Meta-analysis of equine gastro-intestinal microbiome research and evaluation of the impact of fructooligosaccharide supplementation on the gastro-intestinal microbiome of thoroughbred youngstock during nutritional stress

Abstract

Horses are trickle feeders and hindgut fermenters, and rely on the microbial fermentation of a fiber-rich diet for their energy. The gastro-intestinal (GI) microbiome is not only vital for digestion, it may also have an important role in the overall health of a horse through interaction with the immune system. Disturbances in the GI microbiome, for example through an inappropriate diet, can lead to gastro-intestinal and systemic diseases. To avoid this, prebiotic and probiotic supplementation has been proposed to stabilize the microbiome during times of dietary change. However, little evidence exists for the efficacy of this approach.To understand the role of the GI microbiome in horse health and disease, it is important to determine the composition of the ‘normal’ equine microbiome and what factors can influence it. However, there is large variation between studies investigating the equine GI microbiome, which could be due to technical variation in the scientific methods used and/or small sample sizes that could bias the findings.To address these issues, two studies were performed that examined the influence of different factors on the equine GI microbiome: The first study was a meta-analysis of equine GI microbiome data, in which we re-analyzed the raw 16S sequencing data from 29 studies and performed a batch mean correction to account for some of the technical variation. The second study was a case-control field study that examined the impact of Fructooligosaccharide supplementation in a group of Thoroughbred yearlings undergoing a dietary change.The meta-analysis showed that technical factors, such as the sequencing instrument and gene region of the 16S gene used, have a strong impact on the GI microbial composition, such that the influence of biological factors was not visible at a global scale when comparing different studies using multivariate analysis. However, after batch mean correction of some of the technical variation, there was strong variation between different sample types and regions of the GI tract, as well as differential bacterial abundances between age groups, genders, diets and different diseases.The prebiotic field study showed a stronger shift in microbial composition in control horses than in horses given prebiotics during a time of nutritional stress. This may indicate a stabilizing effect of prebiotic supplementation during dietary change. However, the study was limited by a difference in baseline microbial compositions between horses with prebiotic supplementation and those without, which shows the importance of taking a baseline sample during longitudinal studies.Overall, these studies highlight the need for a more standardized global approach in investigating the equine GI microbiota if studies are to be comparable. This could be achieved by creating a protocol for equine GI microbiome research and a database where the generated data can be shared and compared to advance research in this field