Key Tactics for Scaling Fermentation Bioprocesses with Confidence

Scaling up a fermentation process is a make-or-break moment for synthetic biology companies. It’s either a culminating effort that catapults your bioproduct to market or the death throes of a once great idea.

The financial investment required to scale up and commercially launch a fermentation process is often more than the R&D cost to develop the bioproduction microbe and lab-scale process.? Fermentation performance inefficiencies or encountering unexpected timeline delays during scale-up can make it even harder to keep investors and customers engaged. This perilous period is often called the Commercialization Valley of Death.

As discussed in “Passing the Baton to CMOs to Accelerate Industrial Biotech,” collaborating with experienced Contract Manufacturing Organizations (CMOs) represents a vital mechanism for more reliably scaling fermentation while minimizing risk. Even before scale-up, there’s a lot that early-stage companies can do internally to ensure success, especially for bioprocess data management and tech transfer.

In this newsletter, the Liberation Labs and Invert teams put our heads together to collect concrete tactics for de-risking scale-up efforts, from in-house preparation to best practices for CMO partnerships.

Consistent Data Analysis Workflows

Data is everything to a scientific organization. However, many early-stage companies fail to recognize the sizable challenge of bioprocess data management until teams must make scale-up decisions from a mountain of minimally curated and poorly organized data.

Establishing consistent data management and analysis workflows early on for your bioprocess data creates a steady pipeline for new raw information to be transformed into meaningful knowledge, repeatedly and reproducibly, no matter the user or team. This insulates efforts from bias and inter-user variability to improve scale-up decision-making.

With codified parameter tracking and discrepancy analysis, fermentation and downstream processing teams are more able to refine their bioprocess for scale-up and circumvent potential issues before they occur at the worst possible times.

As part of this, elevate the visibility and access to ALL relevant data. Unfortunately, decision-makers may inadvertently select data that supports preconceived notions simply because they see that information first or because other data is unprocessed or out of sight.

"Ideally, fermentation companies should work towards having one single “source of truth” for their bioprocess so that data is fully accessible and not floundering in disparate and confusing spreadsheets."

Remember that data presentation also matters, so be sure to standardize. Beautiful, easy-to-follow data presentations are more likely to drive understanding and scale-up decisions toward a conclusion than conflicting data of equal quality presented less cleanly. If everyone on your team uses the same data plot and report formats, it helps decision-makers remain consistent and avoid biases associated with visual preferences.

Process Documentation and Version Control

Similarly, it’s essential to meticulously document all bioprocess versions, including parameters, changes made, change justification, and the effect.

Given the many variables that can change throughout bioprocess development, it’s easy to lose sight of seemingly trivial differences that impact outcomes. For example, imagine a fermentation team switching suppliers for a common raw ingredient. Minor differences in the ingredient formulation or impurity profile might affect microbial growth or shift metabolism toward undesired biomolecules. Without documentation, teams would not know why productivity fluctuated between runs.

Fermentation companies should implement a robust version control system to differentiate process iterations and streamline the management of all this information over time. Process documentation and version control systems ensure clear communication and alignment across your team and outside parties, like CMOs. That way, all bioprocess scientists, engineers, and decision-makers can remain on the same page about what they're doing and why.

Robustness Testing at Bench-Scale

Running robustness tests or “scale-down” experiments at lab scale can help a bioprocess team understand process variation and potential failure points.

To illustrate this, consider mixing time as an example. The small volumes of bench-scale reactors allow for nearly instantaneous mixing, providing a fully homogeneous environment in terms of temperature, pH, and nutrient availability. However, the mixing time in an agitated, “well-mixed” 150 kL fermentation bioreactor is likely on the order of several minutes.

This difference might seem inconsequential, but can negatively impact strain performance or create process variability. To get ahead of this challenge, a fermentation development team can trial variable mixing times or pulse-feeding strategies to recreate this effect and see how their microbe fares under longer mixing times.

The ideal robustness tests should mimic expected process limitations at scale to reveal the sensitivity of key performance indicators (KPIs) to variations in critical process parameters. Teams can explore variations in pH, temperature, O2 gradients, and other parameters to simulate expected performance during scale-up and mitigate potential problems before scaling up.

As mentioned above, it’s critical to also ensure vigorous process documentation of robustness testing. Done correctly, well-documented robustness testing empowers CMOs taking on new fermentation scale-up projects by helping them see established process edges and where performance starts to fall off during tech transfer.

If a CMO team already knows what’s been done, they can more rapidly identify what experimental levers remain at their disposal. This helps to eliminate redundant experimentation, which can save client resources and speed up time-to-market.

