Precision fermentation is reshaping biologic manufacturing by enabling the efficient production of high-value biomolecules using genetically engineered microorganisms. While offering potential advantages in scalability, timelines, and cost compared with traditional mammalian cell culture, achieving consistent, high-quality outputs requires addressing the inherent complexities of biological processes. Leveraging process analytical technology (PAT), advanced modeling techniques, and a quality-by-design (QbD) framework can empower manufacturers to optimize process performance, ensure product consistency, and accelerate commercialization.
Transforming Biologics Production with Precision Fermentation
Precision fermentation harnesses the capabilities of genetically engineered microorganisms — such as yeasts, fungi, and bacteria — to produce a wide range of high-value biomolecules. When properly optimized, precision fermentation processes enable the production of biologic substances with high yield, purity, and consistency.
Traditionally, biopharmaceutical manufacturing has relied heavily on mammalian cell culture to produce large biologic drug substances, including recombinant proteins, monoclonal antibodies, bispecific antibodies, and fusion proteins. However, the rise of smaller biologic modalities, such as peptides, antibody fragments, nanobodies, and nucleotides, is driving growing interest in precision fermentation as an alternative manufacturing approach. The attraction for using precision fermentation to produce these smaller molecules compared with mammalian cell culture lies in its cost-effectiveness during production across various scales. Thanks to the relatively lower resource costs and shorter timelines for microbial fermentation processes, precision fermentation is a viable alternative method.
And yet, employing microbial fermentation is not straightforward, as it is important to consider what strategies will be used to produce (generally more complex) active eukaryotic biomolecules using the relatively simpler cellular machinery of microorganisms. Furthermore, as production is scaled, ensuring homogeneous conditions throughout the bioreactor and maintaining stable expression are important.
Several advancements are accelerating this shift. Improvements in bioreactor design, alongside the adoption of automation, digitalization, and process analytical technologies (PAT), have greatly enhanced the efficiency, scalability, and control of precision fermentation processes.1,2 These innovations enable real-time monitoring and optimization of critical process parameters, minimizing variability and ensuring the consistent production of high-quality biomolecules.
The potential of precision fermentation in biopharmaceutical applications is reflected in market growth forecasts. The global biopharmaceutical fermentation market is expected to expand at a compound annual growth rate of slightly more than 6%, increasing from $10.17 billion in 2023 to $16.03 billion by 2031.3 This growth reflects not only increased demand for smaller biologic modalities but also recognition of the scalability and sustainability that precision fermentation can offer.
The underlying processes of precision fermentation share similarities with traditional biopharmaceutical production. Both involve cell line development, optimization during R&D, and scaling to commercial manufacturing. However, precision fermentation differs fundamentally in its use of microbial cells — such as yeast or bacteria — rather than mammalian cells. This shift brings distinct advantages, including shorter production cycles, more flexible production environments, and lower costs. These benefits make precision fermentation an increasingly attractive option for biopharma manufacturers seeking to broaden their product portfolios while improving efficiency and sustainability.
Integrating Quality-by-Design with Advanced Technologies
Achieving high-performance precision fermentation requires meticulous management of process conditions and robust process control strategies to minimize variability and ensure consistent product quality across different production scales. PAT tools play a key role in achieving this level of process control. These tools, including advanced sensors and in-line monitoring systems, provide real-time data on critical process parameters (CPPs), enabling operators to maintain optimal conditions throughout fermentation. By continuously measuring key variables, in-line PAT tools ensure that microbial cells remain in an ideal environment, ultimately enhancing yield and reducing the risk of deviations.
Scaling precision fermentation processes from laboratory to commercial production presents its own set of challenges, but these can be mitigated by investing during R&D to develop scale-down models of larger (production-scale) bioreactors. This allows for screening and optimization of fermentation conditions, accelerating process development timelines and minimizing scaling risks by providing early insights into potential performance issues. During scaling (up or down), digital tools can be invaluable for analyzing large volumes of process data to identify trends, predict potential issues, and optimize process parameters. Furthermore, when combined with advanced models, such as digital twins — virtual replicas of physical systems — the collected data can allow for comprehensive modeling of various aspects of the production value chain, from strain performance to equipment operation. Together, digital tools can provide manufacturers with a deeper understanding of their processes and support more informed decision-making.
However, the full potential of these advanced technologies is best realized within a quality-by-design (QbD) framework. By integrating quality considerations from the earliest phases of process development, QbD minimizes the likelihood of errors and ensures that robust, scalable bioprocesses are established from the start. This proactive approach reduces the need for reactive interventions and fosters the consistent production of high-quality biologics.
Enhancing Precision Fermentation with Process Analytical Technology
Precision fermentation involves several interconnected stages: strain development, upstream fermentation, downstream purification, and final formulation. Each of these stages presents unique challenges in achieving scalability, production efficiency, and consistent product quality — factors that directly impact time to market. Addressing these challenges requires precise process control, which is where PAT tools come into play.
PAT tools are essential for maintaining the "precision" in precision fermentation by overcoming the inherent variability of biologic manufacturing systems. The U.S. Food and Drug Administration (FDA) strongly advocates for the use of PAT in biopharmaceutical processes to monitor CPPs, reduce inconsistencies, and ensure product quality through real-time data collection and analysis.
Applying a QbD approach is essential for effective integration of PAT tools. Once the target product profile (TPP) and critical quality attributes (CQAs) are defined — based on efficacy, safety, regulatory expectations, and patient needs — appropriate CPPs can be identified. PAT tools then support process development, scale-up, and commercial manufacturing by providing real-time insights into process performance. This real-time monitoring capability enables operators to make data-driven adjustments to key variables such as feed rates, temperature, and media composition, resulting in robust processes that deliver higher yields and superior product quality.
