End-to-End Fermentation Training

The BioSuite Virtual experience begins with an overview of biomanufacturing and its expanding role in the bioeconomy, showing how living cells are used to produce medicines, food, and fuels. The user is introduced to the core idea that cells act as biological factories, converting simple inputs into valuable products. Through guided interaction, they explore how these processes connect to sustainability, modern medicine, and everyday products. The introduction also orients the user to the virtual lab environment, building confidence as they learn to navigate the facility, interact with equipment, and begin hands-on work.

With the headplate structure in place, focus shifts to how materials move through the bioreactor and how conditions are maintained over time. The user installs the condenser, then configures ports used to introduce and remove materials during the run. Air and liquid lines are connected and labeled, while reinforcing the principle of sterility. Probes for dissolved oxygen and pH are installed to monitor key conditions. Together, these steps build understanding of how controlled flow, measurement, and system integrity support stable and repeatable fermentation.

Working in the wet chemistry lab, sterile filtration is taught as an alternative to autoclaving for liquid chemicals. The user retrieves acid and base from properly designated storage, reinforcing safe chemical handling and separation. Using filter flasks, vacuum pressure, and fine filters, liquids are pulled through to remove microbes while maintaining sterility downstream. Labeling and PPE use are reinforced throughout. This process builds understanding of how filtration supports sterile preparation when heat sterilization is not appropriate.

Virtual Day 2 begins with moving the sterilized bioreactor into operation in the fermentation lab and connecting it to the control unit. Airflow is introduced to create positive pressure, protecting against contamination and allowing for leak detection. Electric, gas, and water connections are completed, linking probes, the impeller, and temperature control systems. The control unit interface is used to monitor and adjust parameters including airflow, temperature, pH, and dissolved oxygen. This chapter builds understanding of how interconnected systems are used to maintain stable conditions throughout the fermentation run.

Work in the microbiology lab introduces the seed train, beginning with retrieval of a Pseudomonas putida cryostock. The user records key information in the batch record, isolates colonies using the four-quadrant streak method, and incubates an agar plate to produce a pure culture. A single colony is then selected and scaled up in a shake flask, reinforcing aseptic technique and airflow awareness in the biosafety cabinet. The resulting culture is prepared as inoculum and transferred into the bioreactor, completing Day 3 and initiating Day 4. This chapter builds understanding of how controlled culture development supports a successful fermentation run.

Attention turns to interpreting Control Unit data and responding to changing conditions as Day 4 progresses and transitions into Day 5. The user reviews temperature, pH, and dissolved oxygen trends. Deadband and cascade control are observed in action as pumps and agitation respond to maintain setpoints. As foam develops, the user applies antifoam through the septum port using aseptic technique. Sampling continues at the 24-hour mark, reinforcing how real-time data and intervention work together to maintain stable and controlled fermentation conditions.

Virtual Day 1, the user learns the role of personal protective equipment (PPE) in reducing contamination risk before moving into the parts and function of the headplate. Each component is installed with purpose, from the impeller for mixing to the sparger for oxygen delivery and the temperature probe for monitoring conditions. As the system comes together, the user develops a clear understanding of how mixing, aeration, temperature, and sealing work together to support a successful fermentation run.

Sterilization is introduced as a critical step in preventing contamination and protecting the integrity of the fermentation run. The user prepares the bioreactor for autoclaving by clamping lines, applying autoclave tape, and documenting mass in batch records before and after adding media. The autoclave process is then explored in depth, including the liquid cycle, steam sterilization, and pressure control. By the end of the chapter, the user understands how proper preparation, documentation, and sterilization work together to create a controlled, contamination-free starting point.

The biosafety cabinet is introduced as a controlled workspace where airflow and technique work together to maintain sterility. Laminar airflow and HEPA filtration, along with proper sash height, establish the sterile environment, while methodical cleaning with IPA reinforces contamination control. The concept of first air is introduced, emphasizing how clean air must reach sterile materials without obstruction. Aseptic technique is developed through defined clean, working, and dirty zones, with strict one-way movement from clean to dirty. Together, these practices build discipline in maintaining a sterile workflow.

Final setup focuses on connecting liquid lines and preparing the bioreactor for controlled operation. The user connects acid, base, and feed lines to peristaltic pumps, then uses the control unit to label pumps, set flow rates, and initiate flow. Media is completed with glucose and additional components using aseptic technique. Calibration of pH and dissolved oxygen probes follows, along with configuration of deadband and cascade control. This chapter builds understanding of how precise inputs and control logic maintain stable fermentation conditions.

Focus shifts to monitoring microbial growth through sampling and analysis. The user collects a sample, labels vials, and records key data in the batch record. In the analytical lab, microscopy is used to observe cell morphology and detect contamination, while spectrophotometry measures optical density to track cell concentration. These techniques connect qualitative observation with quantitative measurement. This chapter builds understanding of how data is used to assess culture health and guide decisions throughout the fermentation run.

The final chapter begins on Day 6 and focuses on ending the fermentation run, disassembling the bioreactor, and analyzing the final product. The user records key values in the batch record, collects a final sample, and shuts down the control unit by stopping pumps, airflow, and agitation. After disassembly, the sample is processed using centrifugation and dimethyl sulfoxide to extract indigoidine from the cells. Spectrophotometry is then used to measure absorbance and determine yield. This chapter builds understanding of how final data connects process performance to measurable outcomes.