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Dr Craig Watkins

Dr Craig Watkins

Moredun Research Institute
Pentlands Science Park
Bush Loan
Midlothian EH26 0PZ


Craig’s interests are in applying molecular approaches to the understanding of host immune responses to disease, and bacterial genomics with respect to Mycobacterium avium paratuberculosis (MAP) – the infectious agent responsible for Johne’s disease in ruminants. Recently his research has extended to studying the microbiota of the ruminant intestine infected with MAP and/or co-infected with parasites. He is a member of the International Association for Paratuberculosis, the Microbiology Society, UK, the British Society for Immunology, and the American Society for Microbiology.

Craig has supervised a number of post-graduate students and is also closely involved in preparing and presenting science to the farming community as well as the wider public through the STEM (Science, Technology, Engineering and Mathematics) network and the Communications Team at the Moredun Research Institute.

Current Research

Current research interests include:

  • Functional studies of MAP genes for vaccine development.
  • Immune responses of MAP infected sheep, including RNA-seq. In collaboration with Roslin Institute, Edinburgh.
  • MiSeq sequencing of 16S rDNA to assess intestinal microbiomes in sheep with different health conditions and assessing their associated environmental microbiota (soil and water). In collaboration with the School of Biological Sciences, Edinburgh University and James Hutton Institute, Aberdeen.
  • MAP transmission and contamination in milk.


Recent projects (supervisory):


  • MSc student project - Detecting and analysing MAP in milk. In collaboration with School of Biological Sciences, University of Edinburgh.


  • 4th year Veterinary Biosciences BSc Research Project from the College of Medical Veterinary and Life Sciences, University of Glasgow:  Characterizing M.a.paratuberculosis virulence in an in-vitro macrophage cultured system.


  • MSc School of Biological Sciences University of Edinburgh.  Assessment of Environmental Contamination in farms diagnosed with Johne’s disease.


  • MScRes: Infectious Diseases Programme, University of Edinburgh.  Effects of intestinal infection on the microbiome of sheep: a focused study on Johne’s disease and round worms.
  • ERASMUS student & MRI Innovation Fund, Understanding of the interaction between Mycobacterium avium paratuberculosis (MAP) infection and other faecal microbiota

Selected Key Publications