Scaling Up with CMOs: Advice for Effective Partnerships

CMOs help early-stage fermentation innovators de-risk scale-up by providing commercial-scale technical expertise, infrastructure, and operations know-how. However, ensuring scale-up success is not as easy as handing over glycerol stocks of the bioproduction microbe. Here are some useful considerations and strategies for an effective scale-up collaboration with a CMO.

Establish Clear Project Leadership

When working across organizations, it’s important to establish clear project leadership and overall structure at the start of any CMO project or partnership. Well-defined roles and responsibilities for each team and a straightforward communication plan keep everyone on the same page, avoid unnecessary redundancy, and help to limit the possibility of conflict. In other words, use a “best practice” project management approach to build rapport.

Prepare a Detailed Tech Transfer Package

A bioproduct company has built significant institutional knowledge about their bioproduction microbe and production technology. However, data sets, calculations, or “common” assumptions that make perfect sense to your team might not be as intuitive to the CMO partner.

“A high-quality and detailed tech transfer package is the most impactful tool to prepare for scale-up and working with a CMO.”

Detailed tech transfer packages should capture everything known about the fermentation process and performance. Provide relevant process information and profiles, including media recipes, nutrient requirements, expected growth rate, feeding profiles, cell biomass profile, OUR profile, key process transitions (like induction points), and other behavior or trends that are indicative of the fermentation performance.

In addition to an optimized process, it is also critical to share the results of the robustness tests collected at lab-scale. That way, CMOs understand how upsets or process excursions for key process variables impact the fermentation. Decision trees that outline the primary levers available to bring the process back are essential.

"Think of tech transfer packages as operating protocols, cheat sheets, and troubleshooting guides all rolled into one – it should be the go-to source of information on how to run your process and why.”

Yet, collecting and curating a massive amount of data for a tech transfer package takes significant effort and time. Thus, investments in software and automated workflows for managing bioprocess data can offer significant returns.

It’s also worth noting that the tech transfer package must also cover the downstream separation and purification process, all analytical methods required for fermentation and downstream process control, as well as final production analysis. However, these areas are not the focus of this newsletter.

Understand Process Requirements and Identify Gaps

After reviewing the tech transfer package, the CMO will perform a facility gap assessment, identifying potential gaps between the client company’s process requirements and the CMO’s capabilities. Once identified, the CMO shares the assessment with the client company, and the teams work together to find solutions, mitigate risks, or, in some cases, align on accepting potential impacts to process performance. Oftentimes, issues identified in the gap assessment warrant additional robustness tests or tweaking of process conditions to best fit the CMO facility.

CMOs are not one-size-fits-all, especially legacy CMOs that were built for a different product and retrofitted to operate as a fermentation CMO today. To that end, Liberation Labs previously shared how to evaluate some of the key fermentation parameters in the “Fermentation Facility Retrofit” issue.

On the other hand, a built-for-purpose CMO site (like Liberation Labs’ first launch facility in Richmond, Indiana) can accommodate highly aerobic, aseptic fermentations and make use of alternative feedstocks (including methanol).

Perform Tech Transfer in-Person

After aligning on process fit and agreeing to move forward with scale-up and commercialization at the selected CMO, it is highly recommended that the lab-to-lab tech transfer is performed in person through direct demonstration and face-to-face interaction.

What do we mean by direct demonstration? Ideally, the CMO’s fermentation experts should learn the fermentation process directly at their client’s lab, providing an opportunity to ask questions and observe how it’s done. Then, the CMO should replicate lab-scale fermentation at their site with the clients present to observe and provide additional support. This allows the teams to cross-validate key procedures and test potential changes (like media formulations or the use of a new feedstock source), as well as build a general familiarity with the process.

Conclusion

Scale-up is where rubber meets the road for fermentation start-ups and synthetic biology companies. It’s the point where a biotech company determines whether its innovation is truly a real-world solution or merely an interesting idea. To come to grips with reality, fermentation teams should implement strategies to diligently challenge their approach and de-risk it throughout every stage of bioprocess development.

Sophisticated data management and a scale-down approach to robustness testing, coupled with diligent process documentation and version control, will help accelerate meaningful lab-scale development. These assets will also be invaluable when creating high-quality, detailed tech transfer packages. Building a strong relationship with your selected CMO and following tech transfer and scale-up “best practices” will ensure that scale-up and commercialization efforts stay on the expected timeline and budget.

Although lab-scale development and CMO operations require substantially different skill sets and core competencies, understanding how to speak the language and work together effectively keeps everyone pointed in the right direction.

Liberation Labs and Invert both believe that implementing these strategies can provide a smoother, more predictable, and ultimately, more successful scale-up journey.

About the Authors

Alex Felt is the Head of Business Development at Invert, a leading software company that is reshaping data management and analytics in the bioprocess industry. Rachel Pacheco is a Senior Director of Process Engineering at Liberation Labs.