Characterising the equine faecal microbiota in health and disease

Maintenance of the gastrointestinal microbiota is understood to play a critical part in health and disease in horses and foals. Changes to the gastrointestinal microbiota have been associated with a several factors including diet, geography, transport, medication administration, general anaesthesia and diseases of the gastrointestinal tract including causes of colic, colitis and diarrhoea. Anthelmintics are commonly used in the husbandry of horses, and administration of certain anthelmintics can cause changes to the gastrointestinal microbiota. Further characterisation of these changes could assist in an improved overall understanding of the host-parasite-microbiota relationship and influence recommendations for anthelmintic use in the future. Diarrhoea is an important cause of clinical disease in foals and is a common presenting problem in veterinary practice. The treatment of diarrhoea in foals currently is non-specific supportive care, with no current recommendations for targeted treatment of the gastrointestinal microbiota and dysbiosis. Faecal microbiota transplantation (FMT) has been used by equine veterinarians with anecdotal success as a treatment to aid restoration of the gastrointestinal microbiota in adult horses and foals with colitis and diarrhoeas. Recently, FMT administration in horses with diarrhoea has been reported, with a beneficial impact on clinical recovery. The efficacy of FMT is yet to be assessed in foals. Solutions for FMT are typically prepared immediately prior to administration and lack of access to donor horses may pose limitations on its use. Storage of equine FMT preparation and the impact of storage conditions on the microbiota has received limited attention.
The aims of the research undertaken in this thesis were to (i) investigate the effects of FMT administration to foals with diarrhoea and evidence of systemic inflammation (ii) investigate the effects of storage of FMT in conditions of 4°C and -20°C (iii) investigate the effects of anthelmintic administration to horses with cyathostomin infection.
The results of (i) showed that administration of FMT was associated with improvement of some clinical and clinicopathological variables in foals but did not result in increased resolution of diarrhoea or survival.
The results of (ii) showed that storage of FMT at 4°C for 72 hoursand -20°C for 28 days had minimal effect on the microbiota composition.
The results of (iii) showed that changes to the faecal microbiota were limited following anthelmintic administration. Removal of cyathostomins resulted in greater changes to the microbiota compared to maintenance of cyathostomin burden.
The thesis provides important contributions to the understanding of the outcomes associated with FMT in foals and the effects of storage on equine FMT solution. This thesis also contributes to understanding of the effects of anthelmintic treatment on the faecal microbiota of healthy horses. The research improved the current knowledge of the effects of use of anthelmintics with and without removal of cyathostomins and reported the first clinical trial of FMT administration as a targeted treatment for diarrhoea in foals. It is also the first equine study investigating the effects of short term storage on the microbiota of equine FMT.