During the fermentation stage, where cells are amplified within a controlled bioreactor environment, optimizing both the mechanical/physical and chemical conditions is essential. Biological systems are inherently complex, and real-time monitoring of CPPs — such as pH, dissolved oxygen (DO), dissolved carbon dioxide (DCO2), and oxidation-reduction potential (ORP) — provides valuable insights into cellular health and metabolism. These insights enable operators to make immediate adjustments to fermentation conditions, ensuring that cells remain in their optimal growth phase and that product synthesis is maximized.
Fermentation process optimization can involve several strategies. For instance, measuring viable cell density throughout the fermentation cycle helps maximize product yields by identifying the ideal balance between cell proliferation and product synthesis. Monitoring respiration indicators — such as partial oxygen pressure — further enhances process understanding by providing a clear picture of how cells consume nutrients and produce target molecules.
The type of fermentation process — whether batch, fed-batch, or continuous — and the design of the bioreactor must also be carefully considered when developing a process monitoring and control strategy. PAT tools play a crucial role in optimizing several key factors for successful scale-up. A well-designed bioreactor, combined with a robust PAT framework, ensures that processes run efficiently, predictably, and at scale.
To further enhance the precision fermentation process, integrating multiple sensor technologies and advanced data analytics is essential. The combination of diverse PAT tools provides a more comprehensive view of the process, reducing variability and increasing efficiency. By leveraging these technologies, manufacturers can develop more efficient microbial production systems, minimizing waste and maximizing product yields.
Employing Advanced Modeling Techniques to Optimize Precision Fermentation
Incorporating advanced modeling technologies into precision fermentation process development can significantly reduce timelines and improve process outcomes. By providing accurate predictions of process performance and behavior, computational models help minimize the need for extensive physical experimentation. However, to deliver reliable insights, these models must be built and trained with high-quality, relevant data.
PAT tools enable real-time monitoring and data collection throughout process development and manufacturing, ensuring a continuous flow of robust data that is essential for refining computational models. By leveraging this data, manufacturers can create predictive models that enhance process control, optimize production parameters, and improve overall efficiency.
One example of this approach involved the development of a computational model for Saccharomyces cerevisiae fermentation. Initially, the model’s predictions were hindered by variability in the original experimental data and inconsistencies in its structure. A local sensitivity analysis was conducted to identify the most influential parameters affecting fermentation performance, guiding subsequent model refinements. Additionally, coupling the model with spatial transport simulations enabled a more accurate representation of large-scale fermentation conditions. As a result, six critical parameters were identified, allowing for targeted optimization efforts and significant improvements in the model’s predictive capabilities. With further refinements, this model is expected to be particularly valuable for optimizing feeding regimes in fed-batch and continuous fermentation processes at commercial scale.
Advanced modeling also plays a critical role in addressing the challenges of scaling up precision fermentation processes. One common issue is the discrepancy between the homogeneous conditions of lab-scale bioreactors and the heterogeneous environments found in large-scale production equipment. A mechanistic model developed to define gradient profiles for various scale-down conditions allows researchers to design experiments that replicate the stress responses experienced in large-scale bioprocesses. For instance, using this approach with Escherichia coli bioprocesses has proven effective in evaluating different process conditions and identifying potential performance issues.
Advancing Precision Fermentation at Hamilton
At Hamilton, we recognize the growing importance of precision fermentation within the biopharmaceutical industry and understand the inherent complexity of these processes.4 Successful implementation of precision fermentation requires effective monitoring and control strategies throughout development and commercial production. Our commitment to process optimization focuses on providing advanced solutions that enable manufacturers to overcome challenges and improve efficiency.
Our approach prioritizes the continuous monitoring and control of as many critical process parameters as possible. We are dedicated to the development of new PAT tools that empower biopharmaceutical manufacturers to adopt a comprehensive QbD approach. By integrating intelligent sensors and real-time analytics, we help enhance bioprocess efficiency, improve product quality, and increase overall productivity.
A key example of this strategy is sensor fusion — the combination of data from multiple sensors to provide a more comprehensive understanding of bioprocesses. This deeper insight is essential for developing robust precision fermentation processes that deliver high yields of high-quality products with consistent performance. By integrating advanced sensor technologies, manufacturers gain greater visibility into their processes, allowing for real-time adjustments that optimize efficiency and minimize variability.
Looking to the future, Hamilton is actively exploring innovations in PAT to further advance precision fermentation capabilities. Our focus areas include developing next-generation sensors with enhanced sensitivity, accuracy, and reliability — empowering our customers to leverage data generated by these tools for deeper application insights.
Through our ongoing efforts to drive innovation in process monitoring, Hamilton aims to remain at the forefront of precision fermentation, providing solutions that enable biopharmaceutical manufacturers to achieve their production goals more effectively and efficiently.
References
1. Puri, Arzoo. “What Role does Fermentation Play in the Pharmaceutical Industry?” AZO Life Sciences. 6 Mar. 2024.
2. Graham, Cameron and Gregor Awang. “High-Growth Microbial Fermentation for the Manufacture of Biologics.” Pharmaceutical Technology. 21 Feb. 2024.
3. “Biopharmaceutical Fermentation Market Size Expected to Reach USD 16.03 Billion to 2031.” Insight Analytic. Biospace. 17 Apr. 2024.
4. “The PAT Pathway to Scalable and Sustainable Precision Fermentation.” Hamilton. Nov. 2024.