Industrial Microbiology


Written by MicroDok



Moulds are filamentous fungi. They are known as filamentous fungi because they have hyphae which are long branching filaments of fungi. Moulds are multicellular fungi that are non photosynthetic in nature. Unlike yeasts that are single celled or unicellular moulds have  multiple cells and thus are known as multicellular fungi. Moulds grow as filamentous branching strands of hyphae. Hyphae is a long branching structure (filament) of some fungi (i.e. moulds).  Moulds grow by the expansion of their interconnected hyphae, and water is important in their growth. Moulds are common contaminants of household appliances, furniture and food. They are generally saprophytic in nature and thus derive their energy and nutrient from thus organic matter on which they live or are growing.

Some common moulds genera include:

  1. Acremonium
  2. Rhizopus
  3. Fusarium
  4. Penicillium
  5. Mucor
  6. Aspergillus
  7. Cladosporium
  8. Trichophyton

Moulds grow on dead organic matter and they can become visible to the naked eyes especially when they form large colonies. They thrive at various temperature conditions and can even survive some harsh conditions in the environment.

Importance of moulds

  1. They cause disease in humans and animals.
  2. Moulds secrete hydrolytic enzymes that can degrade high molecular weight materials or biopolymers such as starch, lignin and cellulose into simpler substances.
  3. They play important roles in the production of various foods and beverages.
  4. Moulds are important in the production of some antibiotics such as penicillin sourced from Penicillium chrysogenum.
  5. Moulds are important are spoilage of food and raw materials for food production.
  6. Moulds are important in most fermentation process involved in wine production, food and other beverages.
  7. Moulds reproduce by both sexual and asexual reproduction methods; and their reproductive parts or structures are spores: mould produce their spores in large numbers; and these spores are readily spread by air. Spores that fall or settle on favourable substrates can initiate a new phase of growth and develop into a new mycelium. A mycelium is a mass of branching intertwined or connected filaments. The whole mass of the hyphae formed by moulds is known as mycelium (pleural : mycelia)
  8. Citric acid for soft drink production and some enzymes for bread making are from moulds.

The use of moulds in food industries is however limited unlike yeasts that have a wider application. Most moulds despite their importance in fermentation are mainly concerned in the spoilage of foods.


Yeasts are the single celled growth forms of most fungi. Yeasts are unicellular fungi. They are heterotrophic organisms that require organic carbon as its common source. Most yeasts are facultative e anaerobes and are able to grow even in the absence of oxygen. Many yeasts especially Saccharomyces cerevisiae are important industrial micro organisms because of the important roles that they play in the production of foods and other product s of economic importance. Most yeasts exhibit dimorphism a phenomenon in which a yeast cell exhibit two growth forms i.e. the yeast form and the filamentous (mould) form. Only few yeasts such as Cryptococcus neoformans (which causes a rare form of meningitis) and Candida albicans are animal/ human pathogens

Saccharomyces cerevisiae: S. cerevisiae is a species of yeast that is also called the bakers yeast. It is one of the most useful yeast because it has been used in baking and brewing since ancient times. S. cerevisiae cells are usually round to oval in shape, and they measure about 5-10 um in diameter. Scerevisiae reproduce asexually by a process known as budding in which daughter cells are produced as off shorts of a parent cell by bud development. Yeasts can also reproduce sexually, and this usually involves two mating haploid yeast cells. Yeasts are common in the environment and are isolated from sugar rich materials. Brewer’s yeast, aye yeast, top fermenting yeast baker’s yeast and budding yeast are other names that S. cerevisiae is known for. S. cerevisiae can grow aerobically on simple carbohydrate sources such as glucose, and maltose. They use ammonia and urea as their sole nitrogen source. Yeasts also require phosphorous and some minerals for their optimal. S. cerevisiae has a short generation (doubling) time which is about 1-2 hours, and they can be easily cultured. These characteristics accounts for their use and preference as the major source of nutritional yeast and yeast extract for most of the fermentation processes in the industry. S. cerevisiae has a small size; they can be easily manipulated or transformed in the lab; they have a short generation time; they can be easily accessed or cultured; their growth requirement can easily be obtained; and S. cerevisiae has tremendous economic benefits, which is why they are they are the most preferred yeast for fermentation processes.


  1. They are used in brewing beer.
  2. They are used in baking bread.
  3. Yeasts are used in wine fermentation.
  4. They are used for the industrial production of ethanol and other industrial fuels.
  5. Yeasts such as boulardii are used in the production of probiotics used to maintain the health of the gastrointestinal tract.
  6. Yeasts convert sugars to carbon dioxide (CO2) and ethanol; and can be used to generate CO2 to nourish plants in aquariums.
  7. Yeasts also cause food spoilage.


