Gut Health: How Your Horse’s Hindgut Microbes Affect Performance

Podcast #68

Did you know the microbes living in your horse’s hindgut may be influencing how well they perform?

In this episode, Dr Nerida explores fascinating research linking hindgut microbiome diversity, fibre fermentation and performance in horses. We look at studies in Thoroughbreds and trotters showing that higher microbial diversity and greater fibre-fermenting capacity are associated with better racing performance, while greater starch fermentation is linked with poorer performance.

You’ll also learn practical ways to support a healthier, more diverse microbiome through forage, fibre diversity and smarter grain feeding.

Whether you own a racehorse, performance horse or simply want to support better gut health, this episode may leave you in a state of mind-bogglement… which will make perfect sense once you listen. 😂💛

Research mentioned in this episode

Leng et al. (2024)
Early-life gut bacterial community structure predicts disease risk and athletic performance in horses bred for racing
Scientific Reports, 14:17124
https://doi.org/10.1038/s41598-024-64657-6

Park et al. (2024)
Comparison of the fecal microbiota with high- and low performance race horses
Journal of Animal Science and Technology, 66(2):425–437
https://doi.org/10.5187/jast.2023.e45

Vasseur et al. (2024)
Fibrolytic efficiency of the large intestine microbiota may benefit running speed in French trotters: A pilot study
Physiological Reports, 12(21)
https://doi.org/10.14814/phy2.70110

Hansen et al. (2015)
High nutrient availability reduces the diversity and stability of the equine caecal microbiota
Microbial Ecology in Health and Disease, 26:27216
https://doi.org/10.3402/mehd.v26.27216

Grimm et al. (2020)
Dietary composition and yeast/microalgae combination supplementation modulate the microbial ecosystem in the caecum, colon and faeces of horses
British Journal of Nutrition, 123(4):372–382
https://doi.org/10.1017/S0007114519002824

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• Full Episode Transcript

  68. Microbiome Diversity and Performance

  Hello there and welcome to the Happy Horse Nutrition Podcast. I’m Dr. Nerida, PhD equine nutritionist, incurably curious human and someone who constantly experiences mind-bogglement – because I needed a noun – when I read anything about a horse’s microbiome.

  My latest adventure into the science around this subject has been taking a deeper look at the relationship between microbiome diversity and performance, and today I’m going to dig into three studies looking at exactly that.

  Most of the research I’m going to talk about has been done in racehorses, but if you have any kind of performance horse, or actually any horse at all, you will want to hear this, because the critters living in your horse’s hindgut are likely to be having at least some impact on their performance.

  A Bit of Background

  I’ve been studying a horse’s microbiome ever since my PhD days, though I never really thought about it like that. In fact, I wouldn’t have even heard the word microbiome back when I was a PhD student. My PhD was looking at how do we process cereal grains so that the starch they contain is digested in the small intestine, and doesn’t end up in the hindgut, where it feeds what we would broadly call the bad bacteria, or the amylolytic starch-loving bacteria, and causes problems for a horse.

  Back then, the problems we knew about were things like horses that had lots of starch fermentation would eat their bedding, chew on things they wouldn’t normally chew on like timber fences or their timber stabling, or they would experience behavioural changes. Though we didn’t really talk about behavioural changes in terms of behaviour under saddle back then – it was more about them developing stereotypies, like wind sucking, when they had starch fermenting in their hindgut.

  So I guess my PhD was very much focused on preserving a horse’s hindgut microbiome. I did talk about the microbes from a starch fermentation or fibre fermentation perspective, but I started my PhD 26 years ago, and so much has happened in that time in this space of research. What I spoke about in my research was so basic compared to the information we’ve got available now.

  Mind-Bogglement: The Numbers

  Speaking of mind-bogglement – don’t you love that word? I don’t think it is actually a word, but I needed a noun for mind-boggling, and it really does boggle my brain when I try to conceptualise the sheer number of microbes living in a horse’s hindgut.

  The estimates are that there are trillions, and it’s hard to actually find an actual number – every horse is going to be different. But trillions, sometimes the estimate is up over 100 trillion microbes. And in a single gram of manure, which is not very much manure, there is estimated to be billions of microbes.

