The horse gut bacteriome and anaerobic mycobiome are influenced by seasonal forages and small intestinal starch digestibility

Aims The equine gut microbiome is a complex and dynamic ecosystem, housing a diverse consortium of bacteria and anaerobic fungi (AF) capable of breaking down complex plant matter and converting it into vital energy sources for their host. The aim of this study was to broaden our current understanding of bacterial and AF diversity in the equine hindgut and how it differs between cohorts and responds to dietary shifts. Methods and Results Faecal samples were collected from 48 horses and the bacteriome and anaerobic mycobiome analysed using long-read amplicon sequencing. Samples were collected from racehorses (RH) on high-concentrate diets and wild-foraging (WF) horses grazing on seasonally variable pastures. Distinct microbial profiles were observed, with bacterial diversity and composition strongly influenced by season. Reduced hindgut starch availability in RH promoted fibrolytic taxa such as Roseburia and reduced amylolytic Lactobacillus. AF communities, though relatively stable across dietary and seasonal changes, differed between the horse cohorts. Piromyces and Khoyollomyces were found to be more strongly associated with WF horses and Caecomyces with RH. Conclusion These findings emphasize the dynamic interplay between diet and microbial composition. Future multi-omics research will enhance our understanding of microbial functionality and inform strategies to optimise equine gut health.