11.2: Bioprocess Engineering

Biotech Focus

You can’t ship a pharmacy to Mars. Pills expire, conditions change, and space is limited. As a result, bioprocess engineers, working with NASA, are designing mini, portable “biofactories” that can make critical compounds on demand using engineering microbes. One application being studied today is the use of engineering yeast to produce essential nutrients, like vitamin B12, which degrades quickly in stored food. Enter the bioprocess engineer.....

Bioprocess engineers are now designing a sealed, automated system comprised of a bioreactor that can provide precise control of culture temperature, oxygen levels, and pH, together with the systems needed to harvest and purify the vitamin. The resulting system will be autonomous, requiring no human operator, would work in microgravity and come equipped with fail-safes and sensors that can adapt the system in real-time to environmental changes.T he whole set-up is being designed to be compact enough to run in a space station—or eventually a base on Mars.

Introduction

Bioprocess engineering uses engineering principles to design industrial biotechnology processes at a scale large enough to make products for commercial sale. In simple terms, bioprocess engineering tries to figure out how to use living cells or biological molecules to make things like medicines, vaccines, food products, and eco-friendly materials like bioplastics. While bioprocess engineering is closely related to industrial biotechnology (Table \(\PageIndex{1}\)), it is not the same thing. Industrial biotechnology focuses on uses biological systems like microbes, enzymes, or other biological materials, in order to develop biologic products for commercial use. To learn more about industrial biotechnology, go to Chapter 11.1 Applications of Industrial Biotechnology.

Table \(\PageIndex{1}\): Industrial Biotech vs. Bioprocess Engineering

Industrial Biotechnology	Bioprocess Engineering
Develops biological tools, like cells and enzymes, for creation of a product	Designs systems to use biological tools at scale
Focuses on innovative biological techniques that are sustainable and eco-friendly	Focuses on implementation and optimization of biological techniques
Often starts in the research & development laboratory	Bridges the gap between the laboratory and industry

In contrast, bioprocess engineering focuses on engineering principles in order to make these biologic products at a high-enough quality and quantity that they be sold commercially (Figure \(\PageIndex{1}\)). Bioprocess engineering designs, optimizes, and scales-up the processes used in industrial biotechnology in order to make these products. Like industrial biotechnology, the processes created by bioprocess engineering aim to be be sustainable and eco-friendly.

Figure \(\PageIndex{1}\): Industrial biotechnology and bioprocess engineering. Industrial biotechnology uses bioprocess engineering principles for the design of a manufacturing process (process design), its optimization and then application of this process at a large enough scale for commercial use (scale-up). The end result of bioprocess engineering is a high-quality product. (Industrial Biotechnology and Bioprocess Engineering by Patricia Zuk; CC BY-SA 4.0)

Without bioprocess engineering, the principles and techniques that form the foundation of industrial biotechnology could not be applied at a large enough scale. The ultimate goal of bioprocess engineering is to make biology easier to engineer—more predictable, reliable, and scalable.

Learning Objectives

Bioprocess engineering takes the biological techniques used in biotechnology and scales them up for use in a biomanufacturing plant. At the end of this page, you will be able to:

• Distinguish between industrial biotechnology and bioprocess engineering
• Understand the differences between bioprocess engineering and other "bio"-based terms like bioengineering, biochemical engineering, and biomedical engineering
• Explain some of the key areas used in bioprocess engineering
• Explain biomanufacturing
• Define and explain the upstream and downstream processes used in biomanufacturing
• List some areas critical to upstream processing
• List some downstream processing steps

"Bio" Engineering Terminology

Many words have been used to describe engineers that work with biotechnology. For example, the term bioprocess engineering is often used interchangeably with other terms like biomedical engineering, biochemical engineering, bioengineering, and biomolecular engineering. However, each of these terms are different and distinct and are often misunderstood.

