How To Set Up A Bioreactor


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The first step in setting up a bioreactor is to choose the appropriate type of bioreactor for your application, followed by preparing the culture media. Then sterilization of the bioreactor components is required. After sterilization, the bioreactor is assembled according to the manufacturer’s instructions and the type of bioreactor. Lastly, various parameters such as temperature, pH, dissolved oxygen, and partial pressure of oxygen (pO2) are monitored and controlled.

As the demand for biotechnology products continues to grow, bioreactors have become a crucial tool for the production of biological substances such as enzymes, vaccines, and antibiotics. A bioreactor is a device that provides a controlled environment for the growth of microorganisms or cells. It is also used in various industries such as food processing, pharmaceuticals, and environmental monitoring. 

In this article, we guide you through what a bioreactor is, its components, and the steps involved in setting up and operating a bioreactor.

What Is A Bioreactor?

A bioreactor is a device that supports the growth of microorganisms or cells by providing a controlled environment for their growth. Bioreactors can be classified based on their design, size, and mode of operation. The most common types of bioreactors are batch, fed-batch, and continuous bioreactors.

Setting up a bioreactor may seem like a daunting task, but it is actually quite simple with the right tools and knowledge.

Bioreactor Components And Their Function

A bioreactor consists of several components, each with its particular function. The vessel is the main component of the bioreactor and is where the microorganisms or cells are grown. The agitator is used to mix the contents of the vessel, ensuring that the microorganisms or cells are evenly distributed. Sensors are used to monitor the temperature, pH, and dissolved oxygen levels of the system.

Other components of the bioreactor include the sparger, which is used to introduce air or other gases into the system, and the controller, which is used to regulate the various parameters of the system.

Bioreactor Installation Processes

Setting up a bioreactor involves the following steps:

  • Preparing the culture vessel
  • Installing and calibrating bioreactor sensors
  • Autoclaving
  • Adding media to prepare the bioreactor for cultivation
  • Inoculation
  • Bioprocess control 
  • Decontamination and cleaning 

Preparing The Culture Vessel

Before you think about setting up the bioreactor, you need to check that the culture vessel is undamaged. This includes thoroughly checking all the O-rings, and that the vessel seal is in the correct position and intact. Failing to check these parts of the culture vessel could lead to contamination after the autoclaving process, which would affect the whole bioreactor process.

You also want to check that you have followed the instructions correctly to install, connect, and secure all of the sensors, gas inputs, ports, and corrective reagents before you proceed to cell harvesting or sampling. Once you have autoclaved the bioreactor, any changes that you make must be performed using a sterile cabinet. 

Below we have some steps and tips to help you prepare the culture vessel:

  • You want to check the impeller’s installation height and check they are firmly fastened to the bioreactor’s drive shaft. 
  • Avoid fitting the impeller at the same level as the medium surface, as this can cause unnecessary foam formation. 
  • Check if the planned process requires baffles, if so insert them following the manufacturer’s guidelines. 
  • Inspect that the O-rings on the top plate are not damaged and that they are in the correct position. 
  • Check the rest of the components are properly installed on the top plate. 
  • Ensure the installation height of all adjustable-height fittings is in the recommended position. These include dip tubes, sensors, and impeller shafts.
  • Check that the sparger is immediately below the bioreactor’s drive shaft.
  • If required, fill the bioreactor vessel with heat-stable water or culture medium. This allows steam development and it sterilizes the vessel. 
  • Carefully secure and align the top plate. You want to check that the installed parts and baffles are not in contact with each other. 
  • Finally, do not use a tool to tighten knurled screws. This can be done by hand. 

Installing & Calibrating

Once the mechanical components of the bioreactor are set up and the top plate is secured, the sensor ports will be open. This is because they are usually installed last, as they are prone to mechanical damage. You also need to calibrate the sensors before the bioreactor process. 

As laboratories usually have standard instructions, when calibrating the sensors check the guidelines as these can differ between manufacturers. 

Usually, pH sensor calibration before autoclaving and installation is the same as a ‘typical’ pH meter in that two reference buffers ( pH 4.0 and pH 7.0) are used. 

