*EASTBIO* Effect of Nematode and Mycobacterium avium subspecies paratuberculosis Infections on the Ovine Intestinal Microbiome

Disease in the agricultural industry is a problem for farmers as it negatively impacts their income as well as reducing the welfare of their livestock. Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease in sheep and found in other economically relevant ruminants such as cattle and goats. The disease is characterised by emaciation as a result of thickening of the intestinal wall, reducing nutrient absorption and causing the animal to starve despite appearing to eat normally. MAP is also known to co-occur with parasitic nematode worms such as Teladorsagia circumcincta and Oesophagostomum columbianum which can have a synergistic or mechanical vectoring effect on the disease (Whittington et al., 2001). Farmers face many challenges when trying to control MAP or prevent it from entering their flocks. MAP is transmitted via the faecal-oral route and shed from infected animals in faeces to the surrounding environment where it can survive for over a year (Whittington et al., 2005). Transmission may also occur via wildlife reservoirs including wild deer, foxes and rabbits.

Sheep will often become infected with MAP in their first few months of life either from faecally-contaminated soils, water, surfaces or shedding from their mother’s milk. This infection can go undetected as many cases are sub-clinical; problems with diagnostic testing can also lead to Johne’s disease being under-diagnosed. MAP is also controversially associated with Crohn’s disease in humans and so represents a potential public health threat (Sechi and Dow, 2015).
Johne’s disease presents a problem for sheep farmers as it can result in the loss of 5-10% of the flock. Due to problems with diagnosing Johne’s disease in sheep it is difficult to estimate the economic burden of the disease. However, the estimated annual cost of Johne’s disease in the UK’s cattle industry is £13 million, around £45 for every infected animal. As the animals affected by Johne’s disease are typically destined for slaughter to become food it is not possible simply to treat the infection with antibiotics. Vaccination presents a possible alternative, however farm-raised sheep are often co-infected with parasitic worms. The effect of gastro-intestinal nematodes (GINs) on the immune response has been reported to interfere with childhood vaccination efficacy in humans and recent work in mice has also implied that the intestinal microbiota plays an important role in vaccine efficacy. This project will investigate the effect of GINs and their treatment with anthelmintic drugs on the intestinal microbiota of sheep and the effectiveness of vaccination against Johne’s disease in a commercially-managed flock.

Preliminary studies carried out by the supervisor, Dr. Free and co-supervisor Dr. Watkins have shown that treating sheep with anthelmintics leads to changes in the intestinal microbiota, specifically that an unresolved nematode infection leads to reduced levels of the potentially-beneficial Actinobacteria. In other work leading up to this project, faecal samples have been collected from a flock of farm-raised sheep in Angus with co-occurring nematode and MAP infections over a three-year period, providing a longitudinal profile of the changes in the microbiota within individual sheep and the flock as a whole. These baseline data will form the reference against which the effects of worm treatment and vaccination against Johne’s disease will be assessed. By studying the fluctuations in the intestinal microbiota, the effect of anthelmintic treatment on the efficacy of vaccination against MAP in farm-raised sheep will be investigated.

The project will aim to:
• Characterise the prokaryotic component of the gut microbiota in a farm-raised sheep flock using Illumina metataxonomic DNA sequencing.
• Investigate the persistence of MAP in soils at different locations on the study farm using qPCR and culture techniques, and link this to soil conditions, other soil microbiota and disease in the sheep which graze these areas.
• Investigate the relationship between MAP infection, parasitic worm infection and intestinal microbiota in a farm-raised sheep flock.
• Assess vaccine efficacy against Johne’s disease using diagnostic testing and microbiota profiling.
• Evaluate the impact of anthelmintic treatments on vaccine efficacy.

This information will be used as a basis for improving diagnostic and treatment strategies for MAP and nematode infection to improve animal health and welfare.