The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans.
Authors: Bull Katie, Davies Gareth, Jenkins Timothy P, Peachey Laura
Journal: Equine veterinary journal
Summary
# Editorial Summary: The Faecal Microbiome of Exmoor Ponies Shows Step-Wise Compositional Changes with Increasing Levels of Management by Humans Bull et al. (2024) investigated how human management practices shape the equine gut microbiome by comparing faecal samples from 29 adult female Exmoor ponies across three contrasting management regimes: low management (grazing-based, n=10), medium management (n=10), and high management (domesticated, n=9), using 16S rRNA gene sequencing and functional metagenomic analysis. The research revealed striking compositional shifts moving from low to high management, with the high-management group displaying elevated Proteobacteria and Tenericutes, the low-management group showing higher Methanobacteria, and the medium-management group exhibiting intermediate taxa abundance alongside considerable within-group microbial diversity variation. Functionally, ponies under high management demonstrated increased amino acid and lipid metabolism capacity, those under low management showed enhanced energy metabolism, whilst the medium-management group revealed enriched carbohydrate metabolism and immune/metabolic disease pathways—findings suggesting dietary differences were the primary driver of microbiome divergence. For equine practitioners, these results underscore that housing, feeding and handling interventions fundamentally restructure the gut microbiome architecture, potentially explaining why domesticated horses experience heightened gastrointestinal disease susceptibility, and highlighting the importance of gradual dietary transitions and management changes to maintain microbial stability and health. Future work controlling for individual management variables separately would help clarify whether specific interventions (diet, medication, exercise) warrant particular attention during transition periods.
Read the full abstract on PubMed
Practical Takeaways
- •Management-related dietary changes have significant and measurable effects on equine gut microbiota composition; consider gradual dietary transitions when increasing management intensity to minimize microbiome disruption
- •Medium management transition periods show the most microbiota variability, suggesting this phase may carry increased risk for GI disease—implement careful management protocols during step-wise changes in husbandry
- •Understanding your specific management approach's impact on gut health may help prevent GI disease episodes in domestic horses; dietary composition appears more influential than handling or exercise level alone
Key Findings
- •Step-wise changes in faecal microbiota composition observed across low, medium, and high management groups, with high management associated with increased Proteobacteria and Tenericutes abundance
- •Low management ponies showed higher abundance of Methanobacteria compared to high management groups
- •Medium management group exhibited high within-group variation in alpha diversity and intermediate microbial composition
- •Functional predictions suggest dietary differences between management groups were likely the primary driver of microbiome differences, with distinct metabolic pathways enriched in each group