Bacteria are prokaryotic cells. They are single celled microorganisms that are ubiquitous in nature. Morphologically, bacteria measure between 0.5 to10 in diameter. Bacteria exist in three different shapes. Some are cocci (spherical), rod-shaped (bacilli) or spiral in shape. Bacteria are of economic importance because they cause disease in plants, animals and humans. They are also employed in various industrial processes for the production of goods/products that are of significance to man, animals and the environment. Their mode of nutrition is simple and they can derive their energy and carbon from organic and inorganic materials in their environment. They grow in the presence of oxygen (aerobic bacteria) or in the absence of it (anaerobic bacteria). Some bacteria are facultative organisms since they can thrive either in the presence or absence of oxygen. Bacteria reproduce by binary fission, in which a bacteria cell wall divides into two cells. Bacteria have a simple cell structure and they lack a membrane bound organelles since they are prokaryotic cells. Bacteria can also exist as single cells in pairs (diplococcic), in chains or in clusters. Comma shaped bacteria (e.g. Vibrio cholerae) and bacteria with corkscrew shape (spirochetes) also exist. Bacteria have extrachromosomal genetic elements known as plasmids; and these plasmids are different from the chromosome or DNA of the organism. Bacteria also cause food spoilage and some infectious diseases.

Based on the product of their fermentation, bacteria can be classified as:

  1. Lactic acids bacteria- they produce lactic acid from fermentative reactions.
  2. Acetic acid bacteria- production of acetic acid
  3. Propionic acid bacteria.
  4. Some bacteria break down protein and may be called proteolytic bacteria. Those that break down lipids are called lipolytic bacteria while those that breakdown sugars are called saccharolytic bacteria.

Streptococcus, lactobacillus, and bacillus produce lactic acid.

Escherichia coli produce ethanol and acetic acid including CO2 and hydrogen.

Vinegar, wine and beer are some foods and beverages in which the fermentative actions of bacteria are applied in their production.


  1. Bacteria produce enzymes that drive fermentation.
  2. They are important for the production of proteins.
  3. Bacteria are important for the production of amino acids and vitamins.
  4. They take part in the production of acetic acid.
  5. Bacteria produce lactic acid
  6. They produce antibiotics.

Bacteria of industrial importance are found in the genus Bacillus, Streptomyces, Lactobacillus, Clostridium, Escherichia, Leuconostoc, Acetobacter, and Azotobacter and Xanthomonas amongst others.


Actinomycetes are fungi-like bacteria. They are widespread in nature, and can be found in the soil, water and in compost. Actinomycetes form branching hyphae or mycelium (which is typical of fungi), and this is why they are often called fungi-like bacteria. Actinomycetes are chemoorganotrophic organisms that derive their carbon from organic molecules or substrates. They degrade chitin, agar cellulose, paraffin, rubber and keratin. Actinomycetes also produce antibiotics. Actinomycetes are gram positive bacteria, and they are spore forming bacteria. The bacteria genera in the group of organisms known as actinomycetes includes: Nocardia, Actinomycetes, Corynebacteria, Streptomyces and Micromonospora. Not all members of actinomycetes are known to produce mycelium. Actinomycetes are filamentous bacteria because they form mycelium. Actinomycetes are aerobic bacteria that produce asexual spores. Actinomycetes have mycelia morphology (that makes them have similar resemblance to fungi); and majority of bacteria in this group of actinomycetes are known for their antibiotic production, especially those in the genus Streptomyces.


  1. Actinomycetes are well recognized because they produce primary and secondary metabolites that are of economic significance.
  2. Actinomycetes produce enzymes such as lipase, cellulases and amylase which are used in fermentation processes.
  3. They produce some valuable antibiotics including, amphotericin, neomycin, vancomycin, gentamicin, tetracycline, erythromycin, nystatin, novobiocin and chloramphenicol.
  4. Actinomycetes are also used as plant growth promoting agents.
  5. They produce biopesticide agents used to control pests in farmlands.
  6. Actinomycetes also have application in bioremediation.
  7. Actinomycetes produce protease enzyme which is used as anti-inflammation agents and also in cancer treatment.
  8. Actinomycetes produce enzymes that have application in wine production.


