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EASTBIO Revealing new insights into the holobiont of host genomics and rumen microbiome in beef cattle

PHD Opportunities

About the Project

The PhD student will carry out research on the hot topic of symbiotic relationships between cattle and the essential nutrient providing microbial community living in their large stomach, the rumen. Our research has revealed that this holobiont has a substantial impact on feed conversion efficiency (Lima et al., 2019, Frontiers in Genetics), animal health (Auffret et al., 2017, Microbiome) and emissions of the greenhouse gas methane (Roehe et al., 2016, PLOS Genetics) in beef cattle. In particular, the host cattle genomic interactions with the rumen microbiome are strong, so that the abundances of the microbiota or its genes are of great interest for cattle breeding. Therefore, the world-wide leading beef breeding company Genus is interested to use microbiome information in its breeding programme. This studentship is aligned to an ongoing BBSRC LINK project entitled “Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria“ a collaborative research project involving SRUC, University of Edinburgh and Genus, which will provide data, samples and expertise for this studentship. Preliminary results of this project highlight that the cattle genomics is closely linked to the abundances of many microbial genes associated with methane emissions and feed conversion efficiency. In this PhD studentship another omics level will be added to genomic and metagenomic information, the metabolomics of the microbiota and the host based on rumen and blood samples respectively. The main aim of the PhD project is to improve our understanding of the symbiotic links within the holobiont based on host genomic, metagenomic and metabolomic information and to use these links for breeding of animals emitting less methane, require less feed per kg growth and have a healthy rumen microbial ecosystem so that animals are not susceptible to acidosis. This breeding strategy will contribute to the reduction of climate change because methane is a highly potent greenhouse gas (28 times of CO2) and 39% of the global greenhouse gas emissions from livestock are due to enteric methane emissions (mainly from cattle). This strategy will also improve the sustainability of beef production since 70% to 80% of the variable cost of beef production in the UK is associated with feed and will enhance animal health and welfare. In addition, the PhD student will have access to novel identified species of rumen microbes (Stewart et al., 2019, Nature Biotechnology) to analysis their effects on the above described environmentally and economically important traits. Besides EASTBIO doctoral training as well as postgraduate training at SRUC and Edinburgh University, the student will be trained in host genomics, ruminant science, rumen microbial community/genes, microbial and animal metabolism. The student will further benefit from training in microbiology, genetics, metabolomics, bioinformatics and animal nutrition at SRUC and the University of Edinburgh. The exposure to two academic partners, together with regular interactions with the biggest breeding company worldwide (Genus) as well as the farming and agri-food industries, will broaden the students’ horizons and place he/she in an excellent position for future employment in academia or industry.

Applicants should download the required forms from http://www.eastscotbiodtp.ac.uk/how-apply-0 and send the following documents to :
a. EASTBIO Application Form
b. EASTBIO DTP Equality Form
c. CV
d. Academic transcripts (a minimum of an upper second class or first class honours degree or equivalent is required for PhD study
e. Two references should be provided by the deadline using the EASTBIO reference form (http://www.eastscotbiodtp.ac.uk/how-apply-0). Please advise your referees to return the reference form to .
f. If you are nominated by the supervisor(s) of the EASTBIO PhD project you wish to apply for, they will provide a Supervisor Support Statement.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership View Website. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (Please state if your institution will provide funding to cover the difference in fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.


Two references should be provided by the deadline using the EASTBIO reference form (http://www.eastscotbiodtp.ac.uk/how-apply-0). Please advise your referees to return the reference form to pg.research@sruc.ac.uk.

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