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Advancements in bioprocessing technologies test microbial fermentation adaptability.
Fermentation, the oldest biological process used to produce biopharmaceutical products, may have a challenging road ahead in adapting to innovations in bioprocessing technologies. Significant investments needed to update hardware and, in some cases, software, in older, legacy facilities to meet modern automated processing requirements, for example, would cause hesitancy. In addition, training is required to run and manage updated systems to get the most out of process optimization. Furthermore, fermentation processes require close scrutiny to ensure that the integrity of whole batches of product are not compromised.
While there is a general belief that fermentation is simple, well understood, and well characterized because it is an old bioprocess, there are aspects of it that require careful consideration, such as the environment in which fermentation takes place and the process itself—factors that can impact results.
For instance, the scientists who modify and construct the microbial strains used in the fermentation for a particular product are not necessarily the same people who perform the fermentation itself or who analyze the data generated, explains Zsolt Popse, CEO of GPC Bio, a US-based bioreactor manufacturer. “I did observe at some times a lack of communication between departments and mutual understanding on goals and expectations. There remain many opportunities to increase the yields by understanding and characterizing the vessels and the various gas, feeding, and mixing strategies, for example,” he says.
The current challenges of needing upfront investments for hardware improvements and the lack of project management skills is another stumbling block to the modernization of fermentation, Popse notes. “We are talking about complex projects with multiple stakeholders and technical/budget decisions [that need] to be made,” he says, adding that there is a need to coach small and mid-size companies and educate them on the pros and cons of each element of the hardware and the process.
Another difficulty in upgrading fermentation systems involves troubleshooting future problems. Many end users need to make decisions that could impact their facility for years to come, for example, and they may have limited visibility about the future projects they may handle, Popse points out. Future projects could involve new biological hosts, scaling-up, or simply ordering a system that will take a month to install and qualify before having the process fully optimized, he emphasizes.
Popse further states that software and data generation, or workflow creation, is one aspect that is often neglected. Many end users, he notes, need to be trained on software and will require information technology flexibility as well as flexibility of communication between various ancillaries, existing equipment, and sensors. In addition, scientists need to learn many new tools within a short timeframe, Popse adds. To that end, vendors should become partners and coaches.
Over the years, however, there have been numerous improvements in optimizing the fermentation process, such as the genetic engineering of host microorganisms to generate enhanced cell-lines, using scale-down models for process development, and the advent of high throughput screening techniques, Popse says. He also notes that design of experiment is now a well-established practice with specific programs and that there has been a key focus on media formulation and feeding strategies. On the hardware itself, some experiments allowed producers to anticipate and better control process challenges related to shear stress, foaming, oxygenation, and other factors. Meanwhile, new sensors have been developed, which increased the number of parameters that can be monitored, Popse explains.
One of the most interesting innovations in the bioprocessing field has been the ability to generate significantly more data nowadays, which in turn has led to the ability to lead with data-driven decisions, Popse says. The evolution of data collection, management, and interpretation has opened up advantages in fermentation as well as mammalian cell culture. “We are not just collecting data to ensure we have collected data and are remaining within the desired range, but we are now capable of intelligently using that data insight to positively impact the culture in real time,” Popse emphasizes.
However, another recent innovation, single-use technology (SUT), which has had a largely positive impact on mammalian cell culture bioprocesses, does not necessarily offer the same benefits for fermentation systems. SUTs have led to major improvements in terms of adding flexibility, avoiding cross contamination between batches, speeding up the overall process, and, in some instances, reducing costs, Popse says, but those benefits remain true for mammalian cell cultures. For bacterial fermentations, those benefits would be less valid because, for example, there are technical blocks that would make the switch to SUT very challenging or impossible, he states. “First, bacterial fermentations are often operated at a scale where SUT is either not compatible or not convenient. There are numerous applications in cell culture where SUT vessels are used up to 2000 L now, but, for fermentations, this range of volumes is not always sufficient,” Popse explains.
Other issues in switching to SUT for fermentation involves pressure and temperature, Popse also points out. Much of the ferementation process would require that the equipment used not only have good heating capability but also cooling capability, since processes could be exothermic. Popse notes that plastic (e.g., single-use plastic bioreactor bags) is not a good conductor for these temperature variations, so glass or stainless steel remain the best options. “Glass and stainless steel also remain the best options when there is a need for pressurized vessels, since SUT is not suited for high pressure,” he adds.
SUTs are, therefore, not particularly popular for fermentation today, Popse says. Furthermore, the cost of consumables might become an issue because the batch duration is shorter than mammalian cell culture, making the cost per batch difficult to justify. “Some fermentation processes, such as those that use fungi, would also expose the scientist to challenges related to high viscosity, for example; traditional fermenters can be designed accordingly, whereas SUT would offer less opportunity in terms of mixing mechanisms,” he states.
Lately, the COVID-19 situation also highlighted the key challenges related to the supply chain. “When you use SUT, you rely entirely on a vendor to deliver the consumables and on the forecasting team. The increase in demand demonstrated that challenges arose due to many delays in delivery. Most end-users we know today would not consider SUT for fermentation; they prefer to remain in control because a supply disruption could lead to major problems. Traditional and SUT fermenters have both valid pros and cons,” Popse explains.
The likelihood that fermentation would move toward an innovation such as a cell-free process for commercial-scale production is tempting, but so far unlikely. Cell-free processes offer numerous interesting solutions, and can sometimes be a better solution, but remains process- and scale-related, Popse states.
Popse notes that there are numerous limitations using cellular systems, as it is always a challenge to scale-up and ensure a robust expression level as well as achieve standardized reactions outcomes with a cell-free system. Thus, he believes that cell-free systems are something to consider for the research phase. “However, it has been my observation that there is little collaboration between the differing approaches,” he adds. “Cell-free experts should interact more with traditional producers to develop a hybrid approach. I am not envisioning the cell-free approach to displace traditional approaches at large scale since there remain some challenges related to the need for enzyme synthesis and co-factors, which lead to some expensive scale-up modeling. But I would absolutely see the benefits in using cell-free systems for screening and optimizing your process and then switching to living organisms for further improvements and production,” Popse concludes.
Feliza Mirasol is the science editor for BioPharm International.
Vol. 34, No. 9
When referring to this article, please cite it as F. Mirasol, “Bioprocessing Innovations Pose New Challenges for Fermentation,” BioPharm International 34 (9) 22–23 (2021).