by DrChika

Industrial Microbiology

The use of microbes by man to produce beneficial products is an ancient practice that has continued till date. Industrial microbiology is the branch of microbiology that uses microbes to produce industrial products in large quantities. Here, the potentials of microorganisms are harnessed for industrial productions and for other related services. Some microorganisms are known to produce various useful end-products such as acids, alcohols, hormones, enzymes and antimicrobial agents (e.g. antibiotics) as part of their metabolic activities. These potentials of microorganisms have been greatly exploited by man, and today there are many fermentation industry across the globe that produce beer, bread, wine and other beverages through the application of certain microorganisms that actively facilitate the process of fermentation.

Industrial microbiologists work in a variety of companies including biochemical industries, biotechnology companies, pharmaceutical companies and food production industries where they exploit the metabolic products of microorganisms (especially their secondary metabolites) to produce a wide variety of useful products. Large fermenters or bioreactors are used in beer and wine production plants for the production of quality wine and beer as well as other beverages that are mediated by microbial action.

Industrial microbiologists work on the exploitation of microorganisms in the manufacturing of food and other useful industrial products including pharmaceutical products and drugs, chemicals and fuel/energy (e.g. biofuels or bioethanol). Industrial microbiology is the application of scientific and engineering principles to the processing of materials by microorganisms including bacteria and fungi to create products that are of economic importance to man.

Industrial microbiologists amongst other things ensure the quality control and assurance of products generated from microbial origins. Some groups of microorganisms are of tremendous importance because they are exploited in the production of products such as organic chemicals (e.g. citric acid, acetone, methanol, butanol and ethanol), enzymes, amino acids, antibiotics and detergents. Industrial microbiologists are needed by governments, industries, the academia, and other agencies where they proffer regulatory and other supervisory roles as it relates to the harnessing of microbial cells for the production of beneficial products. 

The fermentor which can also be called bioreactors is the vessel within which the fermentation reaction during a Fed batch or batch fermentation process is conducted; and such vessels ensure an even mixture of the microbes or inoculums and other reactants in it in such a way that fermentation proceeds unperturbed. Bioreactors also have channels through which nutrients or substrates can be added as well as openings via which the products can be recovered and wastes retrieved. Industrial fermenters are large vessels that usually range from 10,000 liters to 100,000 liters and even larger depending on the purpose it is meant to serve; and industrial fermenters as shown here are fitted with special components such as impellers and spargers that ensure even mixture of the reaction mixture as well as adequate supply of oxygen for the fermentation process. Most bioreactors are used in the industry are computer-controlled and monitored in order to determine vital parameters of the fermentation process such as pH, buildup of metabolic products and wastes and temperature levels amongst other physical or environmental factors that may affect the fermentation process.

Environmental Microbiology

Environmental microbiology is the branch of microbiology that studies the role of microorganisms in the maintenance of a healthy, quality, and sustainable environment. It is the study of the composition and physiology of microbial communities in the environment inclusive of the soil, water and air; and environmental microbiologists examine the environment and test it for possible microbial contamination that may pose a public health threat. Microorganisms play tremendous roles in the environment especially as it relates to nutrient recycling, biodegradation of organic matters, and even in bioremediation such as the use of specific group of microorganisms to control and remedy the untoward effects of oil spillage in the environment.

Bioremediation is simply defined as the biotechnological clean-up of pollutants in the environment that is microbial-based or driven. Microbial degradation of pollutants (e.g. chemical contaminants, pesticides and hydrocarbons) in the environment unlike other physical degradation processes releases environmentally-friendly substances (e.g. carbondioxide and water) that have minimal or no negative effect on the ecosystem. Most physical degradation processes though rapid may adversely affect the environment negatively when compared to other biological techniques of degradation that employs microbes for pollutant degradation. Some microorganisms are also used to reduce the microbial loads of industrial wastes and sewages, pesticides, and other heavy metals before their release into the environment; and waste waters from industries and domestic homes are also treated with microbes in like manner.

