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The wild mammalian microbiome: host-microbe interactions in a natural mouse model

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  • Full or part time
    Dr S C L Knowles
    Prof J Webster
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Supervisors: Dr Sarah Knowles and Professor Joanne Webster

Department: Pathology and Pathogen Biology

It is now recognised that all mammals carry a vast and diverse community of symbiotic microbes – the microbiome – which have pervasive effects on animal development, behaviour, health and disease. However, with much microbiome research focussing on laboratory animals, there is a pressing need to understand what shapes these communities and their consequences in natural animal populations. This project will study the ecology of the gut microbiome in a wild rodent model system (wood mice, Apodemus sylvaticus). It will take advantage of a well-established population of marked wild individuals at Wytham Woods in Oxfordshire, monitored in collaboration with Prof. Tim Coulson, University of Oxford. The student will be able to address key questions such as:
- How do host genetic and environmental effects combine to shape the wild mammalian gut microbiome?
- How important are social interactions among hosts for gut microbe transmission?
- Do seasonal shifts in the microbiome allow animals to adapt to a seasonally variable diet?
- To what extent do gut microbial communities interact with other common gut inhabitants, such as eukaryotic helminths and protozoa?
Several elements of the wood mouse system provide a rich framework in which to address such questions, including (1) regular trapping and PIT-tagging of all mice, so individuals can be followed throughout their lives to monitor microbiota dynamics and host survival (2) availability of mobile data loggers that allow estimation of the host social network and individual space use, and (3) optimised methods for reconstructing the host population pedigree. Alongside observational data collection from a wild population, complimentary experiments in both field and controlled captive settings (a wood mouse colony) can probe the impact of environmental factors like diet and eukaryotic gut parasitism on the microbiome.

The student will be based at the Royal Veterinary College (Hawkshead Campus), and will gain experience in techniques such as field data collection and experiments, Illumina 16S rRNA-based sequencing, bioinformatics and social network analysis.
The studentship will commence in the 2016/17 academic year.

Ihttp://www.rvc.ac.uk/study/postgraduate/phdnterviews for studentships - will be held on 16th March or in the w/c 21st March 2016 at the RVC’s Camden or Hawkshead Campuses

Funding Notes

This is a three year fully funded studentship. It is open to Home/EU applicants only. International students are welcome to apply but must be able to pay the difference between UK/EU and international tuition fees.


Amato KR (2013). Co-evolution in context: The importance of studying gut microbiomes in wild animals. Microbiome Science and Medicine, 10-29.
Maurice CF, Knowles SCL, Ladau J, Pollard KS, Fenton A, Pedersen AB & Turnbaugh PJ (2015). Marked seasonal variation in the wild mouse gut microbiota. ISME Journal 9: 2423-2424
Tung J, Barreiro LB, Burns MB, Grenier J-C, Lynch J, Grieneisen LE, Altmann J, Alberts SC, Blekhman R & Archie EA (2015). Social networks predict gut microbiome composition in wild baboons. eLife;10.7554/eLife.05224

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