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Dr Craig Watkins

Dr Craig Watkins

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


Craig Watkins joined the Moredun Research Institute in 2003 after 5 years of working in the Royal (Dick) School of Veterinary Studies (R(D)SVS, at Edinburgh University. He is a member of the International Association for Paratuberculosis, the Microbiology Society, UK, and the British Society for Immunology.

Over the past 17 years, Craig’s interests have been 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 and anaerobic digestion as a tool for disease control.

He has supervised a number of post-graduate students and is also closely involved in preparing and presenting science to the 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.
  • 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, the University of Edinburgh and James Hutton Institute, Aberdeen).
  • MAP transmission and contamination in milk.
  • Effect of nematode and Mycobacterium avium subspecies paratuberculosis infections on the sheep intestinal microbiome.
  • On farm MAP control measures to reduced infection and improve welfare and productivity in the farming industry.


Recent and Current Projects supervised:

2019 - 2022:

Veterinary Medicines Directorate PhD studentship. Molecular tools for identification of livestock helminths and detection of anthelmintic resistance in collaboration with the R(D)SVS.


University of Edinburgh MSc studentship. Optimizing killing and detection of Mycobacterium avium subspecies paratuberculosis (MAP) in milk in collaboration with School of Biological Sciences, University of Edinburgh.


Honours 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