogen- commensal microbiome interactions, and the host genetic variability underlying microbiome composition in chickens.  In this project we will analyse data from Indian-raised indigenous and commercial chickens and validate our findings by generating additional samples and data from UK-raised ones. 

Our hypotheses are 1) pathogen colonisation is influenced by host-genetic susceptibility and interactions with the commensal-microbiome; 2) QTLs affecting resistance to enteric-pathogens and gut-microbiome composition are segregating in indigenous and commercial chicken populations.

With access to gut microbiome data and DNA from indigenous and commercial chickens, the student will perform genome-wide association studies, next generation sequencing and metagenomics profiling, and assess the results in conjunction with extensive pre-existing and collated metadata. The student will be trained in cutting-edge genetic and bioinformatic technologies, and relevant wet lab techniques to explore DNA array, WGS sequencing, 16S- and Shotgun-sequencing data to identify genetic markers, causative genes and gene networks underlying gut microbiome composition and host resistance to pathogen colonisation.

This project offers an exciting opportunity to increase fundamental knowledge about genetic control of resistance to pathogen colonisation and the influence of gut microbiome composition on host pathogen resistance, and will increase our understanding of gut-microbiome function and genetic control in birds. Outputs offer immediate relevance to food-security and safety in Low and Middle-Income Countries, as well as a direct comparison with birds raised in the UK.

Subject Areas/Keywords:

chickens, gut health, infection, zoonosis, one-health, microbiome, genetics, genomics, metagenomics

Key References:

1. JM. Bettridge, A. Psifidi, et al.2018. Nature Sustainability/

2. R. Pandit, AT. Hinsu, et al.2018 Microbiome

3. A. Psifidi, M. Crotta, et al.2018. Proceedings of the 11th WCGALP conference/Auckland/New Zealand

4. A. Psifidi, M. Fife, et al.2016. BMC Genomics DOI: 10.1186/s12864-016-2612-7

Principal Supervisor: Dr Androniki Psifidi (

Co-Supervisor: Professor Fiona Tomley (

Professor Damer Blake (

Further information about PhDs at RVC is available from:

Application forms and details about how to apply are available from:

If you encounter any problems please email

Closing date for applications is:      
10th February 2019