The following is a list of some of the commonly used "bio" engineering fields:

• Bioengineering: a broad title that includes work in medical and agricultural systems
  • applies engineering principles to biological systems for the development of technologies and products
  • practitioners include many types of engineers, including agricultural, electrical, mechanical, industrial, and chemical
• Biological engineering: similar to bioengineering but emphasizes applications to plants and animals
• Biochemical engineering: the extension of chemical engineering principles to biological systems in order to bring about a specific chemical transformation
  • subdivided into bioreaction engineering and bioseparation engineering
• Biomedical engineering: the application of engineering techniques and design concepts to medicine and biology for healthcare purposes, such as diagnosis, treatment, and rehabilitation
• Biomolecular engineering: deals with the interface of biology and chemical engineering with a focus on the molecular level
• Bioprocess engineering: applies engineering principles to processes based on living cells or biological components (e.g. organelles, enzymes)
  • includes the work of mechanical, chemical, and industrial engineers

Key Areas in Bioprocess Engineering

Bioprocess engineering is a highly interdisciplinary field of engineering, combining the principles of chemical engineering, biology, and biotechnology. Key areas of bioprocess engineering include:

• Fermentation Technology: focuses on the use of microbes to convert raw materials into products
  • optimizes the fermentation process, including the design of bioreactors and the control of fermentation at a large scale
• Bioreactor Design: focuses on the design and optimization of bioreactors for efficient cell growth and product formation
  • includes bioreactors for the fermentation of microbes (e.g. bacteria, yeast, fungus) or the growth of plant and animal cells
• Downstream Processing: focuses on the development of methods for separating and purifying products produced from a bioprocess
  • includes the field of bioseparation - the development of methods for separating and purifying biological molecules
• Cell Culture Engineering: focuses on understanding and optimizing cell culture conditions for specific industrial biotechnology applications
• Bioprocess Modeling: uses mathematical models to understand and predict bioprocess behavior
• Biomanufacturing: focuses on the design and implementation of processes for the large-scale production of bioproducts
  • critical for moving the bioprocess from the lab to industrial production

Biomanufacturing

Bioprocess engineering is a key aspect of biomanufacturing. Biomanufacturing facilities use bioprocess engineering principles to commercially produce materials made through synthetic biology (e.g. therapeutics like antibodies, vaccines, biofuels, and food ingredients) at very large scales. The process of biomanufacturing begins with research and development within a laboratory. The lab is responsible for determining the biological system that will be used to make the product and creating the workflow using this system. Once the workflow has been created, bioprocess engineering focuses on how to design and run the process at a large enough scale. A biomanufacturing facility (Figure \(\PageIndex{2}\)) then runs these scaled-up processes.

Figure \(\PageIndex{2}\): A biomanufacturing facility. The biomanufacturing facility in this picture contains numerous large bioreactors connected to one another(Copyright; author via source)

Biomanufacturing involves both upstream and downstream processes (Table \(\PageIndex{2}\)).

"Upstream" is the growth and production phase and refers to the steps involved in growing and preparing the microbes, plant or animal cells that will produce the desired product. Upstream processes happen before the downstream extraction and purification steps. Because of this, the design of the upstream steps can have a significant effect on what takes place downstream.

The following are critical to upstream processes:

1. Cell Line Development
   • the appropriate cells are chosen and/or engineering to make the product
   • cells include prokaryotic (bacteria) or eukaryotic (yeast, plant, animal)
2. Media Preparation & Optimization
   • precise mixtures of nutrients (e.g. amino acids, sugars, vitamins, salts) that are critical for cell growth
   • dependent upon the cell chosen for production
   • compositions are optimized for cell viability, growth, and expression of new genes
3. Bioreactors
   • where cells grow and make the product
   • provide cells with controlled external conditions - temperature, pH, oxygen (i.e., aeration), agitation/mixing
   • designed for fermentation of microbes or culture of plant of animal cells
4. Monitoring & Control Systems
   • sensors and systems track the process in real-time to ensure optimal growth and product formation

"Downstream" in biomanufacturing are the steps that follow production. In general, downstream processes focus on extraction, purification, and packaging of the product. The design of downstream processes are critical to ensuring that the product meets purity, quality, and safety standards.

