The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans.

The research study investigates the effects of varying degrees of human intervention on the gut microbiota of Exmoor ponies. Increasing levels of management, including diet and medication changes, showed marked step-wise changes in the structure of the faecal microbiome of these ponies.

Objective and Methodology

• The main goal of this research was to dissect the impact of different management conditions on the faecal microbiota of adult, female Exmoor ponies. The levels of management being studied were classified into low (LM), medium (MM), and high (HM), with each level representing different degrees of human intervention concerning diet, drug usage, handling, and exercise.
• This was cross-sectional descriptive research. The faecal samples collected from the three distinct groups of ponies were studied using high-throughput sequencing of the bacterial 16S rRNA gene to profile their faecal microbial composition, followed by functional metagenome predictions.

Results

• The study detected significant step-by-step alterations in microbiome architecture from LM transitioning to MM and then to HM. The faecal microbiota of the HM group was marked by an increased occurrence of Proteobacteria and Tenericutes. In contrast, the LM group showed a higher abundance of Methanobacteria. The MM group showed intermediate levels of these bacterial taxa and exhibited a higher within-group variation in alpha diversity.
• The functional metagenome predictions indicated enhanced amino acid and lipid metabolism in the HM group. On the other hand, the LM group showed elevated energy metabolism, while carbohydrate metabolism and immune/metabolic disease pathways were more pronounced in the MM group.

Conclusions

• Some limitations of the study included small group sizes and incomplete knowledge of bacterial genomes in the equine gut microbiota, as well as the inability to assess the comparative impact of diet, drug use, handling, and exercise on the microbiome due to confounding variables.
• Nevertheless, the study concludes that human-led management factors significantly influence the structure of the horses’ faecal microbiome. The researchers hypothesize based on the functional metagenome predictions that the dietary differences between the management groups were the primary influence leading to the observed microbiome differences.