Ask the Founder: Inside the Science of Scientia Sport Horses

A conversation with Professor Joanne Santini on genetics, gut microbiomes, and why breeding a brilliant sport horse and a genuinely well one should never be two different projects.

Scientia Sport Horses was founded on an unusual premise: that breeding a brilliant sport horse and breeding a genuinely well sport horse should be the same project, not two competing ones. Behind that premise is Joanne Santini — Professor of Microbiology, and the person asking, at every stage of the programme, the same question she'd ask in a laboratory: what does the evidence actually say?

We sat down with Joanne to talk about where the science began, why pedigree alone was never going to be enough, and what her five pillars — Genetics, Microbiome, Environment, Training, and Luck — really mean in practice.

Background & Path

What first drew you to microbiology as a career?

I was fascinated by the microscopic — this enormous, complex world all around us that we simply cannot see. Microorganisms influence almost every aspect of life, yet for most of human history we didn't even know they were there. I loved the idea of understanding something hidden and extraordinary, and using evidence to explain why biological systems behave as they do. That curiosity has never left me.

Was there a specific moment or turning point where horses and science started to intersect for you?

It was probably less a single moment than a gradual realisation. Once I became involved in breeding horses, I found myself approaching every decision the way I approach a research question: why are we making this mating, what evidence supports it, how much is genetic and how much is influenced by nutrition, development, management or environment? The more I looked, the more apparent it became that breeding an elite athlete is not simply a pedigree exercise. Genetics creates potential, but whether that potential is realised depends on everything that happens to the horse from conception onwards. Scientia Sport Horses grew out of wanting to bring those pieces together.

What does a typical week look like when you're balancing academic work with the yard?

There probably isn't a typical week. My academic work involves research, teaching, supervising students, and writing grants and papers. The horses fit around that — early mornings, evenings, and a lot of organisation. But I value the contrast. Academic life can be cerebral and screen-based; at the yard, the priorities become immediate — is everyone sound, is the grazing right, is a youngster developing as expected, is a mare happy in the herd. Horses are also remarkably effective at making your diary irrelevant.

Did colleagues in academia react differently to you starting a breeding programme?

Mostly with curiosity — especially once people realise this isn't a hobby that happens to sit alongside my career, but something I approach with the same critical thinking I use in science. What often interests colleagues is how familiar the underlying questions are: genetics versus environment, developmental effects, microbiomes, phenotype, uncertainty, bias. The organism happens to be a horse rather than a bacterium, but the questions about how biology produces an outcome are surprisingly similar.

Why the Science Had to Come First

What's the biggest misconception in traditional breeding that your scientific background made you question?

Probably the idea that pedigree alone predicts outcome. Pedigree matters enormously, but it isn't destiny. A foal inherits a unique combination of genes, not an average of its parents, and those genes interact continuously with the environment it develops in. It's very easy to construct a convincing story after the fact — this horse is good because of a famous stallion, or an ancestor three generations back. As a scientist, I'm instinctively cautious about that kind of reasoning. I want to know what the wider family has actually produced, how consistently traits are transmitted, and what weaknesses come with the strengths. That doesn't make pedigree less important — it makes using it intelligently far more important.

Can you point to a scientific principle that changed how you approach breeding decisions?

Gene-environment interaction, probably more than anything else. Genetics establishes a range of possibilities, but the outcome emerges from the interaction between genetics and environment — and in a sport horse, that environment begins before birth: maternal health, nutrition, the developing microbiome, growth rate, pasture, movement, social experience, training. None of those factors act independently. That changes the question from “which stallion will give me the best foal?” to “which mating creates the potential I want, and what do I then need to do over the following years to give that horse the best chance of expressing it?” That second question is far more interesting to me.

How does thinking like a microbiologist show up in the small, day-to-day decisions at Alderton?

Mostly through observation, record-keeping, and questioning assumptions. I compare individuals rather than assuming what works for one horse works for all, and I try to think in systems rather than treating nutrition, health, behaviour and training as separate subjects. Food is central to that — what a horse eats doesn't just nourish the horse, it feeds the enormous microbial community in the gut. Forage quality, diet and feeding pattern can alter that ecosystem as much as the animal's own metabolism. It also means resisting the urge to intervene simply because an intervention exists. Sometimes the right decision is to change something; sometimes it's to provide good diet, movement, company and time, and let normal biology do its job.

Were there things you had to unlearn from “how breeding has always been done”?

Yes — particularly the tendency to treat convention as evidence. The horse world holds enormous practical knowledge, and dismissing it would be foolish. But tradition and evidence aren't the same thing, and I've learned to ask why something is done and whether the horse in front of me actually needs it. Horses have also taught me something scientists occasionally need reminding of: not everything important has been measured properly yet. Good horsemanship and good science should inform each other, not compete.