Depending on the product made and the upstream processes used, downstream steps might include:

1. Cell Harvesting: separates cells from the culture medium using techniques like centrifugation or filtration
2. Cell Disruption/Lysis: produces a cell lysate containing the product; required if the product is located within the cell
3. Filtration: removes large particles or debris from the culture medium or the cell lysate
4. Chromatography: purifies the compound of interest from a mixture
5. Ultrafiltration/Diafiltration: concentrates and purifies the product; used to improve the yield of the product
6. Sterilization: ensures the product is microbe-free
7. Formulation and Testing: designs and prepares the product so that the active ingredient(s) can be delivered in a safe, stable, and effective way; mixes the product with stabilizers, preservatives, etc...; tests for stability
8. Quality Control: ensures product meets all specifications, including formulation and safety
9. Filling and Packaging: transfers the product into the appropriate package for distribution (e.g. vials, syringes, ampules, bottles)

Table \(\PageIndex{2}\) below summarizes the differences between upstream and downstream processing.

Table \(\PageIndex{2}\): Upstream vs. Downstream Processing

	Upstream Processing	Downstream Processing
Definition	First part of the bioprocess. Results in the crude production of a product	Second part of the bioprocess Involves extraction and purification of the product
Major Event(s)	Creation of the product in bioreactors	Harvesting, purification, and formulation of the product
Steps Involved	Selection of microbes or cell line Development of media conditions Growth of cells in bioreactors	Centrifugation, filtration, chromatography, and concentration steps Quality control Formulation Packaging
Challenges	Sterility Optimal cell growth Scalability	Separation techniques Purity standards Quality control

Biomanufacturing facilities must contend with government regulations, production logistics, and quality control. Products that are manufactured for medical or food use must be produced in facilities designed and operated according to Good Manufacturing Practice (GMP) regulations. Cleanrooms, that use sterilization and aseptic techniques, are a key component of both upstream and downstream processes. To read more GMP and quality control, go to Chapter 12.1 Quality Assurance and Quality Control in Biotechnology. To learn more about sterilization and aseptic technique, go to Chapter 6.2 Principles of Aseptic Techniques.

Today, thousands of products, including medicines like cytokines, fusion proteins, growth factors, monoclonal antibodies, and vaccines, are made in biomanufacturing facilities across the world. Numerous food and beverages products like amino acids, enzymes, and proteins supplements are also made. Finally, biomanufacturing has played a key role in industrial biotechnology applications such as bioremediation, and the production of detergents and bioplastics.

Key Concepts

Bioprocessing engineering allows for the production of industrial biotechnology products at a large, commercial scale. Some important points to remember are:

• Bioprocessing engineering bridges the gap between a biological system developed in a research and development lab and the biomanufacturing facility that will make this biological system's product
• Key areas of bioprocess engineering include, fermentation system development, bioreactor design and optimization, and cell culture engineering
• Bioprocess engineering is a field that is distinct from many other similar sounding "bio" engineering fields
• The processes designed by bioprocessing engineering are applied at commercial scales in a biomanufacturing facility
• Biomanufacturing is comprised of upstream and downstream processes

Glossary

Biomanufacturing - the production of biological products, such as vaccines, therapeutic proteins, or enzymes using living cells or organisms in industrial settings

Bioprocess - any process that uses living cells to create a product

Bioprocess engineering - an engineering field that designs and develops the processes that use biologic systems to make a product

Bioreactor - a container or vessel used to grow cells, microorganisms, or tissues under controlled conditions

Downstream - refers to the steps in a bioprocess after the cells have made the desired product

Engineering - the science of designing and building complex processes or machines

Fermentation - a biological process where microbes (like bacteria and yeast) convert sugars into other products like alcohol, gases, or acids

Upstream - refers to all the steps involved in preparing and growing the biological system that will produce the desired product