Industrial Microbiology

Industrial Microorganisms

There are various types of microorganisms that are used for large-scale production of industrial items.

Learning Objectives

Describe how microorganisms are used in industry to manufacture food or products in large quantities

Key Takeaways

Key Points

  • The ability of specific microorganisms to produce specialized enzymes and proteins has been exploited for many purposes in industry.
  • Industrial microorganisms are used to produce many things, including food, cosmetics, pharmaceuticals and construction materials.
  • Microorganisms can be genetically modified or engineered to aid in large-scale production.

Key Terms

  • exopolysaccharide: a type of sugar-composed polymer secreted by a microorganism into the external environment
  • archaea: a taxonomic domain of single-celled organisms lacking nuclei that are fundamentally from bacteria.

Industrial microbiology includes the use of microorganisms to manufacture food or industrial products in large quantities. Numerous microorganisms are used within industrial microbiology; these include naturally occurring organisms, laboratory selected mutants, or even genetically modified organisms (GMOs). Currently, the debate in the use of genetically modified organisms (GMOs) in food sources is gaining both momentum, with more and more supporters on both sides. However, the use of microorganisms at an industrial level is deeply rooted into today’s society. The following is a brief overview of the various microorganisms that have industrial uses, and of the roles they play.

Archaea are specific types of prokaryotic microbes that exhibit the ability to sustain populations in unusual and typically harsh environments. Those suriving in the most hostile and extreme settings are known as extremophile archaea. The isolation and identification of various types of Archaea, particularly the extremophile archaea, have allowed for analysis of their metabolic processes, which have then been manipulated and utilized for industrial purposes.

Extremophile archaea species are of particular interest due to the enzymes and molecules they produce that allow them to sustain life in extreme climates, including very high or low temperatures, extremely acid or base solutions, or when exposed to other harmful factors, including radiation. Specific enzymes which have been isolated and used for industrial purposes include thermostable DNA polymerases from the Pyrococcus furiosus. This type of polymerase isa common tool in molecular biology; it is capable of withstanding the high temperatures that are necessary to complete polymerase chain reactions. Additional enzymes isolated from Pyrococcus speciesinclude specific types of amylases and galactosidases which allow food processing to occur at high temperatrues as well.

Corynebacteria are characterized by their diverse origins. They are found in numerous ecological niches and are most often used in industry for the mass production of amino acids and nutritional factors. In particular, the amino acids produced by Corynebacterium glutamicum include the amino acid glutamic acid. Glutamic acid is used as a common additive in food production, where it is known as monosodium glutamate (MSG). Corynebacterium can also be used in steroid conversion and in the degradation of hydrocarbons. Steroid conversion is an important process in the development of pharmaceuticals. Degradation of hydrocarbons is key in the breakdown and elimination of environmental toxins. Items such as plastics and oils are hydrocarbons; the use of microorganisms which exhibit the ability to breakdown these compounds is critical for environmental protection.


Corynebacterium: Corynebacterium species are often used to mass produce amino acids utilized in food processing.

Xanthomonas, a type of Proteobacteria, is known for its ability to cause disease in plants. The bacterial species which are classified under Xanthomonas exhibit the ability to produce the acidic exopolysaccharide commonly marketed as xanthan gum, used as a thickening and stabilizing agent in foods and in cosmetic ingredients to prevent separation.

Another type of microorganism utilized by industry includes various species of Aspergillus. Thisgenusincludes several hundred types of mold. Aspergillus has become a key component in industrial microbiology, where it is used in the production of alcoholic beverages and pharmaceutical development. Aspergillus niger is most commonly used to produce citric acid, which is used in numerous products ranging from household cleaners, pharmaceuticals, foods, cosmetics, photography and construction. Aspergillus is also commonly used in large-scale fermentation in the production of alcoholic beverages such as Japanese sake.

Molecular Products from Microbes

The isolation of molecular products from microbes is considered to be a key component of molecular biology research.