  This week we’ve been filming a nutrition series for Racing Queensland around the feeding of thoroughbred and standardbred racehorses, and one of the things I wanted to show in these videos was one gram of manure – to talk about how many microbes are in a gram. A gram of manure really is a tiny little bit of manure, and yet in that one gram there are estimated to be billions of microbes. It just boggles my brain.

  I had an experience during a Tony Robbins event with Ryan a few years ago, where Tony was talking about the difference between billions and trillions – he was actually talking about the economy – and he was trying to give us a concept of just how big the difference is. So I’ll go back a step further and throw million in here as well.

  To give you a concept of how big those numbers are, I’ll use a timescale:

  • A million seconds is just over 11 and a half days.

  • A billion seconds is just over 31.7 years.

  • A trillion seconds is 31,709 years.

  So when you think about trillions of microbes living in your horse’s hindgut, if it took you a second to meet each one, it would take you more than 31,000 years. There are a lot of microbes in the hindgut.

  A Brief History of Microbiome Research

  It was all the way back in the late 1800s when researchers started to realise there were microbes in the hindgut of a horse, and that those microbes actually broke cellulose down. So we’ve known for a long time that the microbes in a horse’s hindgut have a role in fibre fermentation.

  In the 1970s, researchers showed that if you dump a whole heap of starch into a horse’s hindgut – undigested starch – that causes a lot of fermentation, a lot of acid build-up, and it will actually cause laminitis. We’ve known that since the 1970s.

  In the late 1990s and early 2000s, when I was doing my PhD research, there was more understanding around their impact on things like behaviour. But it wasn’t really until we started to see the increase in technology that allowed us to actually see which microbes were in a horse’s hindgut – to start describing them by function and group them into family, genus, species – and to measure who was living in the hindgut with technology that was a lot more specific than just culturing them. Because so many of these microbes are sensitive to oxygen and die in its presence, it wasn’t possible to easily culture a lot of them.

  As technology improved in the early 2000s, we started to be able to see all of these different microbes living in the hindgut. And we started to understand they were having impacts far greater than just digestion. In humans and a whole bunch of animal species, we started to see there was this gut-brain axis and that they controlled behaviour, that they were very involved in inflammatory responses, involved in immune function. We discovered that a large part of the immune system is actually resident in the gut.

  So we’ve known for the last 20 to 25 years that these microbes have got a lot of roles in controlling – or at least influencing – health and behaviour. But the exciting thing for us as horse owners, horse nutritionists, and people who train performance horses professionally is that we’re starting to discover now that these microbes actually have quite a big impact on performance.

  The Research: Three Studies

  There’s been some really cool research in the last few years – back to 2024 – where papers started coming out to show us that the diversity of microbes living in a horse’s hindgut is actually having an impact on performance. And that’s what I want to dig into today, because I love these studies. They’re so fascinating.

  It is really cool to think – as a nutritionist, and hopefully for you as equine industry professionals and horse owners – that what these studies are showing is that the closer we can keep a horse’s microbiome to what it would have been as a horse was evolving, so very focused on fibre fermentation as opposed to starch fermentation, the better their performance.

  Study 1: Leng et al., 2024 (Nature Journal)

  The first paper was published in the Nature Journal in 2024. A lot of you will have already heard of this one, because it got really well publicised, and I have spoken about it a couple of times already in various podcasts.

  Essentially, what Leng and co-authors found was that the faecal microbial diversity of a foal at 28 days was actually predictive of their future racing performance. They showed that horses with greater diversity at 28 days of age went on to have significantly better placings and race earnings as two and three year old racehorses.

  So the microbiome that foal ended up with, when it was less than a month old, was actually then having an influence on that horse’s future racing performance.

  They also showed that horses with lower diversity – and especially horses that had been treated with antibiotics or antimicrobials at an early age – had poorer performance and were at a much higher risk of respiratory disease. There weren’t a lot of foals in that group, I think it was maybe six foals that had been treated with antibiotics when they were quite young, but most of those foals had actually had a respiratory condition compared to the foals that hadn’t received any antimicrobial treatment.

