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EASTBIO Understanding the role of the gut microbiome in chickens under feed restriction and its interplay with the host transcriptional response to nutritional stress

Project Description

Royal (Dick) School of Veterinary Studies / The Roslin Institute

Improving productivity in the poultry industry is one of the key global challenges to be addressed with regard to feeding an increasing worldwide population. In this context, there is a growing awareness that the gut microbiome plays a role beyond feed efficiency to involvement with the stress response and welfare [1,2], but the relationship between the gut and the stress response is not yet well understood. Here, we propose to investigate the effect of feed-restriction in chickens, a commonly-used practice to control weight gain in founder broiler populations [3] and relevant to all birds in areas of the developing world where feed availability may be variable. In particular, we will investigate the interplay between gut microbiome (and its potential imbalance, or dysbiosis) and expression profiles in highly metabolic tissues (brain and liver) in shaping the host transcriptional response in the context of this environmental stress.

We hypothesise that the gut microbial communities will differ between feed-restricted birds and those maintained on an ad libitum diet, and that a feed-restricted diet will trigger a stress response in the host in terms of both HPA-related gene expression profiles in the brain and an activation of immune pathways. This study is based on samples we have already collected: gut (from three distinct sections: cecum, ileum, jejunum), brain and liver samples from 42 birds (24 broilers; 18 layers).
- Identify the gut samples and specific areas within the gut that have the greatest apparent variance in microbial populations between the two treatment groups (restricted and ad libitum feeding).
- Establish whether the microbial variability is more evident in broilers or layers.
- Investigate whether the host transcriptomic profiles in brain, gut and liver correlate with microbial changes in feed-restricted chickens.
- Identify which phenotypic data (expression data, gut microbial diversity) shows the most discriminatory power between feed-restricted and control animals.
- Build machine learning models to predict gut microbiota dysbiosis.

The PhD student will benefit from a wide range of expertise at The Roslin Institute and within the CTLGH (Center for Tropical Livestock Genetics and Health). The studentship will provide training in Bioinformatics, including metagenomics and transcriptomics data analysis, building pipeline; and depending on funding and interest could include some lab-based work (e.g. DNA/RNA extraction). The student will benefit from a collection of samples already collected (incl. 42 chickens, 2 breeds, 3 tissues) and sequencing data available for analysis at start.

All candidates should have or expect to have a minimum of an appropriate upper 2nd class degree. To qualify for full funding students must be UK or EU citizens who have been resident in the UK for 3 years prior to commencement.

Funding Notes

Completed application form along with your supporting documents should be sent to our PGR student team at

Please send the reference request form to two referees. Completed forms for University of Edinburgh, Royal (Dick) School of Veterinary Studies and the Roslin Institute project should be returned to by the closing date: 5th January 2020.

It is your responsibility to ensure that references are provided by the specified deadline.
Download application and reference forms via:
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[1] de Weerth, C. (2017). Do bacteria shape our development? Crosstalk between intestinal microbiota and HPA axis. Neuroscience and Biobehavioral Reviews, 83, 458–471.
[2] Foster, J. A., Rinaman, L., & Cryan, J. F. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiol Stress, 19(7), 124–136.
[3] Decuypere E, Bruggeman V, Everaert N, Li Y, Boonen R, de Tavernier J, Janssens S and Buys N (2010). The Broiler Breeder Paradox: ethical, genetic and physiological perspectives, and suggestions for solutions. British Poultry Science 51(5), 569-579.

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