Microorganisms have also been used to treat and recycle organic and inorganic wastes. The activities of microorganisms which help to clean-up the environment and keep it safe and free from contaminants are exploited and studied under this very important branch of microbiology. Pseudomonas species, Sphingomonas species, Wolinella species and other facultative anaerobic or microaerophilic bacteria are some of the microorganisms employed for the degradation of pollutants in the environment. The hydrocarbon-degrading activities of microorganisms have helped to contain the oil spills of coastal regions and the open sea areas where oil spillage is common; and these microbes have assisted in remediating the ecological damage caused by oil pollutants and other wastes. Understanding the impact of microbes in the environment assist environmental microbiologists to prevent environmental problems via adequate detection of the harm.

Food Microbiology

Food microbiology is the area of microbiology that studies the interactions of microorganisms and food; how this association can be exploited to produce or process food; and how microbes cause food spoilage. It generally studies beneficial and non-beneficial microbes that impact foodstuffs and beverages from the point of processing, production, storage and usage. Microorganisms cause food spoilage, and they are also exploited in fermentative processes to produce a variety of foods such as single cell proteins (SCPs), yoghurt, cheese and beverages (e.g. wine, beer) amongst other food products. Food microbiologists are also concerned with the involvement of microorganisms known as food-borne pathogens in causing food-borne diseases and food spoilages as well. They are also at the center of preventing food spoilage by developing sustainable ways by which processed foods can be preserved and stored for long period.

Food spoilage is one of the most prevalent microbiological problem facing the food industry; and this problem have cost the food industry fortunes in terms of the amount of food products that get spoiled by bacteria and yeasts or molds on an annual basis. The canning and pasteurization of dairy products such as milk, yoghurt and cheese, and how they can be preserved to avoid microbial contamination and spoilage is also explored in food microbiology. Currently, some foods have probiotics imbedded in them during production, and whole foods have also been produced from microbial origin as well due to improved techniques in food microbiology, biotechnology and industrial microbiology.

Probiotics are live cultures of bacteria which boost the normal microbial flora of the human gastrointestinal tract, and thus improve the general health of the gut. Food microbiologists also ensure that all safety and hygienic measures are observed during food production in food related industries; and they work in related industries where they use their expertise to ensure aseptic techniques during food processing, production and storage. Knowledge of food microbiology acquaints microbiologists of the relationship that exist between microorganisms and food; and it also give emphasis to food safety, food quality and food shelf-life so that adequate measures will be put in place to develop techniques that may contain the spoilage of food especially during food production to food storage. Food microbiologists ensure a safe food supply for mankind; and through appropriate microbiological testing they promptly detect food spoilage organisms and pathogens that cause food borne diseases (Figure 1).   

Figure 1. A food microbiologist analyzing food products for possible microbial contamination. Food microbiologists test finished food products in order to ensure that imported or exported food products meant for human or animal consumption are actually free of any possible microbial contaminants. The ubiquity of microorganisms and their potential to cause food spoilage as well as the possibility of food to transmit disease necessitates the importance and need for adequate and proper microbiological control of food products in order to prevent food spoilage and food borne diseases in human population. Adapted from: Online Textbook of Bacteriology by Dr. Kenneth Todar: Department of Bacteriology University of Wisconsin, USA.

Public Health Microbiology

Public health microbiology is the branch of microbiology that deals with the monitoring, control and spread of infectious diseases and pathogens from community to community, country to country and around the world. Public health microbiologists (also known as epidemiologists) are disease detectors, and they use their profession to improve the quality of health worldwide through timely detection and prevention of disease outbreak or spread in human populations. They also inspect restaurants, food vendors and food from the factory to make sure they are pathogen free and are not sources of food-borne diseases.

Public health microbiologists are specialists that utilize key health data to forestall and reverse the spread of an epidemic; and they play critical roles in cases of disease outbreak such as in the recent epidemic of the ebola virus disease (EVD) in parts of West Africa and other imported diseases/infections in other countries of the world. Public health microbiologists share timely, reliable and comparable microbiological or epidemiological statistics with other health professionals including doctors and other government public health specialists in order to efficiently prevent and control communicable diseases amongst defined human populations.

