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Understanding the contribution of host genetics, intestinal structure and microbiome diversity to gut health in broiler chickens

Pathobiology and Population Sciences

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Prof D Blake , Dr A Psifidi No more applications being accepted Funded PhD Project (UK Students Only)

About the Project


The threat of antimicrobial resistance has led to increasing societal and media pressure on livestock producers to minimise the use of antibiotics in production. Poultry breeders are responding to this challenge, however, production in the absence of antibiotics results in considerable variation in gut health with immediate relevance to farm productivity and animal welfare. More than 1 billion broiler chickens (chickens reared for meat) are produced in the UK every year, indicating that even small advances can provide dramatic improvements.

Phenotypic variation has been described in humans and animals for disease resistance, enteric microbiome composition and immunocompetence, all of which contribute to intestinal health. Here, we propose to combine microbiome and transcriptome ‘omics technologies with measures of pathology and productivity to assess variation in pure pedigree and hybrid chicken lines that represent extremes of ‘good’ and ‘bad’ intestinal health. This studentship will take a holistic approach to investigating intestinal health, using morphometry and histology to develop a gold standard for a healthy gut in high performing individuals and identifying biomarkers within morphological, microbiological and host transcriptomic datasets that can have broader utility in a range of commercial as well as low and middle income country (LMIC) settings. Output from the work will be used to inform breeding and husbandry practices, increasing productivity and welfare, and decreasing requirements for antibiotic intervention.


Variation in intestinal morphology, microbiology and transcription associates with intestinal health in commercial broiler breeder chickens and can be used to identify early-life biomarkers useful for breeding programmes and reducing reliance on antimicrobial drugs.


1. Use morphometry, histology, biochemistry and selective bacterial culture to define intestinal morphology and integrity in chickens with ‘good’ and ‘bad’ gut health.
2. Employ next-generation transcriptome sequencing to assess and compare gene transcription and micro/lncRNA profiles in chickens with ‘good’ and ‘bad’ gut health.
3. Define and compare enteric microbiome populations from distinct intestinal compartments using 16S rDNA deep amplicon sequencing from chickens with ‘good’ and ‘bad’ gut health.
4. Identify associations between data generated from Objectives 1-3, and performance and welfare indicators.
5. Assess and validate candidate biomarker performance in commercial chickens.

Agriculture and food security are recognised as areas of key economic and societal importance to the UK and the rest of the world. Here, we will work with leading broiler breeder Cobb Europe Ltd., offering experience within a commercial research team as part of the iCASE package. Together, we will utilise recent advances in ‘omics technologies and precise digital morphometry to explore and define gut health with a view towards increased productivity, reduced antimicrobial use, improved quality and safety, and better animal welfare. Aligning with the GCRF One Health Poultry Hub (, the international reach of the project will provide resources and strong opportunities for student network development in a dynamic industrial sector.

Fully funded place including home (UK) tuition fees and a tax-free stipend in the region of £17,285.

Funding Notes

Fully funded place including home (UK) tuition fees and a tax-free stipend in the region of £17,285.


Boulton et al. (2018) Dissecting the genomic architecture of resistance to Eimeria maxima parasitism in the chicken. Frontiers in Genetics. 9:528. PMID: 30534137.
Boulton et al. (2018) Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis. Genetics Selection Evolution. 50:63. PMID: 30463512.
Bush et al. (2018) Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. BMC Genomics 19, 594. PMID: 30086717.
Macdonald et al. (2017) Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology. PLoS One 12:e0184890. PMID: 28934262.
Pandit et al. (2018) Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing. Microbiome. 6:115. PMID: 29935540.
Reade et al. (2018) Potential role of fecal volatile organic compounds as biomarkers of chemically induced intestinal inflammation in mice. FASEB JOURNAL. 33:3. PMID: 30359099.
Shah et al. (2019) Interaction of gut microbes and host transcriptome modulates physiology and metabolism of full-sibs broilers with divergent feed conversion ratio. NPJ Biofilms and Microbiomes. 5:24. PMID: 31552140.

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