The Five Pillars

Of the five pillars — Genetics, Microbiome, Environment, Training, Luck — which took you longest to fully appreciate?

Probably Environment, because it covers so much more than I first appreciated. It isn't just the field a horse lives in — it includes nutrition, movement, social contact, pasture, climate, disease exposure, and everything else that shapes a young animal as it develops. Nutrition is especially important, because food is one of the main ways environment acts biologically: it influences growth and metabolism directly, but also determines what reaches the gut microbes, which then produce metabolites that interact with the horse. Diet, microbiome and environment aren't really separate pillars — they're deeply connected. You can't alter the genes after conception, but you influence the developmental environment every single day.

Why did “Luck” earn a place alongside the more scientific pillars?

Because pretending randomness doesn't exist would be very unscientific. You can choose two exceptional parents, manage the pregnancy meticulously, raise the foal carefully and train it beautifully — and something can still happen that nobody could have predicted. Equally, an unremarkable mating can occasionally produce something extraordinary. Biology contains variation and uncertainty, and breeding certainly does. Including Luck is an acknowledgement of intellectual humility: the objective isn't to guarantee an elite horse — nobody can — it's to keep shifting the probabilities in the right direction, while recognising that living systems will never be entirely predictable. Our five pillars aren't a formula for manufacturing champions. They're a framework for giving each horse the best possible chance.

Is there a pillar you think other breeders underrate?

Environment — and particularly the relationship between nutrition and the microbiome. A huge amount of effort quite rightly goes into stallion selection and pedigree analysis, but breeding doesn't end when the foal is born. How a young horse eats, moves, grazes, plays and interacts with people all form part of its developmental environment. The microbiome sits at an interface between diet, metabolism, immunity and environment — we're not just feeding the horse, we're feeding an ecosystem. We're still learning exactly what an optimal equine microbiome looks like, so this is an area where good breeding programmes should be curious, but scientifically cautious too.

Personal & Reflective

Is there a moment — a mare, a foal, a setback — that felt like proof you were on the right track?

Watching Petra and Venus develop, and seeing desirable characteristics appear repeatedly rather than just once — athletic movement, confidence, curiosity, and their own distinct personalities. But more important than any spectacular trot or canter has been seeing young horses that are relaxed, sociable and genuinely interested in people. Athletic ability matters enormously to me, but not at the expense of a horse's psychological wellbeing. Seeing both develop together is probably the closest I've come to thinking: this is exactly what I wanted the programme to be about.

What surprised you most about running a breeding operation, versus studying the science of it?

How much uncertainty remains even when you do everything carefully. Science trains you to control variables; horses are very good at demonstrating that real biological systems refuse to cooperate. Pregnancy, foaling, development, injury, weather, grass and herd relationships each introduce variables you can't fully control. Running the programme has made me even more interested in evidence, but also more accepting that good decision-making often means making the best call possible with incomplete information. And there's considerably more mud involved than in most microbiology laboratories.

If you could tell your younger academic self one thing about where this would lead, what would it be?

That curiosity doesn't need to stay within disciplinary boundaries. I'd never have predicted that questions I first encountered through microbiology — genetics, microbial communities, environmental interactions, variation and biological uncertainty — would eventually shape the way I think about breeding horses. But in retrospect, it makes perfect sense. Biology is biology. The scale and the organism change; the fundamental questions largely don't.

What do you hope people take away from SSH, beyond “good breeding”?

That elite performance and excellent welfare shouldn't be competing objectives. I want Scientia Sport Horses to show that ambition and compassion can coexist — that we can aim to breed horses capable of performing at the highest level while giving equal weight to soundness, longevity, appropriate development and psychological wellbeing. I'd also like people to come away asking more questions: why was this mating chosen, what evidence supports it, how was this youngster raised, what do we know about the female family as well as the fashionable sire? If SSH encourages a slightly more thoughtful conversation about how sport horses are bred, that matters to me almost as much as producing successful horses.

What's Next

What is next for SSH, and for you?

Building slowly, and letting evidence determine the direction of the programme. Scientia Sport Horses is deliberately low-volume — the aim isn't to maximise the number of foals produced, but to make each mating purposeful and follow each youngster carefully enough to actually learn from the outcome. The programme has strong eventing foundations, and the emerging performance evidence within Flairginia PF's female family has also opened up a compelling dressage opportunity.

Longer term, my ambition is to make Scientia Sport Horses a genuinely evidence-led breeding programme — following horses over time, recording health and development as carefully as performance, and being prepared to change our practices when better evidence emerges. The objective isn't to breed more horses. It's to understand how to breed and raise better ones — athletes that are talented, sound, durable, and psychologically equipped for the lives we ask them to lead. That's what science-led breeding means to me.