Learning Objectives

Describe how Taq polymerase, restriction enzymes and DNA ligase are used in molecular biology

Key Takeaways

Key Points

  • Various enzymes can be isolated from microorganisms and utilized in recombinant – DNA production.
  • The ability of some archaea to thrive in extreme environments has led to analysis and isolation of important molecular components of the organisms, such as Taq polymerase, that have contributed to modern molecular biology techniques.
  • Modern-day molecular biology techniques rely heavily on specific enzymes and molecular components derived from microbes, including DNA ligase and restriction enzymes.
  • DNA ligase functions by covalently linking, or ligating, DNA fragments.
  • Restriction enzymes function by recognizing and cutting specific sequences within DNA.

Key Terms

  • polymerase chain reaction: A technique in molecular biology for creating multiple copies of DNA from a sample; used in genetic fingerprinting etc.
  • restriction enzymes: an endonuclease that cuts DNA at specific recognition sequences

The expansion and growing popularity of the field of molecular biology has resulted in a higher demand for tools used to study molecular biology. The field of molecular biology specifically deals with the molecular mechanisms of a cell and focuses on the regulation of cellular interactions. Topics of particular interest within the field include gene expression (transcription and translation) and protein synthesis. Studying these mechanisms in the laboratory has been made possible by the use of molecules derived from microbes. The following is a brief overview of some of the molecular products derived from microbes that allow for the performance of popular molecular biology techniques.

Taq Polymerase

Taq polymerase is an enzyme that was first isolated from the microbe Thermus aquaticus. T. aquaticus is a specific type of bacterial species, a DNA polymerase, that is thermostable — it can withstand extremely high temperatures. The isolation of this polymerase has resulted in the ability to perform polymerase chain reactions (PCR), a process used to amplify DNA segments, in a single step. Prior to the isolation of Taq polymerase, a new DNA polymerase had to be added to the reaction after every cycle because of thermal denaturation. With the addition of Taq polymerase to the reaction tube, the cycle can be performed much more quickly, and less enzyme needs to be used. Currently, Taq polymerase is manufactured and produced on a large scale and is available for commercial sale.

Restriction Enzymes

Restriction enzymes are a specific class of enzymes isolated from various bacteria and archaea, in which they grow naturally as a means of protection against viral infection. These enzymes have the ability to cut DNA at specific recognition sequences and have served as invaluable tools in DNA modification and manipulation. The enzymes have the ability to recognize foreign DNA and cut it up. The bacteria and archaea from which these enzymes are isolated from have innate mechanisms to protect their own DNA sequences from these enzymes, such as methylation. The isolation of approximately 3000 restriction enzymes has allowed molecular biologists to utilize them in processes such as cloning and the production of recombinant DNA.


EcoRI Restriction Enzyme: An example of a specific restriction enzyme, EcoRI, which exhibits the ability to target specific sequences within DNA.

DNA Ligase

Another enzyme that was isolated from T. aquaticus and that has been undeniably important to the field of molecular biology is DNA ligase. DNA ligase plays a key role in molecular biology processes due to its ability to insert DNA fragments into plasmids. The process of DNA ligation is defined as the ability of DNA ligase to covalently link, or ligate, fragments of DNA together. In molecular biology — specifically, during the process of developing recombinant DNA — DNA ligase can be used to ligate a fragment of DNA into a plasmid vector. The most commonly used DNA ligase is derived from the T4 bacteriophage and is referred to as T4 DNA ligase.


Example of a DNA Ligation: Diagram of a DNA ligation.

Primary and Secondary Metabolites

Primary and secondary metabolites are often used in industrial microbiology for the production of food, amino acids, and antibiotics.

Learning Objectives

Describe how primary and secondary metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals for organic synthesis

Key Takeaways

Key Points

  • Primary metabolites are considered essential to microorganisms for proper growth.
  • Secondary metabolites do not play a role in growth, development, and reproduction, and are formed during the end or near the stationary phase of growth.
  • These metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals necessary for organic synthesis.