  I was reading that this morning in a lot more detail, and it made me think about weaning thoroughbred foals in the Hunter Valley of New South Wales, where so many of them would get snotty noses and respiratory conditions around the time of weaning. I’d love to look at the relationship for those foals – whether they had received any antimicrobial treatment early in life. So if any stud managers are listening to this, it would be really interesting to go back and look at your weanlings, at the ones who did experience a respiratory condition versus the ones that didn’t, and see if you find a relationship between that and whether they might have been treated with some sort of antimicrobial early in life.

  But certainly from a microbiome diversity perspective, those researchers showed that the more diverse the microbiome of a foal, the better the racing performance later in life.

  Study 2: Park et al., 2024

  Park and co-authors showed that high-performance thoroughbred and also high-performance Jeju horses had significantly higher Shannon diversity. The Jeju horses also had significantly higher richness.

  I always forget what Shannon diversity means – I had to look it up again this morning, sorry Dr. Belinda if you happen to listen to this, because you’ve taught me this so many times. Shannon diversity is a combination of the number of different microbial species in a horse’s hindgut, and the evenness of the microbial species. So how evenly are they distributed? Is one or two microbes sort of dominating, or are they all roughly the same number in a horse’s hindgut?

  So these high-performing thoroughbred and Jeju horses had significantly higher Shannon diversity – more microbes that were more evenly distributed in their hindgut than the low-performing horses. Looking at the box and whisker plots for the thoroughbred horses, the high-performing horses did look to have higher diversity, but when they ran the statistical significance on it, it wasn’t quite significant in the thoroughbreds. The Jeju horses did show a really clear increase in the number of species.

  But the really cool thing in this paper was that they then started looking at what do those microbes actually do in the hindgut. They showed that the high-performing horses had significantly more abundant fibre-fermenting bacteria – more bacteria in there doing the work of digesting fibre for the horses.

  The high-performing horses also had enriched production of butyrate, which is a volatile fatty acid that the gut lining uses as an energy source. The horse’s muscles can also use it as an energy source, but it’s typically known as a volatile fatty acid that is really important for maintaining gut health. And they also had more vitamin K production, as well as enriched production of polyamines. I need to go and do a bunch more research on polyamines, because I don’t know a lot about them. From a quick bit of reading this morning, it sounds like they have something to do with maintaining gut lining integrity – so making sure the tight junctions, the little zippers between gastrointestinal cells that hold the cells together so that the gut doesn’t leak, are maintained. So the high-performing horses had more of those polyamines, more butyrate, more vitamin K compared to the low-performing horses.

  They also showed that the low-performing horses had more pathogenic bacteria – more disease-causing bacteria in their hindguts.

  So Leng and co. showed that at 28 days, greater microbial diversity improved performance. Park and co. have shown a similar thing – the high-performing horses having greater microbial diversity – but also that their guts are better set up for fibre fermentation, which from an evolutionary perspective means they’re more like what a natural gut should be like in a horse. Very set up to digest a high-forage, high-fibre diet as opposed to being set up to digest a high-starch, high-fructan, high-sugar diet.

  Study 3: Voisin et al., 2024 (France)

  Voisin and co-authors, working in France in 2024, looked at maximum running speed in French trotters. They showed that maximum running speed was correlated with in vitro capacity – so in a test tube, in a lab – for fibre digestion. They would have taken the hindgut contents from these horses and done a lab fermentation to see what the fermentation patterns were. The maximum running speed in these horses was correlated with an individual horse’s in vitro capacity for fibre digestion. So the horses that had a hindgut that was more effective at fermenting fibre were also faster.

  Like the Park paper, they also looked at some of the metabolites and vitamins produced by the microbes in the hindgut. The faster horses had more butyrate production – the same volatile fatty acid involved in maintaining gut wall integrity and supplying energy for the muscles. And in this one, thiamine production – vitamin B1 – which is so tied up with muscle energy generation. We know that the fibre-fermenting microbes are the ones that produce the B vitamins horses need for muscle energy generation. So it’s really cool that this paper showed horses with a higher maximum running speed also had greater capacity for vitamin B1 production in their hindgut.

