How Breed, Location And Management Affect The Gut Microbiota | Equine Science Matters™

This week, we have broken down a research paper written in July 2026: 'Differential shaping of equine gut microbiota structure and function by breed and feeding regimen' (Lin et al.) So that you can stay up to recent research on the gut microbiota and the practical applications for your own horses. 

Introduction 

Horses are known as hindgut fermenters, meaning they rely heavily on the fermentation of fibre in their hindgut to release energy from their naturally high-fibre diets. This process is carried out by the hindgut microbiota – the community of bacteria, viruses, fungi and yeasts that live in the digestive tract. 

The gut microbiota does much more than help horses extract energy from their feed. It is also thought to play a role in overall health, immunity, performance, recovery and even behaviour through what is known as the gut-brain axis. 

There is a growing body of research looking at what a "healthy" gut microbiota might look like. However, our understanding of what is normal or abnormal, and what those differences actually mean for a horse's health, is still at an early stage. 

One of the challenges researchers face is that many different factors can influence the gut microbiota. Breed, diet, management, geographical location and age may all have an effect, but it can be difficult to work out how much influence each factor has individually. 

This study set out to investigate those factors and, where possible, tease apart their relative effects. 

What the researchers did 

The researchers collected samples from 139 male horses aged between two and eight years, divided into six groups: 

• Thoroughbreds (TH) 

• Thoroughbred × Mongolian hybrids that were stabled (HH1) 

• Thoroughbred × Mongolian hybrids that were grazing (HH2) 

• Mongolian horses (MH) 

• Warmbloods from Beijing (WBH1) 

• Warmbloods from Xing'an League (WBH2) 

Keeping all the horses male and within a similar age range helped the researchers reduce the potential influence of sex and age on the results. 

Because the different groups were living under different conditions, the researchers could make some useful comparisons: 

The researchers then used a range of techniques to examine: 

• The diversity of bacteria within each group of horses. 

• How different the overall microbial communities were between groups. 

• How much of those differences could potentially be explained by breed, location and management. 

• The specific "core" groups of bacteria associated with each group. 

• What functions the different bacterial communities might have, particularly in relation to gut health and fibre fermentation. 

What they found 

Of all the factors investigated, breed was associated with the largest differences in the composition of the gut microbiota. 

The Thoroughbred × Mongolian horses had microbial communities that appeared to be a blend of those seen in their parent breeds. Feeding regime and management – including whether horses were stabled or grazing – were associated with the next largest differences. 

One of the most interesting findings was the difference between the Warmbloods and all of the other groups. Both groups of Warmbloods had a noticeably different hindgut microbial community, with less microbial diversity, fewer fibre-fermenting bacteria and more types of bacteria that have been associated with inflammation in other species. However, this finding needs to be interpreted carefully. 

The study did not provide detailed information about the Warmbloods' diets or management, and all of the horses were considered healthy by veterinarians. Therefore, we cannot conclude from this study that Warmbloods have poorer gut health. 

The results do, however, raise some interesting questions for future research. In particular, it would be useful to understand why the Warmbloods had such a different microbial community and whether these differences have any practical consequences for digestion, health or how they respond to different diets. 

Practical Takeaways 

This was an observational study, which means the researchers looked at what was happening naturally and compared the different groups. They didn't deliberately change the horses' diets or management to see what effect those changes had. This is important because it means we can't say that one factor directly caused another. We therefore need to be cautious about making practical feeding recommendations based on this study alone. 

That said, the findings are still interesting and reinforce some important principles when it comes to feeding and managing horses. 

1. Don't underestimate the importance of making changes gradually 

Horses rely on their gut microbes to ferment fibre and provide much of the energy they need. These microbes need time to adapt when a horse's diet changes. 

Making sudden changes to feed or forage can disrupt this process. The new feed may not ferment as efficiently, so the horse may not get the full benefit, and it may also increase the risk of digestive upset. 

This is one reason why gradual dietary changes are so important, even when the new diet appears to be perfectly suitable for the horse. 

2. We can't yet use microbiota tests to tell us exactly what to feed 

Although we know considerably more about the gut microbiota than we did 10 or even five years ago, there is still a lot we don't understand. 

We don't yet know exactly what an "ideal" gut microbiota looks like – and it is increasingly possible that what is normal for one breed may not be the same as what is normal for another. 

For example, the Warmbloods in this study had higher levels of Proteobacteria, a group of bacteria that can be associated with disturbances in gut health. However, these horses were considered healthy. 

This is a good reminder that we shouldn't look at one group of bacteria in isolation and assume that it tells us whether a horse has good or poor gut health. The microbiota is a complex community, and the different bacteria need to be considered in the context of the whole ecosystem. 

At this stage, microbiota testing can provide interesting information, but we don't yet have enough evidence to use it on its own to determine what an individual horse should be fed.

3. Treat each horse as an individual 

Perhaps the most useful takeaway is that there is no one-size-fits-all approach to feeding horses. Breed is likely to influence how a horse responds to changes in diet and management. If different breeds have different gut microbial communities, two horses of a similar size, living under similar conditions, could potentially respond quite differently to the same feed. 

This doesn't mean that every breed needs a completely different diet. Rather, it reinforces the importance of looking at the individual horse and considering their breed, workload, forage, management and response to their diet when making feeding decisions. 

Conclusion 

The findings of this study fit well with what we already know about the gut microbiota, which is reassuring. They also highlight just how much we still have to learn. 

We don't yet have a clear definition of what a "healthy" gut microbiota looks like in horses, or how much variation between individual horses and breeds is completely normal. Until the science develops further, microbiome testing should therefore be interpreted with caution, particularly if it is being used to make specific feeding or health recommendations. 

Reputable equine nutritionists will always advocate adapting feed, forage and management to the individual horse, and the results of this study further reinforce that approach. Breed appears to have a significant influence on the gut microbiota, which may in turn affect how well individual horses adapt to different feeds and types of forage, as well as how much energy they can extract from their diet, as well as wider health implications. 

Ultimately, understanding these differences could help us make better, more personalised feeding and management choices for individual horses, supporting their health, wellbeing and performance.