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The gut microbiome - the diverse community of bacteria, fungi, viruses and other microorganisms that inhabit the gastrointestinal tract - has become a major focus of research in both human and veterinary medicine.
Far from being passive inhabitants, these microorganisms play a crucial role in host health, influencing digestion, metabolism, immune function and even neurological processes. Growing evidence suggests that the composition and diversity of the gut microbiome can affect susceptibility to a wide range of conditions, including obesity, cardiovascular disease, autoimmune disorders and inflammatory diseases.
In human medicine, among the many factors that influence the microbiome, regular physical activity has emerged as one of the most important. Exercise is widely recognised for its benefits to digestive and systemic health, and research indicates that many of these effects may be mediated through changes in the gut microbiota. Regular moderate-to-vigorous exercise has been shown to increase microbial diversity, a characteristic strongly associated with better physical and mental health.
In contrast, reduced microbial diversity has been observed in individuals with obesity, cardiometabolic disease and certain autoimmune conditions.
While these effects are increasingly well documented in humans, less is known about the relationship between exercise and the gut microbiome in horses. A recent study, published in Microbial pathogenesis, investigated this question by examining the effects of exercise on equine gut bacterial and fungal communities using 16S rDNA and ITS gene amplicon sequencing.
The results demonstrated that exercise significantly increased bacterial diversity, as reflected by higher ACE, Chao1 and Shannon diversity indices - commonly used measures of microbial diversity in ecological and microbiome studies. The increases in ACE and Chao1 suggest that exercise was associated with a greater number of bacterial taxa in the gut, while an increase in the Shannon index indicated that the bacterial community became both richer and more evenly distributed. Together, these findings suggest that exercise promoted a more diverse gut bacterial ecosystem.
Exercise also altered the overall composition of the bacterial community. Specifically, the relative abundance of eight bacterial phyla and 187 bacterial genera increased, while three phyla and 197 genera decreased significantly.
In contrast, exercise had little effect on the overall diversity and abundance of the fungal community, although significant changes were observed in the abundance of specific fungal taxa. Exercise increased the relative abundance of five fungal phyla and 105 genera, while reducing two phyla and 82 genera.
These findings indicate that exercise can substantially modify the composition and structure of the equine gut microbiota, particularly the bacterial component. The study supports the growing concept that exercise may promote health by shaping the gut microbial ecosystem.
Future research examining different exercise types and intensities may further clarify how physical activity can be used to optimise microbiome health and improve management strategies in both humans and horses.
For more details, see:
Ma, Rufei., & Wang, Chong.
Microbiome analysis reveals the positive effects of exercise on the gut microbiota in horse.
Microbial pathogenesis (2026) , 216, 108501.
https://doi.org/10.1016/j.micpath.2026.108501
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