The horse is a hindgut fermenter which relies on microbial digestion to provide more than half of its energy requirements. Disturbances to the microbiota can lead to colic (abdominal pain), diarrhoea and other disorders in horses. Advances in techniques to characterise the equine gut microbiome have revealed that this is a complex population and many factors are thought to contribute towards the composition of species present. Epidemiological studies have identified various horse and management risk factors for colic including season (and associated management changes), foaling and tapeworm infections. The contribution of the intestinal microbiota to the development of colic in relation to these risk factors is unknown. The aim of this thesis is to investigate the association of these factors with the intestinal (or faeces as a proxy) microbiome and metabolome. Few studies to date have attempted to understand the equine gut mycobiome and functional equine microbiome (metabolome). The faecal metabolome may provide simple, cost effective markers for microbial shifts that may be associated with equine disease including increased likelihood of colic. A method to extract volatile organic compounds (VOCs) from equine faeces for gas chromatography mass spectrometry (GCMS) was developed and applied to longitudinal studies in healthy horses. The VOC profile and mycobiome (18S rRNA and internal transcribed spacer region 1 DNA sequences) of horses grazing at pasture over 12 months was characterised as well as the VOC profile of mares around the time of foaling. The optimised extraction method (with some modifications) and 16S rRNA gene sequencing was also applied to hindgut and rectal contents collected from horses identified as either positive or negative for Anoplocephala perfoliata (tapeworm) at post-mortem. Horses grazing at pasture over 12 months showed a marked difference in VOC profile over time. Notably, there was a marked increase in fungal compounds and a shift in fungal species was observed in the autumn, a high-risk time of year for both colic and tapeworm infection. The VOC profile of periparturient mares remained stable throughout the sampling period, providing baseline data to assist identification of mares at increased likelihood of developing colic. Variations in the intestinal VOC profile and bacterial microbiome between horses with and without A. perfoliata infection were observed, even without the ability to control for extrinsic factors such as diet and other management factors. Furthermore, a combination of 10 VOCs emitted from rectal contents generated a sensitivity of 80% and a specificity of 70% when the model was tested on a sub-set of samples. These pilot results warrant further study of parasites and their interactions with the equine intestinal microbiome using controlled study designs. Where multiple -omics were used, correlations of VOCs with both bacterial microbiome and mycobiome data were observed. These data indicate that VOCs have the potential to act as cost-effective markers for microbial shifts in horse intestinal contents and faeces.