ProDigest: the truth behind the gut

Are there more microbes in your gut than stars in the galaxy?

Yes — and that simple fact reveals just how complex the human gut really is.

With around 100 trillion microorganisms, the human gut is one of the most complex ecosystems in the body. It shapes digestion, immunity, metabolism, and even mood. Understanding how it works is essential — but studying it is anything but simple. 

For decades, researchers have relied on tools that aren’t quite fit for purpose — animal models that don’t fully translate, and clinical studies that come too late in the process. More importantly, they don’t reflect the growing demand — both scientific and societal — for better, more ethical models. 

That’s the gap ProDigest was created to fill.

What began as a university prototype — a dynamic simulation of the gastrointestinal tract — evolved into a purpose-built CRO offering the world’s most advanced ex vivo platforms with its technologies validated in over 200 publications. Today, ProDigest helps innovators in food, health, and pharma explore how their products interact with the gut microbiome — without relying on animal models, and without waiting months for data.

That commitment to scientific quality has also been recognised externally. In 2023, the U.S. FDA awarded ProDigest a contract to provide SHIME® as a preclinical gastrointestinal model — a milestone that highlights SHIME®’s value in regulatory research and the growing role of advanced in vitro tools in preclinical decision-making.

“ From the beginning, our goal wasn’t just to simulate the gut — it was to create tools that help people make better, faster, and more responsible decisions in science. That’s what drives everything we do.”
— Massimo Marzorati, CEO, ProDigest

Why building good gut models is hard

The gut doesn’t work in isolation. Microbes break down food, produce metabolites, interact with immune cells, and influence the gut lining — all at the same time. Studying just one part in isolation risks missing how these systems connect and influence each other.

That’s the core challenge of gut research: capturing complexity without losing clarity. A good model needs to reflect what’s happening in the body, but still be focused enough to deliver usable insights.

This balance shapes how we design our systems. We aim to capture not just the composition of the microbiome, but its function — what microbes are doing, how their activity affects the host, and how those effects unfold over time.

It also shapes how we work. We’re scientists by training, but we work alongside people making real-world decisions. That means staying curious, questioning assumptions, and designing studies that lead to real understanding — not just data. It also means collaborating closely, improving constantly, and staying focused on what matters: doing science that’s honest, useful, and built to solve problems.

Why one size doesn’t fit all

There’s no single way to study the gut — because there’s no single question being asked.

One team might be exploring how a new ingredient affects fermentation. Another might be focused on barrier integrity, or how the microbiome influences immune response. Some need quick answers to guide early decisions. Others are digging deep into mechanisms to support a clinical trial.

That’s the reality of gut research: it’s varied, specific, and often messy. And no one model can do everything.

So instead of trying to make one system fit every need, we work differently. We start with the question. Then we shape the model around it — choosing the right setup, the right readouts, and the right level of complexity to get to a clear answer.

That’s how we approach every project: not with a fixed formula, but with the flexibility to meet science where it is.

“ For me, one of the biggest strengths of ProDigest’s offering is the combination of flexible study design, deep expertise, and the versatility of our technology platforms. That mix allows us to tailor each project to the product and the question — and to deliver the best possible value. ”
— Bart Roucourt, Business Development Director, ProDigest

Why our technology keeps evolving

At ProDigest, innovation doesn’t start with a product roadmap — it starts with a research challenge. Each platform we’ve built began with a pressure point in science: a gap in speed, scalability, predictability, or insight. And each one was designed not just to generate data, but to enable real decisions earlier in development.

When researchers needed to rapidly screen ingredients for microbiome effects, we created Colon-on-a-plate® — a high-throughput tool that delivers fast, predictive insights with clear relevance to in vivo outcomes. Paired with our host interaction and metabolomics platforms, it opens the door to system-wide understanding, well beyond the gut.

To help teams dig deeper into mechanisms of action and the link to health effects, we developed MetaKey® — a metabolomics engine built to surface meaningful biological shifts and reduce uncertainty before clinical trials.

And when the need arose for in depth side-by-side comparisons — of probiotic strains, formulation tweaks, or repeat dosing regimens — we introduced Screening SHIME®, combining parallel microbiomes with a flexible, controlled setup to support rigorous early-stage testing.

These weren’t just smart tools. They were scientific responses to real-world bottlenecks — built through internal R&D, close collaboration, and a deep understanding of what researchers actually need. Last year alone, we invested over €1 million into our own R&D — not because we had to, but because that’s what serious science demands.

“ The science around the human gut is evolving quickly, and staying ahead of it requires constant innovation. For us, R&D isn’t a department — it’s a core value. It’s how we link in vitro and in vivo insights, connect mechanisms to outcomes, and help shape the future of gut health research “.

— Massimo Marzorati, CEO, ProDigest

Our technology evolves because we stay close to the questions researchers are asking — and we build what’s missing, before it’s asked for again.

Why our team is different

You don’t build flexible scientific tools by working in silos. At ProDigest, our teams — from microbiologists and data analysts to project managers — work side by side from start to finish. Not because it sounds good, but because gut research is complex, and solving complex problems takes conversation.

Whether we’re setting up a SHIME® study or digging into microbial shifts, we work together to make sure every decision is grounded in both context and expertise. That same mindset shapes how we work with clients: listening first, asking the right questions, and shaping the study around what really matters.

It’s how we stay focused, adaptive, and honest about what good science actually requires.

Why you’ll want to see what’s next

Every platform we’ve built — SHIME®, Colon-on-a-plate®, MetaKey®, Screening SHIME® — has been shaped by the same principles: scientific depth, practical value, and a refusal to oversimplify what the gut does.

But we’re not finished.

At Vitafoods Europe, we’ll be previewing our next step forward in flexible throughput gut research — a new generation of our short-term platform, designed to bring even more speed, consistency, and clarity to early-stage screening.

It’s built for teams who need fast insight but can’t afford to compromise on relevance. And it reflects everything we’ve learned so far — from two decades of asking better questions, designing smarter models, and helping our partners move science forward.

Come find us at Vitafoods. We’d love to show you what’s coming.

Want to make gut research easier and add more value for your customers? Let’s explore how ProDigest can collaborate with you.