Unveiling the strategic secrets of the Screening-SHIME®

What if the most extraordinary ecosystem on the planet has never seen sunlight — because it’s inside you?

Your gut is home to about 100 trillion microbes, spanning up to 400 gut microbiome species – 3,000 species for the global population – and weighing nearly 2 kilograms. That’s roughly ten times more microbial cells than human ones — forming one of the most intricate biological communities ever known.

These microbes digest, ferment, communicate, and influence everything from immunity to metabolism. They’re essential to human health — yet remarkably difficult to study outside the body.

At ProDigest, we’ve spent years recreating that hidden world through advanced ex vivo gut models — turning complexity into results researchers can act on. Our mission is simple: to make the invisible visible, helping scientists understand how products interact with the gut and microbiome under realistic physiological conditions, and to generate in vitro data that reliably predict what happens in vivo.

That mindset has shaped our entire portfolio. From the full SHIME® — a dynamic, long-term simulator of the entire gastrointestinal tract validated in over 300 peer-reviewed publications — to Colon-on-a-plate® and Kinetic Colon-on-a-plate®, designed for high-throughput and time-resolved studies, ProDigest offers the broadest portfolio of validated gut models available today, each proven to reliably predict in vivo outcomes and drive confident R&D decisions

The Screening-SHIME® builds on that foundation — leveraging SHIME®’s physiological depth, including dynamic control of digestive parameters, compartmentalized simulation of the GI tract, and maintenance of a complex, stable human microbiome — into a mid-throughput, automated system that delivers faster, high-quality insights into gut-level product activity.

And recently, that legacy took its next step forward, with the Screening-SHIME® featured in its first peer-reviewed paper — a quiet milestone in a story that’s only just beginning.

The best of two worlds

Some studies call for speed — others for depth. The Screening-SHIME® was created to bring both together.

It bridges the rapid, high-throughput insight of single-dose fermentations with Colon-on-a-plate® and the deeper, time-resolved understanding of the full SHIME® — the most detailed long-term gut simulation model available today. By combining the proven depth of SHIME® technology with the efficiency of Colon-on-a-plate®, the Screening-SHIME® offers the best of both worlds — a dynamic, mid-throughput system that captures how the microbiome reacts and adapts under life-like conditions.

Using a single colonic reactor that represents the entire colonic microbiome, it streamlines complexity without losing accuracy. Fully automated and designed for parallel testing, the model allows multiple experiments to run side by side — capturing how microbial communities evolve, adapt, and respond over time.

Whether you’re exploring the promise of probiotics, the complexity of prebiotics, or the potential of novel dietary ingredients and therapeutic candidates, the Screening-SHIME® offers the swiftest and most reliable path to understanding the microbiome. It’s the critical link that ensures discovery moves at pace while remaining firmly grounded in sound biology.

Screening-SHIME®: The Essential Advantage

The Screening-SHIME® isn’t just another model—it’s a strategic advantage. We engineered this platform to cut through the complexity, delivering accelerated, trustworthy, and budget-smart insights into how your product truly impacts the gut microbiome. This mid-throughput platform is the streamlined solution for researchers in need of high efficiency without ever compromising the quality of their foundational data.

Optimize Volume and Variability

Two major bottlenecks in early R&D are low throughput and capturing complexity. The Screening-SHIME® solves both. The system is designed for parallel testing, allowing you to test multiple donor microbiomes simultaneously. This is crucial for gaining early, necessary insights into interindividual variability while letting you run numerous products side-by-side to maximize resource efficiency.

Accelerate Critical Decisions

In product development, time is money. With a typical turnaround of just nine weeks from experiment start to  reporting, the Screening-SHIME® delivers actionable data quickly. This speed enables faster decision-making and significantly shrinks your product development timeline. As a budget-friendly alternative to our larger models, you gain the flexibility to run more experiments within the same budget, maximizing scope without sacrificing rigor.

Insight That Mirrors Life

The best data is data you can trust to reflect reality. We ensure that by building in features that closely reflect human physiology. The model accounts for the influence of diet and lifestyle, ensuring your test products are assessed under conditions that are practically relevant. Furthermore, we give you the full story: The Screening-SHIME® lets you monitor microbial responses across the entire digestive system—including the stomach, small intestine, and colon—providing a holistic view of your product’s interaction with the microbiome from start to finish. 

The milestone in print

The ultimate test of any model is its performance under peer review. The Screening-SHIME® was recently put to work studying the prebiotic potential of two whole mushroom powders (M2 Cordyceps 116™ and Myco-Multi™).

Using microbiota from three healthy donors, researchers ran a twelve-day repeated-dosing study designed to mirror daily exposure within the colon. In every donor, the Screening-SHIME® successfully traced clear shifts in how the gut community behaved and adapted, including:

• Increased butyrate production, a critical metabolite linked to gut, immune, and metabolic health.
• Distinct microbial and metabolic profiles, showing how each product uniquely shaped community activity.
• Reduced Bilophila wadsworthia, a bacterium often associated with inflammation and dysbiosis.
• Greater abundance of butyrate-producing species, supporting a balanced, resilient gut ecosystem.

These observations confirmed the model’s sensitivity to subtle microbial and metabolic changes—the kind that reflect real biological processes, not just experimental noise. The study illustrates that the Screening-SHIME® can translate complexity into clarity, providing researchers with results that are fast, reproducible, and real.

Why It Matters

As microbiome research expands across nutrition, health, and therapeutics, scientists are consistently asked to do more with less—less time, less budget, but with an unrelenting demand for rigor and increased level of detail. The Screening-SHIME® was built for this reality.

This demand is driven by explosive market growth: the global human microbiome market, estimated at US$0.94 billion in 2024, is projected to soar to US$13.87 billion by 2034.

For ProDigest, this publication is a quiet affirmation of what drives our work: the belief that progress in gut research should move quickly, but never carelessly; efficiently, but never at the expense of truth. It brings the proven physiology of the SHIME® into a mid-throughput, cost-efficient platform, allowing you to uncover mechanisms faster and still generate data you can confidently take to the next stage of pre-clinical development or clinical translation.