Sexually transmitted diseases (e.g. gonorrhea and syphilis), HIV/AIDS, Ebola virus disease (EVD), lassa fever, tuberculosis (TB), lyme disease, plague, diphtheria, influenza, rabies, hepatitis infection (especially B and C), malaria and food borne illnesses are some of the diseases that are of public health importance and must be reported to the authorities for appropriate containment measures; and the public health microbiologist play critical role in ensuring that vital data regarding infectious diseases are well shared and reported.

Research conducted by public health microbiologists is used for the control and prevention of infectious diseases in the community; and they use a wide variety of laboratory techniques which incorporates a multidisciplinary investigation in identifying and characterizing pathogenic microorganisms that directly affect the wellbeing of the general public. Public health microbiologists work in research institutions, the academia, government laboratories, hospitals and in other government agencies where there knowledge about the spread of microbes within a defined population is harnessed and utilized to contain infectious diseases. They also sensitize the general public on possible ways of preventing the contamination and spread of infectious diseases so as to lead a healthier lifestyle.

Petroleum Microbiology

Petroleum microbiology studies microbes that metabolize hydrocarbons and how they could be employed in oil prospecting and oil spillage control. Petroleum is a complex mixture of hydrocarbons(i.e. aliphatic and aromatic compounds) and other organic or inorganic constituents such as sulphur, oxygen and carbon; and some microbes metabolize hydrocarbons to generate their energy as well as other growth factors. Some microorganisms (e.g. Homoconis resinae) depend solely on crude oil or other refined petroleum products which they degrade to generate nutrient molecules required for their nourishment and growth. H. resinae, a fungus produces more biomass than any other fungi, and this is likely to cause obstruction of pipes in the fuel tank of aircrafts where they colonize.

The organism also has the potential to grow between fuel and water and produce suspended solids in fuels, thus giving it the opportunity to cause microbial corrosion in aircraft tanks. Pseudomonas, Arthrobacter, Burkholderia, Sphingomonas, Acinetobacter, Bacillus and Rhodococcus are some bacterial genus that can metabolize and degrade hydrocarbon or organic compounds. However, it is the job of petroleum microbiologists to periodically check aircraft fuels and tanks for possible microbial contamination, and thus ensure that the microbial load of microorganisms are within accepted limits to avoid possible damage to the fuel tanks. In addition, this field of microbiology deals with the use of microbial action to control oil spillage and clean-up of the environment.

Microorganisms play significant roles in the oil industry (especially in microbial enhanced oil recovery); and they also have the ability to degrade hydrocarbons and clean up the environment especially in oil spillage scenarios as is commonly obtainable in oil rigs and other oil processing and storage facilities. Hydrocarbon contamination of the terrestrial habitat and waterfronts resulting from the activities related to the petrochemical industry is one major environmental problem that is of global concern; and this is largely because hydrocarbons are carcinogenic in nature and some organic pollutants are neurotoxic and thus affect the health of humans, animals and even the aquatic life. However, bioremediation and/or biodegradation technology (which employs the metabolic activities of microbes) is currently been exploited for the treatment of hydrocarbon contaminated sites since it leads to complete mineralization of the hydrocarbons i.e. the transformation of organic compounds including hydrocarbons into simple inorganic molecules such as carbondioxide and water amongst others. 

Agricultural (Soil) Microbiology

Microorganisms are ubiquitous and they are densely found in the soil where they play important roles as it relates to crop yield and development. A handful of microorganisms that produce antibiotics and other antimicrobial agents that are used in medicine to contain the negative effects of pathogenic microorganisms (i.e. microorganisms that cause disease) are largely found and isolated from the soil. Though there are different categories of microorganisms that cause diseases in plants, microorganisms found in the soil help a lot in nitrogen fixation and many others are used in the compounding of bio-fertilizers.

Microorganisms living in the soil affect the plants and crops on the surface in diverse ways especially by helping them acquire vital nutrients required for their proper growth and plentiful harvest. While some microorganisms can cause disease in crops and farm animals, others can be used a bio-pesticides to control the devastating effects of insect pests and weeds in farmlands. Soil microbiologists also study the relationship between microorganisms and plant with the bid of enhancing crop yield and reducing microbial related diseases amongst plants.

