Building the Bioyard: Scaling Precision Fermentation for Industrial Biomanufacturing
A Conversation with Niels Agerbaek
Arsenale is developing an industrial biomanufacturing platform that integrates precision fermentation, modular infrastructure, and advanced automation to enable scalable production. As Chief Technology Officer, Niels Agerbaek leads the development of the Bioyard, Arsenale’s fermentation facility, designed to bridge the gap between lab-scale innovation and industrial-scale production.
Arsenale’s focus is on building the necessary infrastructure and processes to make biomanufacturing more predictable, scalable, and efficient, thus economically viable.
In this conversation, Niels shares insights on:
The vision behind the Bioyard and how it differs from traditional fermentation facilities
The challenges of scaling precision fermentation from pilot to industrial production
The role of automation, AI, and real-time process control in optimizing fermentation efficiency
Innovations in bioreactor design, aeration, sterilization, and energy efficiency
The future of modular, distributed, and AI-driven biomanufacturing
Niels, you’ve spent your career at the intersection of bioprocessing and technology development. What brought you to Arsenale, and how do you see your role shaping the future of biomanufacturing?
I’ve always been drawn to the challenge of translating biological processes into scalable industrial solutions. My background is in process engineering and industrial-scale operation, and I’ve worked across the entire value chain—from early-stage process development to full-scale biomanufacturing.
Before joining Arsenale, I spent several years at Novo Nordisk, where I worked on finished product development and manufacturing for insulin, needles, and durable pens, ensuring large-scale production met the highest quality and efficiency standards. Later, at Xellia Pharmaceuticals, I, among others, led the establishment of global capacity and business development, focusing on scaling operations for pharmaceutical applications.
Most recently, as Vice President at Zymergen, I was responsible for internal operations and engineering management, overseeing the transition of biomanufacturing processes from early discovery to bench-scale proof of concept. At Zymergen, I was introduced to the vast potential of biology for product manufacturing. This innovative approach leverages the same foundational technology used in the pharmaceutical industry, harnessing the power of living organisms and biological processes to create a wide range of products. This includes everything from bio-based materials and chemicals to novel food ingredients and advanced medicines.
However, the pivotal factor in my decision to co-found Arsenale, was the realization that bringing an innovative biomanufactured product to market at a competitive price required a fundamental rethink enabled by the building of a robust, scalable, automated, and efficient end-to-end fermentation platform.
I believe that Arsenale provides the opportunity to develop and implement such a platform.
The Bioyard is a key part of this vision—it’s designed to be a flexible and modular facility that can integrate new technologies and adapt to different production needs. My role is to bridge the gap between biology and engineering, ensuring that our fermentation processes are not only scientifically robust but also scalable, cost-effective, and industrially viable.
The Bioyard is one of Arsenale’s most ambitious projects. Can you explain what it is and how it differentiates from traditional fermentation facilities?
The Bioyard is our platform for industrial-scale precision fermentation. Traditional biomanufacturing sites are often built around bio-pharma and around legacy infrastructure, which can be rigid, costly, and difficult to optimize. At Arsenale, we wanted to take a different approach.
What makes the Bioyard unique is its modular and containerized design, which allows us to scale production dynamically. Instead of relying on fixed, large-scale bioreactors, we use highly controlled fermentation units that can be adjusted based on process requirements. This gives us greater flexibility, faster iteration cycles, and more predictable scale-up from lab to industrial production. Additionally, our standardized operational units, which are developed, produced, and validated in-house in collaboration with our industrial partners, allow us to deploy extra capacity more quickly and cost-effectively than traditional suppliers.
Another key differentiator is automation and the full integration with our benchscale operation and development (our Piccolo system). The Bioyard is fully integrated with our proprietary software, enabling real-time monitoring and control, and an AI-driven process optimization system, allowing us to fine-tune fermentation conditions with a very high degree of precision. This level of control is critical for ensuring high yields, reproducibility, and cost-efficiency at scale.
Scaling fermentation from lab to industrial production is a major challenge. How is Arsenale addressing this?
