The Science of Microbiology

Basic Microbiology

Microbiology is the study of microscopic organisms and how they interact with humans and the environment.

Learning Objectives

Evaluate the science of basic microbiology; understand the fundamental aspects of microbiology.

Key Takeaways

Key Points

  • Microbiology focuses on organisms that are very small using various tools, which is a process done by microbiologists.
  • As microbes are essential for human life and as microbes can cause human diseases, microbiology is therefore very important.
  • The numbers of individual microbes and the number of microbes in and on the earth is staggering in proportions.

Key Terms

  • quantitation: The process of quantitating.
  • immunology: The branch of medicine that studies the body’s immune system.
  • culturable: Able to be cultured (grown in a suitable environment).

Microbiology is the study of microscopic organisms (microbes), which are defined as any living organism that is either a single cell (unicellular), a cell cluster, or has no cells at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.

Microbiology typically includes the study of the immune system, or immunology. Generally, immune systems interact with pathogenic microbes; these two disciplines often intersect which is why many colleges offer a paired degree such as “Microbiology and Immunology. ”


Microbiologist: A microbiology officer aboard a US naval ship examines wound cultures in the ship’s microbiology laboratory.

Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology, and other branches. A microbiologist is a specialist in microbiology and these related topics. Microbiological procedures usually must be aseptic and use a variety of tools such as light microscopes with a combination of stains and dyes. As microbes are absolutely required for most facets of human life (including the air we breathe and the food we eat) and are potential causes of many human diseases, microbiology is paramount for human society.

Research in the microbiology field is expanding, and in the coming years, we should see the demand for microbiologists in the workforce increase. It is estimated that only about one percent of the microorganisms present in a given environmental sample are culturable and the number of bacterial cells and species on Earth is still not possible to be determined. Recent estimates indicate that this number might be extremely high at five to the power of thirty. Although microbes were directly observed over three hundred years ago, the precise determination, quantitation, and description of its functions is far from complete, given the overwhelming diversity detected by genetic and culture-independent means.

Applied Microbiology

The information gained by microbiologists can be applied to many medicinal and commercial endeavors.

Learning Objectives

Explain applied microbiology

Key Takeaways

Key Points

  • Using knowledge gained by microbiologists studying microbes, several fields of applied microbiology have formed.
  • While food and medicinal applications are a big portion of applied microbiology, the study of microbes has lead to entire commercial industries which affect almost all aspects of human life.
  • There are a myriad of practical applications that microbiology contributes to, including several parts of food production and medicinal applications.

Key Terms

  • rhizosphere: The soil region subject to the influence of plant roots and their associated microorganisms.
  • biotechnology: The use of living organisms (especially microorganisms) in industrial, agricultural, medical, and other technological applications.
  • pathogenic: Able to cause harmful disease.

Microbiology is the study of microbes, which affect almost every aspect of life on the earth. In addition, there are huge commercial and medicinal benefits in understanding microbes. The application of this understanding is known as applied microbiology. There are many different types of applied microbiology which can be briefly defined as follows:

Medical Microbiology

Medical microbiology is the study of the pathogenic microbes and the role of microbes in human illness. This includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.

Pharmaceutical Microbiology

The study of microorganisms that are related to the production of antibiotics, enzymes, vitamins, vaccines, and other pharmaceutical products. Pharmaceutical microbiology also studies the causes of pharmaceutical contamination and spoil.

Industrial Microbiology

The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and waste-water treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.

Microbial Biotechnology

The manipulation of microorganisms at the genetic and molecular level to generate useful products.

Food Microbiology and Dairy Microbiology

The study of microorganisms causing food spoilage and food-borne illness. Microorganisms can produce foods, for example by fermentation.


Applied microbiology – Fermentation: One of the oldest and well-known examples of applied microbiology is fermentation. In this picture the large tanks are being used for the fermentation of grapes to make wine.

