Understanding the Relationship between Immune Receptor Repertoires, the Microbiome and Infection

Lead Research Organisation: University of Oxford
Department Name: Interdisciplinary Bioscience DTP


Around 60 billion chickens are reared worldwide each year representing an efficient and vital protein source for a growing human population1. The chicken gut microbes, known as the intestinal microbiota, play key roles in metabolism and resistance to infection and birds lacking a microbiota shown increased susceptibility to colonisation by pathogens2,3. It has been shown that despite its complexity, the microbiota remains relatively unchanged over time4,5. Simulations and unpublished research suggests this phenomena may be facilitated by the population structure of the intestinal microbiota6. This project seeks to further explore this structure and examine how the microbiota changes with age, its universality across different animal species and how it recovers following perturbation by enteric pathogens. These findings will contribute to novel research aimed at understanding the microbiota structure of agriculturally important animals and developing interventions aimed at stabilising it, such as probiotic therapy.

Priority Area: AFS, ENWW


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011224/1 30/09/2015 29/09/2023
1757836 Studentship BB/M011224/1 30/09/2016 30/03/2021 Robert James Dixon
Description Mouse
Confirmed previous findings that Butyrophilin-like molecules in play a role in Vy7 localisation to the gut
Showed that knock out of Butyrophilin-like molecules or gamma delta T cells as a whole has impacts on the gut microbiota
Showed that removal of the microbiota has a minimal effect on the gamma delta T cell repertoire

Showed that Campylobacter co-infection influences the microbiota differently depending on the strains present
Showed that knock out of gamma delta T cells has subtle impacts on the microbiota
Mapped the gamma delta locus and showed the distribution of V segments in different tissues
Exploitation Route Could look more closely at clones identified in sequencing or confirm findings with sorted gamma delta T cells
Sectors Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology

Title IgA Sequencing 
Description Using MACS or FACS to pull down IgA labelled bacteria, then 16S and NGS to sequence them. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact Allows identification of IgA bound bacteria enabling groups to ascertain their importance in certain diseases, eg colitis. 
Description The influence of gamma delta T cells on the microbiota in chickens 
Organisation Technical University of Munich
Country Germany 
Sector Academic/University 
PI Contribution 16S analysis of faecal samples collected by novel TCRd KO chicken strain
Collaborator Contribution Construction of mutant, raising of birds, sample collection
Impact Gamma delta T cells appear to have subtle impacts on microbiota
Start Year 2018