Key Terms

  • bradycardia: the slowing of the heartbeat to below average

Bacterial metabolism can be classified into three major categories: the kind of energy used for growth, the carbon source, and the electron donors used for growth. Pathogenic bacteria are capable of exhibiting various types of metabolism. Metabolites, the intermediates and products of metabolism, are typically characterized by small molecules with various functions. Metabolites can be categorized into both primary and secondary metabolites. These metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals necessary for organic synthesis.

Primary Metabolites

Primary metabolites are involved in growth, development, and reproduction of the organism. The primary metabolite is typically a key component in maintaining normal physiological processes; thus, it is often referred to as a central metabolite. Primary metabolites are typically formed during the growth phase as a result of energy metabolism, and are deemed essential for proper growth. Examples of primary metabolites include alcohols such as ethanol, lactic acid, and certain amino acids. Within the field of industrial microbiology, alcohol is one of the most common primary metabolites used for large-scale production. Specifically, alcohol is used for processes involving fermentation which produce products like beer and wine. Additionally, primary metabolites such as amino acids– including L-glutamate and L-lysine, which are commonly used as supplements– are isolated via the mass production of a specific bacterial species, Corynebacteria glutamicum. Another example of a primary metabolite commonly used in industrial microbiology includes citric acid. Citric acid, produced by Aspergillus niger, is one of the most widely used ingredients in food production. It is commonly used in pharmaceutical and cosmetic industries as well.


Aspergillus niger: Microorganisms such as Aspergillus niger are used in industrial microbiology for mass production of citric acid.

Secondary Metabolites

Secondary metabolites are typically organic compounds produced through the modification of primary metabolite synthases. Secondary metabolites do not play a role in growth, development, and reproduction like primary metabolites do, and are typically formed during the end or near the stationary phase of growth. Many of the identified secondary metabolites have a role in ecological function, including defense mechanism(s), by serving as antibiotics and by producing pigments. Examples of secondary metabolites with importance in industrial microbiology include atropine and antibiotics such as erythromycin and bacitracin. Atropine, derived from various plants, is a secondary metabolite with important use in the clinic. Atropine is a competitive antagonist for acetycholine receptors, specifically those of the muscarinic type, which can be used in the treatment of bradycardia. Antibiotics such as erythromcyin and bacitracin are also considered to be secondary metabolites. Erythromycin, derived from Saccharopolyspora erythraea, is a commonly used antibiotic with a wide antimicrobial spectrum. It is mass produced and commonly administered orally. Lastly, another example of an antibiotic which is classified as a secondary metabolite is bacitracin. Bacitracin, derived from organisms classified under Bacillus subtilis, is an antibiotic commonly used a topical drug. Bacitracin is synthesized in nature as a nonribosomal peptide synthetase that can synthesize peptides; however, it is used in the clinic as an antibiotic.


Erythromycin tablets: Erythromycin is an example of a secondary metabolite used as an antibiotic and mass produced within industrial microbiology.

Large-Scale Fermentations

Large-scale fermentations are key to the production of numerous products ranging from food to pharmaceutical items.

Learning Objectives

Describe fermentation and its applications to produce food, alcoholic beverages, fuel and recombinant products such as insulin

Key Takeaways

Key Points

  • Large-scale fermentations are utilized to create massive quantities of ethanol which are used for food production, alcohol production, and even gasoline production.
  • Fermentation is characterized by the metabolic processes that are used to transfer electrons released from nutrients to molecules obtained from the breakdown of those same nutrients.
  • Fermentation utilizes numerous organic compounds, such as sugars, as endogenous electron acceptors to promote the electron transfer that occurs.

Key Terms

  • oxidation: A reaction in which the atoms of an element lose electrons and the valence of the element increases.
  • amylase: A type of digestive enzyme capable of breaking down complex carbohydrates into simple sugars.