  And Voisin and co. take it one step further. Park showed us that high-performing horses had more fibre-fermenting bacteria. Voisin shows us that maximum running speed was negatively correlated with starch degradation in the hindgut. So horses that had more of a tendency towards the starch degradation metabolic pathways were slower.

  When we start to ferment starch in a hindgut, we are negatively affecting performance.

  The Grain Question

  This is a hard one with racehorses, because I do think – particularly with thoroughbred racehorses – they do need some grain. They need the starch to give them glycogen, to refuel their muscle glycogen supply so that they can train and perform at high levels consistently over periods of time. But what we don’t want is starch getting into their hindgut.

  I see it consistently over and over with racehorse stables I work with – if we push grain too hard and start to dump grain into a horse’s hindgut, we actually negatively affect performance. Some of the big stables, Kiramal Racing being one of them, when there are enough measurements of faecal pH, what we start to see – and this is on a much more crude measurement of what’s going on in the hindgut – is that when pH drops too low, and particularly if it goes below pH 6, performance starts to suffer. What I see in real life lines up really nicely with what these researchers are showing in their much more sophisticated research.

  I also dug out a couple of papers around feeding grain and the impact that has on the hindgut microbiome.

  Hansen et al., 2015 (Norway) looked at a hay-only diet versus hay plus oats. This is interesting because you’ll hear me say over and over again that all cereal grains, with the exception of oats, need to be heat-treated before feeding. But this paper actually showed that when oats were added to the diet, the diversity and stability of the hindgut microbiome were significantly reduced.

  The interesting thing was the hindgut pH didn’t even drop to what we would consider a level of acidosis. It didn’t drop down far enough to where we would say, okay, the fibre-fermenting microbes are going to start dying off now. The classic thing that happens is: you feed too much grain or the wrong type of grain, you dump a lot of starch into the hindgut, the starch-loving bacteria grab hold of that starch, ferment it very quickly, produce a lot of acid, drop the pH of the fluid in the hindgut, and then the poor little fibre-fermenting microbes – the bacteria and the fungi – don’t like a low hindgut pH and start to die off. That’s a very easy way to lose diversity. But this paper showed the diversity was significantly reduced when oats were fed, even without the pH dropping to that level. So whenever you put any starch into the hindgut, it is going to have a negative effect on your horse’s microbiome diversity, and according to this paper, also the stability.

  I actually listened to a podcast the other day talking about resistant starch and feeding it to horses, being sold as something beneficial. It was about to make my head pop off my shoulders listening to it, because we know – there’s so much research in horses and horse nutrition – that shows the negative effect of starch fermentation in the hindgut. This Hansen et al. 2015 paper is a really good demonstration of that, because they’re feeding a grain we would normally consider safe for horses, and yet, without any major impact on the horse’s hindgut pH, it is negatively affecting the health of their microbiome. So do be really careful and take any information about feeding resistant starch to horses with a large grain of salt, because I don’t believe we have any scientific evidence to show it is actually beneficial to them, but we do have an awful lot of evidence to show that putting starch into the hindgut has a negative impact on the microbiome.

  Grimm et al., 2020 (Dijon, France) looked at feeding 100% hay and then transitioning over to a diet that was 56% hay and 44% barley – I believe raw barley, so that 44% would have been putting a lot of starch into the hindgut. They showed that both the number of species and the Shannon diversity in the hindgut of those horses dropped when the barley was introduced, and they showed an increase in starch-digesting bacteria and a decrease in the fibre-fermenting bacteria.

  When we think back to both the Park and Voisin research – they both showed that when there’s greater capacity for fibre fermentation, you get better performance. So when we feed cereal grains incorrectly and put a lot of starch into the hindgut, we are potentially – and I would go so far as to say almost certainly – negatively affecting performance.