Agricultural Microbiology

The study of agriculturally relevant microorganisms. This field can be further classified into the following subfields:

  • Plant microbiology and plant pathology – The study of the interactions between microorganisms and plants and plant pathogens.
  • Soil microbiology – The study of those microorganisms that are found in soil.
  • Veterinary microbiology – The study of the role in microbes in veterinary medicine or animal taxonomy.
  • Environmental microbiology – The study of the function and diversity of microbes in their natural environments. This involves the characterization of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles). This field includes other branches of microbiology such as: microbial ecology (microbially-mediated nutrient cycling), geomicrobiology, (microbial diversity), water microbiology (the study of those microorganisms that are found in water), aeromicrobiology (the study of airborne microorganisms) and epidemiology (the study of the incidence, spread, and control of disease).

This is by no means an exhaustive list of the different types of applied microbiology, but gives an indication of the expansive variety of the field and some of the benefits these studies entail.

Immunization, Antiseptics, and Antibiotics

Understanding microbes gives us the ability to fight pathogens using immunization, antiseptics, and antibiotics.

Learning Objectives

Compare immunization, antiseptics and antibiotics, and how they are used to combat human pathogens

Key Takeaways

Key Points

  • Immunization is the fortification of our own immune system, priming it against potential future infections by specific microbes.
  • Antiseptics are broadly defined as substances we can use on our body or surfaces around us to slow or kill microbes that could potentially harm us.
  • Antibiotics, like antiseptics, can slow or kill microbes. However, unlike antiseptics, antibiotics can circulate in the human blood system and be used to fight microbial infections.

Key Terms

  • anaphylactic shock: A severe and rapid systemic allergic reaction to an allergen, constricting the trachea and preventing breathing.
  • immunogen: any substance that elicits a immune response; an antigen

Surprisingly, most microbes are not harmful to humans. In fact, they are all around us and even a part of us. However, some microbes are human pathogens; to combat these, we use immunization, antiseptics, and antibiotics.

Immunization is the process by which an individual’s immune system becomes fortified against an agent (known as the immunogen ).


Flu Immunization: A naval officer self-administers a nasal spray that immunizes him against the flu.

When the immune system is exposed to molecules that are foreign to the body, it will orchestrate an immune response. It will also develop the ability to respond quickly to subsequent encounters with the same substance, a phenomenon known as immunological memory. Therefore, by exposing a person to an immunogen in a controlled way, the body can learn to protect itself: this is called active immunization.

Vaccines against microorganisms that cause diseases can prepare the body’s immune system, thus helping it fight or prevent an infection. The most important elements of the immune system that are improved by immunization are the T cells, the B cells, and the antibodies B cells produce. Memory B cells and memory T cells are responsible for the swift response to a second encounter with a foreign molecule. Through the use of immunizations, some infections and diseases have been almost completely eradicated throughout the United States and the world. For example, polio was eliminated in the U.S. in 1979. Active immunization and vaccination has been named one of the “Ten Great Public Health Achievements in the 20th Century. ”

By contrast, in passive immunization, pre-synthesized elements of the immune system are transferred to a human body so it does not need to produce these elements itself. Currently, antibodies can be used for passive immunization. This method of immunization starts to work very quickly; however, it is short-lasting because the antibodies are naturally broken down and will disappear altogether if there are no B cells to produce more of them. Passive immunization occurs physiologically, when antibodies are transferred from mother to fetus during pregnancy, to protect the fetus before and shortly after birth. The antibodies can be produced in animals, called ” serum therapy,” although there is a high chance of anaphylactic shock because of immunity against animal serum itself. Thus, humanized antibodies produced in vitro by cell culture are used instead if available.

In early inquiries before there was an understanding of microbes, much emphasis was given to the prevention of putrefaction. Procedures were carried out to determine the amount of agent that needed to be added to a given solution in order to prevent the development of pus and putrefaction. However, due to a lack of understanding of germ theory, this method was inaccurate. Today, an antiseptic is judged by its effect on pure cultures of a defined microbe or on their vegetative and spore forms.