Fermentation includes the processes by which energy is extracted from the oxidation of organic compounds. The oxidation of organic compounds occurs by utilizing an endogenous electron acceptor to transfer electrons released from nutrients to molecules obtained from the breakdown of these same nutrients.


Common types of fermentation: These are common types of fermentation utilized in eukaryotic cells.

There are various types of fermentation which occur at the industrial level such as ethanol fermentation and fermentation processes used to produce food and wine. The ability to utilize the fermentation process in anaerobic conditions is critical to organisms which demand ATP production by glycolysis. Fermentation can be carried out in aerobic conditions as well, as in the case of yeast cells which prefer fermentation to oxidative phosphorylation. The following is a brief overview of a few types of the large-scale fermentations utilized by industries in production creation.

Ethanol Fermentation

Ethanol fermentation is used to produce ethanol for use in food, alcoholic beverages, and both fuel and industry. The process of ethanol fermentation occurs when sugars are converted into cellular energy. The sugars which are most often used include glucose, fructose, and sucrose. These sugars are converted into cellular energy and produce both ethanol and carbon dioxide as waste products. Yeast is the most commonly used organism to produce ethanol via the fermentation process for beer, wine, and alcoholic drink production. As stated previously, despite abundant amounts of oxygen which may be present, yeast prefer to utilize fermentation. Hence, the use of yeast on a large-scale to produce ethanol and carbon dioxide occurs in an anaerobic environment.

The ethanol which is produced can then be used in bread production. Yeast will convert the sugars present in the dough to cellular energy and produce both ethanol and carbon dioxide in the process. The ethanol will evaporate and the carbon dioxide will expand the dough. In regards to alcohol production, yeast will induce fermentation and produce ethanol. Specifically, in wine-making, the yeast will convert the sugars present in the grapes. In beer and additional alcohol such as vodka or whiskey, the yeast will convert the sugars produced as a result of the conversion of grain starches to sugar by amylase. Additionally, yeast fermentation is utilized to mass produce ethanol which is added to gasoline. The major source of sugar utilized for ethanol production in the US is currently corn; however, crops such as sugarcane or sugar beets can be used as well.


Fermentation in grapes: This is a photograph of grapes undergoing fermentation during the wine-making process.

Recombinant Products

Fermentation is also utilized in the mass production of various recombinant products. These recombinant products include numerous pharmaceuticals such as insulin and hepatitis B vaccine. Insulin, produced by the pancreas, serves as a central regulator of carbohydrate and fat metabolism and is responsible for the regulation of glucose levels in the blood. Insulin is used medically to treat individuals diagnosed with diabetes mellitus. Specifically, individuals with type 1 diabetes are unable to produce insulin and those with type 2 diabetes often develop insulin resistance where the hormone is no longer effective.

The increase in individuals diagnosed with diabetes mellitus has resulted in an increase in demand for external insulin. The mass production of insulin is performed by utilizing both recombinant DNA technology and fermentation processes. E. coli, which has been genetically altered to produce proinsulin, is grown to a large amount to produce sufficient amounts in a fermentation broth. The proinsulin is then isolated via disruption of the cell and purified. There is further enzymatic reactions that occur to then convert the proinsulin to crude insulin which can be further altered for use as a medicinal compound.

An additional recombinant product that utilizes the fermentation process to be produced is the hepatitis B vaccine. The hepatitis B vaccine is developed to specifically target the hepatitis B virus infection. The creation of this vaccine utilizes both recombinant DNA technology and fermentation. A gene, HBV, which is specific for hepatitis B virus, is inserted into the genome of the organism yeast. The yeast is used to grow the HBV gene in large amounts and then harvested and purified. The process of fermentation is utilized to grow the yeast, thus promoting the production of large amounts of the HBV protein which was genetically added to the genome.