  One of the problems in the racing industry is that when horses are fed raw grains, particularly raw corn – barley is almost just as bad, it’s just not as commonly fed in Australia in raw form in large amounts – those horses can actually run really well for a period. They’re half crazy, their gut is in such bad shape, but their hindgut is pumping a lot of fuel out because it’s fermenting so much starch from the raw grain. But what you’ll also see is those horses won’t race for very long. They will start to lose weight, they won’t eat very well, they’ll be in poor shape. They’ll often get foot soreness because they’ll get low-level laminitis. And then they need to go out for regular spells or, unfortunately – and it breaks my heart to see it – they get lost from having all of these raw grains fed, because they just can’t sustain performance.

  Whereas if we feed horses in a much more sustainable way and use their hindgut as a fuel tank – because performance horses have two fuel tanks: the glycogen they store in their muscles, and the volatile fatty acids that the microbes produce for them in the hindgut – when we can feed cereal grain in a way that is digested in the small intestine, it allows them to break it down into glucose and top up their muscle glycogen. And they also have the volatile fatty acids coming out of their hindgut from fermenting fibre and not starch. Those horses can perform at really high levels consistently for a much longer period of time, because their gut is healthy.

  Thinking about it from an evolutionary perspective, the closer we can keep a horse’s hindgut to the way nature designed it over 55 million years, the healthier they will be – and according to this research, also the faster, or the better the performance.

  Practical Tips for Feeding for Diversity

  So if we think about feeding for diversity, there are some really easy things you can do.

  Keep grain meals small. Don’t feed all of a horse’s grain allocation for a day in one meal. Break it up into as many small meals as you can throughout the course of the day, so that their stomach and small intestine can do the job of digesting starch, and then the starch is not ending up in the hindgut. That’s the fastest way to create loss of diversity in a horse’s hindgut – dump a whole heap of starch in there, and that’ll do the job for you very quickly.

  Feed plenty of forage. The published minimum amount of forage horses should be fed is 1.5% of their body weight per day – so 7.5 kilograms for a 500-kilogram horse per day. The closer you can get to 2% of a horse’s body weight per day, the happier the hindgut microbes will be. That’s closer to 10 kilograms per day for a 500-kilogram horse. If you’ve got high-performance horses, use high-quality hay, because high-quality hay is still high in energy and your hindgut microbes will ferment that hay and produce masses of volatile fatty acids. The cool thing with volatile fatty acids is that they are being pumped out of the horse’s hindgut even during a race. So if you’ve got a healthy hindgut with plenty of fibre in there, it will actually be actively fuelling a horse’s muscles during a race.

  Be careful with high-fructan forages. Lots of your cereal hays can be really high in a carbohydrate called fructan, which is not digestible in the small intestine – it’s a little bit like resistant starch in that regard – but it ferments really rapidly in the hindgut. It will have the same negative impact on the microbiome as dumping starch into the hindgut: it’ll ferment quickly, build up acid, and negatively affect your good, friendly fibre-fermenting microbes.

  Feed a diversity of hay. At a minimum, feed a grassy hay and a legume hay. Lots of our racehorses and performance horses in Australia are fed something like an oaten or barley hay plus lucerne hay. But even better than that is to feed two or three different types of grassy hay and a legume hay, or a couple of legume hays.

  People used to say to me, is there any point in feeding clover and lucerne hay? And I used to say no, because if you showed me an analysis of lucerne next to clover, it’d be really hard to tell them apart just based on the numbers – they look so similar from a nutrient perspective. Well, I’ve revised that now, because clover and lucerne are two different plant species, and there are lots of different types of clover as well. The more plant species and the more ingredient variety you can get into a horse’s diet, the more diverse that horse’s microbiome will be. When you bring lots of different fibres to a horse’s hindgut, lots of different microbes will be able to find their favourite foods, and you’ll support a more diverse population of microbes in the hindgut. So if you have access to both clover and lucerne hay, by all means feed both of them.