Antiseptics are antimicrobial substances that are applied to living tissue to reduce the possibility of infection, sepsis, or putrefaction. Their earliest known systematic use was in the ancient practice of embalming the dead. Antiseptics are generally distinguished from antibiotics by the latter’s ability to be transported through the lymphatic system to destroy bacteria within the body, and from disinfectants, which destroy microorganisms found on non-living objects. Some antiseptics are true germicides, capable of destroying microbes (bacteriocidal), while others are bacteriostatic and only prevent or inhibit bacterial growth. Microbicides that destroy virus particles are called viricides or antivirals.


Antibiotic Testing: Discs soaked with various compounds are put onto a lawn of bacteria. If the compound on the disc kills or slows bacteria growth, a “halo” of clear media is seen.

An antibacterial is a compound or substance that kills or slows down the growth of bacteria. The term is often used synonymously with the term antibiotic; today, however, with increased knowledge of the causative agents of various infectious diseases, the term “antibiotic” has come to denote a broader range of antimicrobial compounds, including anti-fungal and other compounds.

The word “antibiotic” was first used in 1942 by Selman Waksman and his collaborators to describe any substance produced by a microorganism that is antagonistic to the growth of other microorganisms in high dilution. This definition excluded substances that kill bacteria but are not produced by microorganisms (such as gastric juices and hydrogen peroxide). It also excluded synthetic antibacterial compounds, such as the sulfonamides. Many antibacterial compounds are relatively small molecules with a molecular weight of less than 2000 amu. With advances in medicinal chemistry, most of today’s antibacterials are semisynthetic modifications of various natural compounds.

Modern Microbiology

Modern microbiology began with the discovery of microbes in the 1600s and the scope and scale of the field continues to expand today.

Learning Objectives

Discuss the fundamental aspects of microbiology

Key Takeaways

Key Points

  • There is some debate as to who was exactly first, but Antonie van Leeuwenhoek, Athanasius Kircher, and Robert Hooke were the first people to view microbes using some of the first self-built microscopes.
  • Ferdinand Cohn, Louis Pasteur, and Robert Koch were pioneers in bacteriology, the discovery and understanding of the subset of microbes that are bacteria. This had a direct and immediate impact on food storage and disease causality.
  • Martinus Beijerinck and Sergei Winogradsky are credited with the discovery of general microbiology, which laid the ground work for our understanding of microbial physiology, diversity, and ecology.

Key Terms

  • chemoautotrophy: When a simple organism, such as a protozoan, derives its energy from chemical processes rather than photosynthesis.
  • pasteurization: heat-treatment of a perishable food to destroy heat-sensitive vegetative cells followed by immediate cooling to limit growth of the surviving cells and germination of spores
  • rabies: a viral disease that causes acute encephalitis in warm-blooded animals and people, characterised by abnormal behaviour such as excitement, aggressiveness, and dementia, followed by paralysis and death
  • animalcule: An older term for a minute or microscopic animal or protozoan.

Modern microbiolgy began with the discovery of microbes, and the scope and scale of the field continues to expand today.

While there is some debate, modern microbiology is accepted by most to begin with observations by the Dutch draper and haberdasher, Antonie van Leeuwenhoek, who lived for most of his life in Delft, Holland. In 1676, van Leeuwenhoek observed bacteria and other microorganisms, using a single-lens microscope of his own design. While van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the fruiting bodies of molds, in 1665.

It has been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms. One of his books contains a chapter in Latin, which reads in translation – “Concerning the wonderful structure of things in nature, investigated by Microscope. ” Here, he wrote “who would believe that vinegar and milk abound with an innumerable multitude of worms. ” He noted that putrid material is full of innumerable creeping animalcule. These observations antedate Robert Hooke’s Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa.


Athanasius Kirche: A portrait of the 17th century Jesuit priest Athanasius Kirche, who arguably discovered microbes.

The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria and discover spores. Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are often considered to be the father of microbiology and medical microbiology, respectively. Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science. Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera, and rabies.

Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms. He developed a series of criteria that have become known as the Koch’s postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis. While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance.

It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky, the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity, and ecology), that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. While his work on the tobacco mosaic virus (TMV) established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemoautotrophy and to thereby reveal the essential role microorganisms played in geochemical processes. Specifically, he was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.


Sergei Winogradsky: An image of Sergei Winogradsky,who discovered nitrogen-fixing bacteria.