Currently, conventional, recombinant DNA technology and monoclonal antibody techniques are used to improve microbial inoculants which serve as bio-fertilizers or plant growth supplements; and these microbial inoculants act by fixing atmospheric nitrogen in order to improve crop yields and they also to serve as plant pest controls by preventing the attack of farm crops by pests. Agricultural microbiologists play tremendous roles in the economy of any nation especially in this current state of global food insecurity.

In order to meet up with the current challenges of food insecurity around the globe and provide sustainable food products for the teaming population of the world; microbiologists have manipulated genes and/or proteins that control the architecture and stress resistance of plants (especially to disease and harsh environmental conditions) at the molecular level in order to improve crop productivity and ensure food security a across the world. Farmers and agriculturists can improve their crop productivity by using bio-fertilizers which incorporates microbes that help to improve the fertility of the soil. Bio-fertilizers help to unlock nitrogen and phosphorus (which are both vital for plant growth) from the soil; and unlike chemical fertilizers they are environmentally-friendly and do not adversely affect the soil. Bio-pesticides, bio-herbicides and bio-insecticides also exist for the control of pests in farmlands.  


Biotechnology is simply defined as the use of cellular and biomolecular processes to produce useful products that are of economic importance. It is the use of biological processes (e.g. microorganisms) to solve practical problems that are beneficial to mankind, plants, animals and the environment. Biotechnology is another vital branch of microbiology that is radically transforming the medical, pharmaceutical and biomedical sciences; and this field of biological sciences harnesses the cellular and metabolic profiles or activities of microbes in particular to improve the quality of life such as in novel drug and vaccine development and in the production of sustainable food products. Beneficial microorganisms have been genetically-engineered through the application of biotechnology to generate medically important products ranging from drugs to diagnostics, human therapeutics and hormones amongst others; and recombinant human insulin for the treatment of diabetes, a non-infectious disease is also based on the application of biotechnology techniques. A handful of food and other industrial products have also been produced through biotechnological applications or techniques.

Through biotechnology, microorganisms can be manipulated at the molecular or genetic level to be more efficient in the production of environmentally friendly products and services. Several high-throughput techniques (e.g. proteomics and genomics) are now available for the manipulation of microorganisms at the molecular level for improved product yield and the development of novel products which have far-reaching economic importance. Biotechnologists work in government agencies, health institutions, research facilities, hospitals and even in educational institutions where their knowledge of microorganisms at the molecular and genetic level are exploited for the synthesis of desired products. Biotechnology is a fast growing field of biological sciences, and microbiologists with practical knowledge of this discipline are highly sourced in many fields of life especially in the pharmaceutical, food, medical and chemical industries amongst others. Yogurt, cheese, chocolate, butter, pickles, sauerkraut, soy sauce, food supplements (such as vitamins and amino acids), foods thickeners (produced from microbial polysaccharides), alcoholic drinks (e.g. beer, whiskeys and wines) sausages and silage for animals are some examples of products of microbial origin or activity. Biotechnology generally involves the industrial application of microbes to produce products that are beneficial to mankind in large quantities.

Medical Microbiology

Medical microbiology is the branch of microbiology that is primarily responsible for the laboratory diagnosis, treatment and prevention of infectious diseases caused by pathogenic microorganisms. Medical microbiologists collaborate effectively with other health professionals and even the patients and their family members in order to provide optimal care of the patient. They also take part in the provision of clinical consultation services both within the hospital and even in the community especially as it relates to pathogenic microorganisms. And medical microbiologists apart from isolating and identifying the causative agents of infectious diseases also help the physicians to administer the appropriate therapy owing to the current rapid evolution of drug-resistant microbes.

Medical microbiology concerns itself with the group or class of microorganisms that cause diseases and other infections in human population. This branch of microbiology specifically deals with pathogenic microorganisms, their life cycle, reproduction and physiology amongst other factors, and how these could be exploited to provide solutions to the many diseases that these microbes cause in humans. Aside their notable usefulness, some microorganisms known as pathogens cause disease and it is the task of the medical microbiologist to isolate and identify disease-causing agents from clinically important specimens so that therapy can be properly guided.