Scaling fermentation is not just about using bigger reactors—it’s about understanding and controlling every variable that affects microbial performance. At Arsenale, we take a data-driven approach to scale-up, ensuring that every step is optimized before moving to the next level.
Our process follows a structured pathway:
Lab-Scale Optimization – We start with small-scale fermentations to fine-tune strain performance, media composition, and process parameters while testing these conditions in our PICCOLO reactor batteries, which allow us to simulate industrial conditions at a smaller scale.
Industrial Scale-Up – Once we have a validated process, we transition to our industrial fermentation units, using real-time data and AI-assisted feedback loops to ensure consistency and efficiency.
Continual improvements - during operation, we are constantly optimizing our operations and lowering costs by incorporating feedback from large-scale operations and utilizing our Piccolo system to validate e.g. new feedstocks and optimize energy consumption.
Automation plays a crucial role here. By integrating advanced sensors, real-time monitoring, and AI-driven analytics, we can predict and adjust process conditions dynamically, reducing variability and improving overall performance.
What are some of the biggest technical innovations you’re implementing in Arsenale’s fermentation infrastructure?
We’re focusing on several key areas of innovation:
We design and develop all our hardware in-house, starting from data and software needs, working closely with industrial partners to optimize data capture and analysis. This focus allows us to improve key operational efficiency factors.
For instance, we are working on enhancing our sparging mixing to boost oxygen transfer, a significant hurdle in large-scale fermentation. Additionally, we're developing advanced heat exchange and energy recovery systems to address the considerable heat generated during fermentation, thereby minimizing waste and improving sustainability.
These innovations aim to make biomanufacturing more predictable, scalable, and cost-effective.
How does automation and AI-driven process control enhance fermentation efficiency at Arsenale?
Automation is at the core of everything we do. Fermentation is a highly dynamic process, and even small fluctuations in temperature, pH, or oxygen levels can have a significant impact on yield and quality. By starting from our proprietary software, we are enabling real-time sensors and AI-driven analytics, we can continuously monitor and adjust process conditions to optimize performance.
For example, our AI-assisted feedback loops analyze fermentation data in real-time, allowing us to:
Predict and prevent process deviations before they impact production.
Optimize feeding strategies to maximize microbial productivity.
Reduce energy consumption by dynamically adjusting aeration and cooling systems.
This level of control not only improves efficiency but also reduces costs and increases reproducibility, making industrial-scale precision fermentation more viable than ever before.
Looking ahead, where do you see industrial biomanufacturing heading in the next decade?
Over the next decade, I see three major trends shaping the industry:
Modular and Distributed Production: The future of biomanufacturing lies in a network of smaller, decentralized facilities rather than massive, centralized plants. These modular biomanufacturing hubs can be rapidly deployed and scaled, offering greater flexibility and adaptability to market demands and reducing the risks associated with large-scale investments. This distributed model also enables localized production, reducing transportation costs and environmental impact while improving supply chain resilience.
AI-Driven Optimization: Artificial intelligence and machine learning will revolutionize biomanufacturing by enabling predictive process control, strain engineering, and real-time optimization. AI algorithms can analyze vast amounts of data from bioprocesses to identify patterns, predict outcomes, and optimize parameters for maximum efficiency and yield. Machine learning can accelerate strain engineering by predicting the effects of genetic modifications and guiding the development of high-performing strains. Real-time optimization using AI can continuously adjust process conditions to maintain optimal performance and respond to changing conditions.
Sustainability and Circular Bioprocessing: As the biomanufacturing industry expands, sustainability and circularity will become paramount. There will be a growing emphasis on reducing waste, improving energy efficiency, and integrating biomanufacturing into circular economy models. This includes developing bioprocesses that utilize renewable feedstocks, minimize water and energy consumption, and generate minimal waste. Circular bioprocessing strategies will focus on recovering and reusing materials from biomanufacturing processes, creating closed-loop systems that minimize environmental impact and maximize resource efficiency. Additionally, advancements in bioprocessing technologies will enable the valorization of waste streams, transforming them into valuable products and contributing to a more sustainable and circular bioeconomy.
At Arsenale, we’re building for this future. The Bioyard is not just a facility—it’s a blueprint for the next generation of industrial biomanufacturing.