One important note is the pO2 and turbidity sensors. As oxygen and turbidity are dependent on operating conditions, you must not calibrate these sensors until after autoclaving and dispensing the culture medium. 


Autoclaving is a fairly straightforward process, however, the steps are very important. 

The first is to get the adjustment agent bottles ready. For corrective agents, such as ammonia, that cannot be sterilized in the autoclave, fill with water. If you use water or a substrate that is prone to caramelizing, after autoclaving, replace the water/substrate with a filter-sterilized corrective agent. 

Next, loosen the pump head’s mounting platform from the base unit and connect it to the bioreactor vessel holder. While ensuring all the connections, attach the tubing from the reagent bottles to the pump heads. From there, connect them to the feeding needles on the lid. Most bioreactors come with a Super Safe Sampler, which allows you to take very small samples without wasting any culture in the vessel. You will need to connect it to the sampling pipe, followed by clamping it off and covering it with aluminum foil.

If you haven’t done so already, connect the air filter(s) and any additional tubes. Lightly cover the filter using aluminum foil. Ensure you do not clamp the exhaust filter off; check that it is open. Failure to do so can cause issues in balancing the pressure during autoclaving. When autoclaving the prepared culture vessel, follow the operating procedure. This is typically 249.8°F for 20-30 minutes for most bench-top bioreactors. 

Adding Media

We are almost ready for the bioprocess, but before you go ahead, you need to connect the culture vessel to the base unit. You may want to fill it with a culture medium and do a final sensor calibration. 

To connect the culture vessel to the base unit, position the culture vessel holder. Some bioreactors will also need the temperature control tubing connected or a heating mat installed. Always follow the manual instructors for the type of bioreactor you are using.

Next, secure the pump head mounting plate to the pump motor shafts (peristaltic pump). Carefully fill the corrective reagent tubes, as filling the tubes with the wrong agent can cause a malfunction in the control unit. Connect the pH, turbidity, pO2, and foam sensors. Note, that when inserting the temperature sensor, push it down into the thermo-well until there is metal-to-metal contact. 

Once the motor is mounted, connect the gas lines, including the exit gas cooler line. If the culture medium is not autoclaved inside the vessel, dispense it following a sterile filling process. 

Finally, start up the bioreactor. Switch on the stirrer and temperature control to the correct target value. When the desired target is reached, sometimes the pH sensor or the culture’s pH needs re-adjusting. You may also need to calibrate the pO2 sensor and turbidity sensor. 


If you have followed the steps above, you are now ready for inoculation! 

Depending on the bioprocess you are working on, the exact procedure can differ, however, we have outlined the most common steps to adding microorganisms/cells to your bioreactor.

As standard practice, you need to first run a blank culture medium sample for a maximum of 24 hours to allow the vessel to equilibrate. Next is the important part, preparing the inoculum and placing it in a vessel for inoculation. 

Microbial Bioprocesses

Using a needled syringe, pierce the cell’s membrane to introduce the cells to the culture medium. 

Note: Even if you were to disinfect the membrane with alcohol or work close to a flame, there is never a 100% guarantee against contaminated samples.

Cell Culture Preparations

Cell cultures are more prone to contamination than microbial bioprocesses because of the nutrient media used. Another contrasting factor is that inoculum is introduced using a sterile tubing connection in a sterile lab cabinet. In some cases, the tubing can be created using a tube welding machine. 

To finish the inoculation process, press the button (or SCADA (Supervisory Control and Data Acquisition) software) to signal that inoculation has been completed so that it can start the bioprocess. 

Bioprocess Control

Throughout the setup of a bioreactor, bioprocess control is extremely important. Before you set up a bioreactor you need to have some knowledge about culture and cell growth so you can correctly complete the bioprocess.

When an essential factor in the bioprocess becomes limited, the growth of the microorganisms becomes limited. By selecting the correct process strategy, you should be able to optimize the bioprocess, maximize the product, and be more time efficient. 