Medical microbiologists also contribute to the development of vaccines, diagnostics and other measures that will help to contain the infectious diseases caused by microbes. They work in hospital laboratories, research institutions, in government agencies and even in the academia where they analyze medically important samples in order to isolate and identify the pathogen(s) that is responsible for a particular disease outbreak. They also conduct antimicrobial susceptibility studies on isolated microbes and give appropriate advice on the treatment cause to follow. Microbiological research as carried out by medical microbiologists will lead to the development of novel diagnostic tools to improve on the prompt detection of pathogenic strains including those that are multidrug resistant.

Pharmaceutical Microbiology

Pharmaceutical microbiology is the branch of microbiology that focuses on all aspects of pharmacy especially as it relates to the manufacture and quality control of pharmaceuticals such as drugs. Microbiological applications are tremendously applied in the pharmaceutical industry to produce a wide range of products including hormones, antibiotics, water for injections, steroids and so on which are used for the treatment and management of both infectious and non-communicable diseases. Irrespective of the suffering of patients due to infectious diseases caused by pathogenic microorganism, healthcare delivery has tremendously improved worldwide owing to the availability of effective medicines and vaccines with which to treat and prevent these diseases. Pharmaceutical companies around the world are investing heavily in research and development (R&D); and they are also in high demand for pharmaceutical microbiologists due to the relevance of this branch of microbiology in the manufacture of safe, effective and good-quality drugs.

Pharmaceutical microbiology also deals with the controlling of microorganisms that cause spoilage of pharmaceutical products, and this area of microbiology is also keenly interested in harnessing the metabolic activities of microorganisms to develop novel and potent medicines and other pharmaceuticals for the health sector. This branch of microbiology is a burgeoning area in the biological sciences due to its importance to not just the health and pharmaceutical sector, but also the central role that it plays in ensuring the improvement of world health and disease prevention. The production of novel drugs from herbal plants and other natural products are also the subject of pharmaceutical microbiologists.           

Water Microbiology

Water microbiology is the branch of microbiology that ensures that the water supply to homes, industries, towns and local communities are of good quality and free from water-borne pathogens such as Escherichia coli, Vibrio cholerae amongst others. Water microbiologists work in water distribution and purification companies where they analyze water from reservoirs and river sources to check for their quality and microbial load before distribution to homes and industries. They also ensure that sewage and other industrial wastes are properly treated before release into water ways and that they are not potential causes of water-borne diseases.

Another aspect of water microbiology is aquatic microbiology which deals with the study of microorganisms and how their metabolic activities could be exploited to improve the health of man and animals in the fresh, marine and estuarine habitat. Water borne diseases such as cholera and dysentery are amongst the child killer diseases; and these infections are prevalent in places where environmental sanitation is poor. It is mainly the task of the water microbiologists to ensure that the water distribution channels are free from water-borne pathogens; and that water meant for domestic use and for other human purposes such as in the industry for manufacturing are free from pathogenic microorganisms.  


Immunology is an aspect of microbiology that concerns itself with the study of the immune system in man and animals. The immune system is made up of cells, tissues and organs that work together in a cooperative manner to protect human host’s from or against the invasion of foreign substances and microbes. They also help to eliminate these foreign molecules and thus minimize their deleterious effects in the body. Immunologists study the immune system (composed of innate and acquired immunity) to better understand it and proffer practical explanation as to how these could be exploited to contain some infectious diseases and their causative agents as well as develop strong and sustainable preventive measures against the acquisition of infections e.g. the production of potent vaccines for various infectious diseases. Vaccines are vital tools in clinical medicine, and they are mainly used to prevent disease occurrence in susceptible human population through the process of immunization/vaccination. Immunologists work in the government, healthcare sector, research institutions and even ion the academia where their knowledge of the body’s immune system are brought to bear to unravel some of the mysteries of infectious diseases especially in humans.       

Molecular Microbiology and Genetics

Microbiologists in this area of molecular microbiology and genetics focus on the nature of genetic manipulation and how it regulates the development and function of cells and organisms. The use of microorganisms has been very helpful in understanding gene function. Microbial genetics play important role in applied microbiology by helping to produce new microbial strains that are more efficient in synthesizing useful products. With tools and techniques in molecular microbiology, microbiologists can detect pathogens more rapidly and accurately from clinical and/or environmental samples based on the genetic signatures of the organisms. 

