Introduction to Microbiology

Defining Microbes

Microbes are organisms that are microscopic, or extremely small.

Learning Objectives

Explain the roles of microorganisms in ecosystems and biotechnology.

Key Takeaways

Key Points

  • While most microbes are unicellular, some multicellular animals and plants are also microscopic and are therefore broadly defined as “microbes.”
  • Microbes serve many functions in almost any ecosystem on Earth, including decomposition and nitrogen fixation.
  • Many microbes are either pathogens or parasitic organisms, both of which can harm humans.

Key Terms

  • symbiote: An organism in a partnership with another, such that each profits from the other.
  • pathogenic: Able to cause a harmful disease.
  • ecosystem: The interconnectedness of plants, animals, and microbes, not only with each other but also with their environment.

What Are Microbes?

A microbe, or microorganism, is a microscopic organism that comprises either a single cell (unicellular); cell clusters; or multicellular, relatively complex organisms.

The study of microorganisms is called microbiology, a subject that began with Anton van Leeuwenhoek’s discovery of microorganisms in 1675, using a microscope of his own design.


A Drawing of Microbes: This is a drawing of what Arthur Hill Hassall saw under a microscope in a sample of water taken from the River Thames at two locations. Hassall was able to identify many microscopic organisms not perceptible to the unaided eye,.

Microorganisms are very diverse; they include bacteria, fungi, algae, and protozoa; microscopic plants (green algae); and animals such as rotifers and planarians. Some microbiologists also include viruses, but others consider these as nonliving. Most microorganisms are unicellular, but this is not universal, since some multicellular organisms are microscopic. Some unicellular protists and bacteria, like Thiomargarita namibiensis, are macroscopic and visible to the naked eye.

Microorganisms live in all parts of the biosphere where there is liquid water, including soil, hot springs, on the ocean floor, high in the atmosphere, and deep inside rocks within the Earth’s crust. Most importantly, these organisms are vital to humans and the environment, as they participate in the Earth’s element cycles, such as the carbon cycle and the nitrogen cycle.

Microorganisms also fulfill other vital roles in virtually all ecosystems, such as recycling other organisms’ dead remains and waste products through decomposition. Microbes have an important place in most higher-order multicellular organisms as symbionts, and they are also exploited by people in biotechnology, both in traditional food and beverage preparation, and in modern technologies based on genetic engineering. Pathogenic microbes are harmful, however, since they invade and grow within other organisms, causing diseases that kill humans, animals, and plants.

The Pathogenic Ecology of Microbes

Although many microorganisms are beneficial, many others are the cause of infectious diseases. The organisms involved include pathogenic bacteria, which cause diseases such as plague, tuberculosis, and anthrax. Biofilms —microbial communities that are very difficult to destroy—are considered responsible for diseases like bacterial infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media (middle ear infection). They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic devices; and infect contact lenses, open wounds, and burned tissue.

Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are a large threat because they are resistant to most of the methods used to control microbial growth. Moreover, the excessive use of antibiotics has resulted in a major global problem since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked havoc recently.

In addition, protozoans are known to cause diseases such as malaria, sleeping sickness, and toxoplasmosis, while fungi can cause diseases such as ringworm, candidiasis, or histoplasmosis. Other diseases such as influenza, yellow fever, and AIDS are caused by viruses.

Food-borne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food. ” Hygiene ” is the avoidance of infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms (bacteria, in particular) are found virtually everywhere, the levels of harmful microorganisms can be reduced to acceptable levels with proper hygiene techniques. In some cases, however, it is required that an object or substance be completely sterile (i.e., devoid of all living entities and viruses). A good example of this is a hypodermic needle.

History of Microbiology: Hooke, van Leeuwenhoek, and Cohn

The development of the microscope, along with the observations of various scientists, led to the discovery of microorganisms.

Learning Objectives

Explain how Van Leeuwenhoek, Spallanzani, Pasteur, Cohn and Koch contributed to the field of microbiology

Key Takeaways

Key Points

  • Van Leeuwenhoek is largely credited with the discovery of microbes, while Hooke is credited as the first scientist to describe live processes under a microscope.
  • Spallanzani and Pasteur performed several experiments to demonstrate that microbial life does not arise spontaneously.
  • Cohn laid the groundwork for discovering and cataloging microbes, while Koch conclusively showed that microbes can cause diseases.

Key Terms

  • classification: the act of forming into a class or classes; a distribution into groups, as classes, orders, families, etc., according to some common relations or attributes.

