Exercise, the gut microbiome and health

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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

 

Free articles on equine infectious disease and Microbiology in EVJ Special Collection

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The March 2026 issue of Equine Veterinary Journal (EVJ) highlights major advances in equine infectious disease and microbiology, with a Special Collection dedicated to the equine microbiome. The issue, which is free to access for 12 weeks, features 30 research papers spanning a wide range of diseases, body systems, and pathogens. Many of the studies involve international collaboration, reflecting the global importance of managing infectious diseases in horses.

Equine infectious disease remains a key research focus for veterinarians and scientists because of its impact on horse health, welfare, and the equine industry. The special issue identifies three major themes: the importance of national disease surveillance programmes, the need for accurate and definitive diagnoses, and the value of comparing diseases across different animal species to better understand how pathogens behave.

Several studies focus on improvements in diagnostic techniques, particularly for equine fever, equine influenza, and gastrointestinal parasites. These advances aim to support faster detection of disease and enable earlier implementation of biosecurity measures, which can help reduce transmission between horses.

Research into gastrointestinal diseases also features prominently. Studies explore the use of metabolic profiling to detect equine proliferative disease earlier in foals, investigate possible causes of colitis, and emphasise the importance of additional diagnostic testing for chronic hepatitis and liver failure in cases linked to hepacivirus infection. Together, these findings may support earlier intervention and improved disease management.

Antimicrobial resistance is another significant area of concern. One survey found that nearly 40% of hospitalised horses received at least one antimicrobial treatment. Research linked to colic surgery suggests that using antimicrobials for more than 24 hours after surgery is unnecessary for preventing complications, highlighting opportunities to reduce antibiotic use and slow the development of antimicrobial resistance.

Several papers examine diseases affecting multiple body systems. For example, updated guidance on equine botulism emphasises its importance as a differential diagnosis when horses show neurological signs. Other studies investigate multisystem diseases by comparing similar infections in other species, helping researchers better understand how diseases develop and present in horses.

Blood-related infectious diseases are also discussed. Two systematic reviews examine equine trypanosomiasis, focusing on its prevalence, management, and control strategies. Another study introduces a new diagnostic tool for detecting Theileria haneyi, a parasite associated with equine piroplasmosis, and reports the first evidence of its presence in China.

Regionally important diseases are highlighted through research on Hendra virus, which uses government and field data to study how domestic horses may act as bridging hosts for zoonotic pathogens. Another study shows that horses infected with African Horse Sickness virus can develop severe blood clotting disorders that cause significant bleeding. Research also suggests that equine encephalosis virus should be considered when diagnosing African Horse Sickness in regions where both diseases occur.

The issue also examines reproductive health, with one study linking Escherichia coli infection to reduced fertility in Thoroughbred broodmares. Another uses multi-omics technology to study nocardioform placentitis, proposing that the condition be renamed mucoid placentitis due to the variety of bacteria involved.

Respiratory disease research forms a major section, including several studies on strangles. Findings emphasise the importance of screening, quarantine, monitoring, and disease reporting to improve prevention. Additional studies investigate respiratory disease caused by Rhodococcus equi, equine influenza vaccination strategies, and the use of air sampling in stables as a non-invasive surveillance method for equine herpesvirus.

Other research explores infectious skin diseases and rare ulcerative conditions, demonstrating the importance of obtaining accurate diagnoses and comparing disease patterns across species when treatment data in horses is limited.

The Special Focus section also includes a dedicated collection on the equine microbiome, updating earlier research published in 2019. This collection highlights rapid progress in understanding the complex communities of microorganisms that influence equine health.

Overall, the research presented in this EVJ issue aims to improve disease detection, diagnosis, treatment, and prevention. These advances are expected to strengthen equine welfare globally while supporting the livelihoods of communities that depend on horses for work and transport.

The Special Focus Issue is available here:

 https://beva.onlinelibrary.wiley.com/toc/20423306/2026/58/2

Study on Deworming Practices

 The University of Connecticut Equine Extension Program has announced a study to better understand how horse owners and equine professionals manage deworming. Through a brief 10-minute survey, the team aims to gather real-world insight into current parasite-control practices and the industry’s overall awareness of effective deworming strategies.

Participation is voluntary, and all responses will remain confidential and used solely for educational purposes. The survey asks for basic information about respondents’ horses and their deworming experiences. Once started, answers cannot be revisited, and participants may stop at any time.

Those interested in contributing to this research can complete the survey at: https://s.uconn.edu/deworming-survey

Impact of environmental exposure and captivity on gut microbial diversity

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Over thousands of years, hosts and their resident microbiota have evolved complex interactions, with microbial communities adapting to the physiological and dietary conditions of their hosts. 

In addition to these evolutionary relationships, genetic factors play a crucial role in shaping microbial colonisation and immune responses. Domestication significantly influences microbiome composition through changes in diet, habitat, and human-driven selection pressures. The external environment also contributes to microbial diversity, as hosts acquire microbes from soil, water, and food sources. 

A study conducted by Victor Hugo Jarquín-Díaz and colleagues, and published in Scientific Reports, explored the contribution of environmental microbiota from freshwater sources to the gastrointestinal microbiomes of wild khulans (Equus hemionus hemionus). 

 The study also compared the faecal microbial diversity of wild khulans to that of captive khulans in Europe and two other equid species—Przewalski’s horses and domestic horses—in Mongolia. By examining these populations, the researchers sought to understand the extent to which environmental exposure and captivity shape equid gut microbiota. 

They used PacBio sequencing (a DNA sequencing technique widely used for microbial genomics) and the LotuS pipeline for 16S rRNA gene sequencing, enabling a detailed analysis of microbial communities. The research team measured alpha diversity (species richness and evenness within a sample) and beta diversity (differences between samples) and conducted differential abundance analysis to identify microbial differences between groups. 

Their findings showed minimal microbial exchange between wild khulans and their water sources, suggesting that freshwater sources have little impact on their gut microbiomes. They point out that this finding also indicates that khulans contribute little to waterborne microbial contamination, despite regular interactions with these water sources. 

 Comparisons revealed that wild khulans have a more diverse and richer gut microbiome than captive khulans. The researchers suggest that this is an adaptation to the harsh nutritional conditions of the Gobi Desert, where wild khulans must digest a wide range of fibrous, low-quality forage. In contrast, captive khulans have reduced microbial diversity, likely due to changes in diet, lower exposure to environmental microbes, and possible antibiotic use. 

They conclude that their findings demonstrate limited microbial sharing between khulans and the waterholes they drink from, challenging the hypothesis that these act as a source of their gut bacteria or that khulans shape the water microbiome through their exudates. Captive khulans exhibit lower microbial diversity compared to their wild counterpart. However, captivity appears to be less of an influence than species differences – as the faecal biomes of captive and wild khulans are more like each other than they are to those of domestic horses and Przewalski’s horses. 

For more details, see: 

 Jarquín-Díaz, V.H., Dayaram, A., Soilemetzidou, E.S. et al. 

 Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids. 

 Sci Rep (2025)15, 2767 (2025). 

 https://doi.org/10.1038/s41598-025-87216-z