Generally, this aspect of microbiology studies the genetic makeup of microorganisms (DNA and RNA inclusive), their heredity patterns and variations that occur amongst members of the same species. Knowledge of the genetic makeup of microorganisms especially those that are multidrug resistant in nature (e.g. bacteria producing extended spectrum beta-lactamases and metallo beta-lactamases) will help to provide clues as to how the emergence and spread of disease-causing microbes particularly those that are drug resistant could be monitored and contained. Since the genome is mainly the control center of the cell, molecular microbiologists (in whose duty it is to study microbes at the molecular level) play critical role in helping the medical community to unravel the genetic basis of some infectious and non-infectious diseases that affect humanity.       


  • Bacteriology: Bacteriology is simply defined as the study of bacteria. Bacteriologists are microbiologists that are devoted to the study of bacteria especially those that are pathogenic i.e. disease-causing bacteria. They work in hospitals, research institutions, veterinary centers, university, government agencies and other areas where pathogenic bacteria are the microorganisms of interest.
  • Virology: Virology is defined as the study of viruses. Microbiologists that exclusively study viruses, their properties and the diseases they cause are called virologists. Virologists work in hospitals, research institutions, educational institutions (as educators and researchers), in government agencies and in pharmaceutical companies where there knowledge about viruses are harnessed to solve infectious diseases caused by viral agents.  
  • Parasitology: Parasitology is the study of parasites or worms and even insects or arthropods that act as transmission vehicles or vectors for infectious diseases and their causative agents in both human and animal populations. Another related area to parasitology is protozoology which is the study of parasites and how their association with plants, animals and humans can cause infection or disease. Protozoalogists study protozoa or parasites.
  • Mycology: Mycology is simply defined as the study of fungi including yeasts, moulds, mushrooms and slime moulds. Microbiologists that exclusively study fungi are called mycologists. They are found in the industries, hospitals, food industries, the academia and pharmaceutical companies amongst other areas where their services as it relates to fungi are required.  
  • Algology/phycology: Algology or phycology is defined as the study of algae. It is noteworthy that algae consist of both microscopic (invisible) and macroscopic (visible) forms. But due to the scope of microbiology, only microscopic algae of utmost importance to algologists (i.e. microbiologists that study algae) are usually studied in the field of microbiology.
  • Geochemical microbiology: Geochemical microbiology is the branch of microbiology that studies the applications of microorganisms in the mining of metals, crude oil and other natural resources from their natural sources or the ground. Microorganisms are currently being exploited in a number of mining and oil recovery activities. They have also been used to prospect for oil, gas and coal in areas deemed to be low in these resources. 
  • Aero microbiology: Aero microbiology is largely concerned with the role of microorganisms in the air and in the contamination and spoilage of food, wine and beverages. It also specializes in the monitoring of dissemination of air-borne diseases in plant, animal and human populations. Aero microbiologists also evaluate the quality and quantity of air available for both human and animal activities; and the significance of bioaerosols in causing morbidity and mortality in human populations. Bioaerosols are microbial suspensions or airborne particles produced by microbes including fungi, bacteria and viruses, and which are mainly found in the atmosphere. Bioaerosols are composed of a variety of microbes and particles inclusive of live, dormant and dead microbes as aforementioned as well as other microbial toxins and other high molecular weight compounds that are of public health importance. Continued uncontrolled exposure of humans to these bioaerosols especially those working in certain occupations (e.g. composters, farmers, abattoir workers and construction workers) that predispose them to significant accumulation or inhalation of toxic biological agents are at a higher risk of becoming ill from exposure to bioaerosols.  Most infectious disease agents are dispersed through the air in aerosols or in their spore or dormant state; and this is particularly the case for pathogenic fungi and other microbes that are mostly dispersed as spores through dust particles in the air.  
  • Exo microbiology: Though still in its infancy, exo microbiology is the branch of microbiology that specializes in the exploration of microbial life in the outer space.


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