Microorganism Speculation

Pre-microbiology, the possibility that microorganisms existed was discussed for many centuries before their actual discovery in the 17th century. The existence of unseen microbiological life was postulated by Jainism, which is based on Mahavira’s teachings as early as 6th century BCE. In his first century book, On Agriculture, Roman scholar Marcus Terentius Varro was the first known to suggest the possibility of disease spreading by yet unseen organisms. In his book, he warns against locating a homestead near swamps because “there are bred certain minute creatures that cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there cause serious diseases. ” In The Canon of Medicine (1020), Abū Alī ibn Sīnā (Avicenna) hypothesized that tuberculosis and other diseases might be contagious. In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seed-like entities that could transmit infection by direct or indirect contact, or even without contact over long distances. All these early claims about the existence of microorganisms were speculative and were not based on any data or science. Microorganisms were neither proven, observed, nor correctly and accurately described until the 17th century. The reason for this was that all these early studies lacked the microscope.

The Microscope and Discovery of Microorganisms


Antoni van Leeuwenhoek: A drawing of Antoni van Leeuwenhoek, one of the first scientists to use a microscope and identify microbes.

Antonie van Leeuwenhoek (1632–1723) was one of the first people to observe microorganisms, using a microscope of his own design, and made one of the most important contributions to biology. Robert Hooke was the first to use a microscope to observe living things. Hooke’s 1665 book, Micrographia, contained descriptions of plant cells. Before Van Leeuwenhoek’s discovery of microorganisms in 1675, it had been a mystery why grapes could be turned into wine, milk into cheese, or why food would spoil. Van Leeuwenhoek did not make the connection between these processes and microorganisms, but using a microscope, he did establish that there were forms of life that were not visible to the naked eye. Van Leeuwenhoek’s discovery, along with subsequent observations by Spallanzani and Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.

Lazzaro Spallanzani (1729–1799) found that boiling broth would sterilise it and kill any microorganisms in it. He also found that new microorganisms could settle only in a broth if the broth was exposed to the air.

Louis Pasteur (1822–1895) expanded upon Spallanzani’s findings by exposing boiled broths to the air in vessels that contained a filter to prevent all particles from passing through to the growth medium. He also did this in vessels with no filter at all, with air being admitted via a curved tube that prevented dust particles from coming in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur’s experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported germ theory instead.


Louis Pasteur.: The famous scientist Louis Pasteur, one of the founders of microbiology.

Ferdinand Julius Cohn (January 24, 1828 – June 25, 1898) was a German biologist. His classification of bacteria into four groups based on shape (sphericals, short rods, threads, and spirals) is still in use today. Among other things Cohn is remembered for being the first to show that Bacillus can change from a vegetative state to an endospore state when subjected to an environment deleterious to the vegetative state. His studies would lay the foundation for the classification of microbes and gave some of the first insights into the incredible complexity and diversity of microbial life.

In 1876, Robert Koch (1843–1910) established that microbes can cause disease. He found that the blood of cattle who were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microbe and a disease and these are now known as Koch’s postulates. Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today.

Pasteur and Spontaneous Generation

Pasteur’s experiments revealed that spontaneous generation does not occur.

Learning Objectives

Explain the concept of spontaneous generation

Key Takeaways

Key Points

  • Before the discovery of microbes, it was widely thought that life, as in the case of rotting food, arose from nothing. This idea was referred to as spontaneous generation.
  • By sterilizing cultures and keeping them isolated from the open air, Pasteur found that contamination of the media only occurred upon exposure to the outside environment, showing that some element was needed to give rise to life. In other words, life does not arise spontaneously.
  • Despite Pasteur’s work and the work of others, it still took a better understanding of germ theory and cell theory to finally displace the concept of spontaneous generation.

Key Terms

  • abiogenesis: The origination of living organisms from lifeless matter; such genesis as does not involve the action of living parents; spontaneous generation.
  • germ theory: The germ theory of disease, also called the pathogenic theory of medicine, is a theory that proposes that microorganisms are the cause of many diseases. Although highly controversial when first proposed, germ theory was validated in the late 19th century and is now a fundamental part of modern medicine and clinical microbiology, leading to such important innovations as antibiotics and hygienic practices.