Viruses are non-cellular microorganisms that consist of nucleic acid (DNA or RNA) and proteins. They can only replicate within a living cell, including cells of animals, plants and bacteria. A virus contains either an RNA or a DNA as its genome. No viruses contain both DNA and RNA as its genome. The size of viruses ranges from 0.015 µm to 0.2 µm and they can only be seen under an electron microscope. Viruses are lacking in cellular components necessary for their independent reproduction or metabolism. And this is why viruses replicate or multiply inside a living cell. Outside a living cell they remain dormant and inactive. Viruses cause diseases in man plants and animals. A virion is defined as an individual virus particle. Because a virion contain only one type of nucleic acid as its genome (DNA or RNA), viruses can be classified into two classes based on their nucleic acid genome. Thus, they are DNA viruses (whose genome is only made of DNA) and RNA viruses (that only contains RNA as its genome).

Viruses are not cells and they do not contain organelles. Viruses are not cultured in the artificial media like the prokaryotic and eukaryotic cells. They are cultured in living cells such as in embryonated egg cell or in cell cultures containing cell lines of living cells extracted from plants animals or humans.


  1. Viruses cause disease in plants animals and man.
  2. They are employed in the production of vaccines.
  3. Viruses are sources of important enzymes such as reverse transcriptase used in molecular biology or biotechnology
  4. Viruses can act as gene vectors for the useful production of useful proteins.


Fermentation is defined as a metabolic process that converts sugars (substrates) to alcohol, acids and gases (e.g. CO2). It can occur both I n the presence of oxygen and in the absence of oxygen. But most fermentation processes occur in the absence of oxygen. Several definitions exist for fermentation. Fermentation occur when organisms including moulds, bacteria actinomycetes and yeasts consume organic substrate molecules as part of their own metabolic processes; and thus produce metabolites of substances that are of economic importance in the process. When spoilage microbes grow in food they cause spoilage and food borne diseases when such food is consumed. However some fermentation processes are highly desirable since they lead to the production of important molecules like alcohol, acids and gases; and microbial by-products are significant in food production.

Yoghurt, cheese, sauerkraut are some examples of food produced via fermentation spurred by microbial activity. Wine and beer are beverages produced by fermentative action of microbe.


  1. Fermented foods can be more nutritious and tasty than unfermented foods.
  2. Fermentation foods products (such as acids and alcohols) that inhibit the overgrowth of spoilage and pathogenic microbes in the food.
  3. Fermentation produced industrially useful end-products such as organic acids, alcohols, aldehydes and ketones.
  4. Fermentation processes leads to the production of important biological molecules including vitamins and antibiotics.
  5. Fermentation leads to the production of products with enhances activity and value.


Microorganisms including bacteria, fungi and actinomycetes are important in fermentation processes because of the metabolites that they produce during and after their growth or development. The production of beer, antibiotics, wine, some beverages, food and pharmaceutical products go through the process of fermentation before the extraction of the final (end) product of fermentation .if these organisms fail to metabolize the nutrients in this growth medium made available to them. The primary metabolites which are central to the growth and the production of organisms will not be produced; and once this is done, the organism will not grow well and at the end the secondary metabolites(which are of economic importance to man, plants, animals and the environment) will not be produced. These organisms drive fermentation processes and it is important that they continue to produce metabolites that encourage their optimal growth during fermentation.


PRIMARY METABOLITES:  Primary metabolites are produced during the growth of an organism. They are produced during the exponential phase of growth of the organism. Primary metabolites are involved in the growth development and reproduction of microorganisms. They act as key components in maintaining the normal physiological and metabolic processes of the organism. Primary metabolites are critical for the optimal or normal growth of the organism. Examples of primary metabolites are alcohol, vitamins and essential amino acids.

SECONDARY METABOLITES:   Secondary metabolites are produced at the end of growth of the organism. They are produced during the stationary phase of growth. i.e. at the stage when the organism is resting and is not actively growing. Secondary metabolites are not in the growth, development and reproduction of the organism. They are organic compounds that are produced through the modification of primary metabolites. Secondary metabolites provide defensive function and they have tremendous economic importance. They play no role in maintaining the physiological and metabolic processes of the organism. Examples of secondary metabolites include: antibiotics steroids and enzymes.

THE MAJOR ROLE OF MICROORGANISMS INCLUDING BACTERIA, YEASTS, MOULDS AND ACTINOMYCETES IN FERMENTATION PROCESSES is to convert or breakdown large substrates (macromolecules to economically important end-products. As the organism is growing in the fermentor or fermentation vessel, it produces primary metabolites- which it uses to maximize the available substrate or nutrient in the growth vessel (fermentor). These primary metabolites are primarily utilized by the organism to manufacturer its secondary metabolites such as antibiotics that are of great economic importance. Most fermentation processes are activated by microorganism including moulds, yeasts, actinomycetes and bacteria; and these organisms act on their own in collaboration with others.


Prescott L.M., Harley J.P and Klein D.A (2005). Microbiology. 6th ed. McGraw Hill Publishers, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA.




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