  Add alternate fibres. Things like sugar beet pulp, lupin hulls, copra meal, hemp hulls and hearts, flaxseed meal, well-processed soybean hulls – do be careful with soybean hulls, because if they’re not heat-treated properly they can still have active trypsin inhibitor, which will negatively affect protein digestion – but there are lots and lots of different alternate fibres you can use. The more of these you add into a horse’s diet, the greater the fibre diversity, and that gives the best chance of maintaining microbiome diversity in the hindgut.

  We want the diversity because research has shown us that horses with more diverse microbiomes have got better performance. And we want the fibre fermentation capacity, because research has shown us that horses with greater fibre fermentation have got better performance. Bringing in some of these alternate fibres – they’ve all got different types of fibre in them, so sugar beet pulp has got a different set of fibres to copra meal, and if you use both of those together you’re bringing in fibre diversity – helps support the microbiome diversity in your horse’s hindgut.

  We can’t recreate a wild foraging horse’s diet, and certainly not easily. They moved across such massive areas, plus they had seasonal changes, so the same plants weren’t available to them all the time. It was constantly changing. But we can try to recreate as much of that as possible by bringing in as many different types of fibre from as many different sources as possible.

  I do get asked on a reasonably regular basis these days: how much of those fibres do I need to feed to actually have an impact? And the reality is, I don’t know. But I figure that any amount of alternate fibre is better than none. If you have a horse that doesn’t need a whole lot of additional energy – say a dressage performance horse where maintenance of microbiome diversity is more important from a colic prevention and behaviour perspective than from a pure speed and strength perspective – and that horse is quite chunky and doesn’t need a whole lot of extra calories, then just put the minimum amount in you can get away with without putting too many calories in the diet. If it’s 50 or 100 grams a day, do that. If you can feed more, do that. A lot of racehorses, and definitely in Japan, nearly every single horse is on sugar beet pulp – when I can use it with racehorses here, I’ll use it at, say, half a kilo to one kilo a day, because we’re also chasing the energy that’s in that amount of high-energy fibre.

  I can’t give you an answer on how much is enough to have a measurable impact. I’d really love someone to do some research in this space so that we can say, you know, 100 grams made no measurable difference but 300 grams did. We don’t have those numbers at the moment. But just go with any variety is better than no variety, and get as much fibre diversity into your horse’s diet as possible.

  Wrapping Up

  That was a lot. There’s a lot of detail and a lot of science just in that one little podcast. But do start to think about your horse’s gut from an evolutionary perspective, and start to think about how do I feed my performance horse in a way that will both fuel them for the performance I need, but also maintain their gut as close as possible to the way that millions of years of evolution actually designed it to be.

  I just love that research is showing us that the more diverse a microbial population, and the more geared up those hindgut microbes are to ferment fibre, the better a horse’s performance.

  Remember that you can use the MyHappy.Horse Nutrition app to assess your horse’s diet from a gut health perspective – fibre diversity is one of the factors it does take into account. So if you’re interested to know what sort of impact your horse’s diet is having on their gut health, definitely put it in. I’ll give you the heads up that if you put any kind of raw corn in, you’re going to immediately get half a red star and be told that your horse’s gut health is very poor, because it does have such a negative impact on their gut health. But it’s a good exercise to give you some kind of measurement on where your horse’s diet is at in terms of how well it’s supporting gut health.

  I hope you found that as fascinating and as mind-boggling as I do. It really is a watch-this-space area of research. I know there’s lots of cool research going on at the moment, and I know there’d be a lot of research that I’m also not aware of in this space, but it’s an exciting time to be a nutritionist. And I hope that in bringing some of those studies to you in that brief format, it has helped you think about how you might feed your performance horses into the future.

  And if you don’t have performance horses, it’s just as relevant for any horse – we know that horses with a more diverse microbiome are at less risk of colic, and I think it doesn’t matter who you are or what you do with your horses, colic is always one of those things in the back of our minds that we’re so conscious of and would do anything to prevent. So feeding for microbiome diversity is relevant to every horse.

  So, with that, I will say thank you so much for being here. If you find the time to follow the Happy Horse Nutrition Podcast, I would absolutely love that. And if you know anyone who has got performance horses or racehorses, please share this episode with them. I will catch you in the next episode.