Decontamination & Cleaning

Once the bioprocess has been completed, you need to decontaminate and clean the bioreactor to prepare it for the next cultivation. 

The protocols for killing organisms can differ depending on the environment or institution you are working in. Yet, the most common decontamination method is to autoclave the culture vessel and properly dispose of the culture broth. 

After that, a complex cleaning process is carried out on the peripheral equipment and the bioreactor vessel itself. Any peripherals that came into contact with any organisms must be thoroughly decontaminated and cleaned. 

The Importance Of Bioreactor Sterilization And Cleaning

Sterilization is an essential step in the operation of a bioreactor. It is done to ensure that the bioreactor is free of any microorganisms that could contaminate the production process. Sterilization can be achieved using various methods such as heat, chemicals, or radiation.

Cleaning is also an important step in the operation of a bioreactor. It is done to remove any residual material or debris that may have accumulated in the system. Cleaning can be achieved using various methods such as hot water, detergents, or disinfectants.

Bioreactor Operation And Monitoring

The operation of a bioreactor involves the growth of microorganisms or cells in a controlled environment. The growth process is monitored using various sensors that measure the temperature, pH, and dissolved oxygen levels of the system. The data collected by the sensors is used to adjust the various parameters of the system.

Monitoring the bioreactor is essential to ensure that the production process runs smoothly and that the product meets the required specifications. Monitoring can be done manually or automatically using a computer system such as SCADA. 

Common Bioreactor Issues

As we have covered a lot in this article, one of the most prevalent bioreactor issues is contamination. Microbial contamination can significantly impact the yield and purity of the product, leading to substantial economic losses. Contaminants can enter the bioreactor through various sources, such as contaminated raw materials, unsterilized equipment, or even through the air. To prevent contamination, bioreactors must be adequately sterilized before use, and proper aseptic techniques (such as working in an autoclave or near a flame in a controlled laboratory environment) must be followed during operation.

Another issue that bioreactors face is foaming. Foaming occurs due to the accumulation of surface-active agents in the culture medium, resulting in the formation of bubbles that can adversely affect cell growth and product quality. To deal with foaming, anti-foaming agents can be added to the culture medium, or mechanical foam control devices can be installed in the bioreactor.

Temperature control is crucial for maintaining optimal cell growth and product yield in a bioreactor. However, temperature fluctuations can occur due to inadequate heat transfer or cooling capacity, leading to a decrease in cell viability and productivity. To tackle this issue, proper monitoring and control of temperature parameters must be implemented.

Lastly, one significant concern for large-scale bioreactors is shear stress. Shear stress results from the agitation of the culture medium during mixing, which can damage and disrupt fragile cells and tissues. Reducing shear stress can be achieved by optimizing impeller speed and design or using alternative mixing strategies such as air-lift reactors.

Bioreactor Applications

One of the most significant bioreactor applications is in the production of biofuels. Biofuels have been gaining popularity among researchers and policymakers as a viable alternative to traditional fossil fuels.

Bioreactors play a key role in the production of biofuels, providing a controlled environment for the microorganisms involved in the process. Bioreactors are used in both first-generation biofuels, which are typically derived from food crops such as corn, and second-generation biofuels, which are produced from non-food sources such as waste biomass or algae.

Apart from biofuel production, bioreactors have several other applications. Bioreactors are extensively used in the pharmaceutical industry. The bioreactor provides a sterile environment for the growth of cells necessary for the production of vaccines and drugs. Bioreactors also find extensive applications in tissue engineering, where they are used to grow cells and tissues for various medical applications.


Bioreactors are a crucial tool for the production of biological substances such as enzymes, vaccines, and antibiotics. Setting up a bioreactor may seem like a complex process, but it can be broken down into simple steps. Choosing the appropriate type of bioreactor, preparing the culture media, sterilizing the bioreactor and components, assembling and setting up the bioreactor, and monitoring and controlling various parameters are key steps in the process.

With proper planning and execution, you can set up a bioreactor and produce high-quality products in a controlled environment.
If you need assistance with setting up your bioreactor, do not hesitate to contact the world-class team at Atlas Scientific.

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