Spontaneous generation is an obsolete body of thought on the ordinary formation of living organisms without descent from similar organisms. Typically, the idea was that certain forms such as fleas could arise from inanimate matter such as dust or that maggots could arise from dead flesh. A variant idea was that of equivocal generation, in which species such as tapeworms arose from unrelated living organisms, now understood to be their hosts.

Doctrines held that these processes were commonplace and regular. Such ideas were in contradiction to that of univocal generation: effectively exclusive reproduction from genetically related parent(s), generally of the same species. The doctrine of spontaneous generation was coherently synthesized by Aristotle, who compiled and expanded the work of prior natural philosophers and the various ancient explanations of the appearance of organisms; it held sway for two millennia.

Today spontaneous generation is generally accepted to have been decisively dispelled during the 19th century by the experiments of Louis Pasteur. He expanded upon the investigations of predecessors, such as Francesco Redi who, in the 17th century, had performed experiments based on the same principles.

Louis Pasteur’s 1859 experiment is widely seen as having settled the question. In summary, Pasteur boiled a meat broth in a flask that had a long neck that curved downward, like a goose. The idea was that the bend in the neck prevented falling particles from reaching the broth, while still allowing the free flow of air. The flask remained free of growth for an extended period. When the flask was turned so that particles could fall down the bends, the broth quickly became clouded. In detail, Pasteur exposed boiled broths to air in vessels that contained a filter to prevent all particles from passing through to the growth medium, and even in vessels with no filter at all, with air being admitted via a long tortuous tube that would not allow dust particles to pass. Nothing grew in the broths unless the flasks were broken open, showing that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. This was one of the last and most important experiments disproving the theory of spontaneous generation.


Pasteur’s test of spontaneous generation.: By sterilizing a food source and keeping it isolated from the outside, Pasteur observed no putrefaction of the food source (top panel). Upon exposure to the outside environment, Pasteur observed the putrefaction of the food source (bottom panel). This strongly suggested that the components needed to create life do not spontaneously arise.

Despite his experiment, objections from persons holding the traditional views persisted. Many of these residual objections were routed by the work of John Tyndall, succeeding the work of Pasteur. Ultimately, the ideas of spontaneous generation were displaced by advances in germ theory and cell theory. Disproof of the traditional ideas of spontaneous generation is no longer controversial among professional biologists. Objections and doubts have been dispelled by studies and documentation of the life cycles of various life forms. However, the principles of the very different matter of the original abiogenesis on this planet — of living from nonliving material — are still under investigation.

Koch and Pure Culture

Robert Koch identified anthrax as a disease agent and formulated postulates that are still used to research diseases today.

Learning Objectives

Explain Robert Koch’s postulates

Key Takeaways

Key Points

  • Koch’s research and methods helped link the causal nature of microbes to certain diseases, such as anthrax.
  • As developed by Koch, pure cultures allow the pure isolation of a microbe, which is vital in understanding how an individual microbe may contribute to a disease.
  • According to Koch’s postulates, for an organism to be the cause of a disease, it must be found in all cases of the disease and must be absent from healthy organisms, as well as maintained in pure culture capable of producing the original infection.

Key Terms

  • anthrax: An infectious bacterial disease of herbivores than can also occur in humans through contact with infected animals, tissue from infected animals, or high concentrations of anthrax spores.
  • metazoa: All those multicellular animals, of the subkingdom Metazoa, that have differentiated tissue.
  • tuberculosis: An infectious disease of humans and animals caused by a species of mycobacterium mainly infecting the lungs where it causes tubercles characterized by the expectoration of mucus and sputum, fever, weight loss, and chest pain, and transmitted through inhalation or ingestion of bacteria.

Robert Koch was born in Clausthal in the Harz Mountains, then part of the Kingdom of Hanover, as the son of a mining official. He studied medicine at the University of Göttingen and graduated in 1866. He then served in the Franco-Prussian War and later became district medical officer in Wollstein (Wolsztyn), Prussian Poland. Working with very limited resources, he became one of the founders of bacteriology, the other major figure being Louis Pasteur.


Robert Koch: An image of Robert Koch, a pioneering microbiologist. Koch’s research and methods helped link the causal nature of microbes to certain diseases, including anthrax.

After Casimir Davaine demonstrated the direct transmission of the anthrax bacillus between cows, Koch studied anthrax more closely. He invented methods to purify the bacillus from blood samples and grow pure cultures. He found that, while it could not survive outside a host for long, anthrax built persisting endospores that could last a long time. These endospores, embedded in soil, were the cause of unexplained “spontaneous” outbreaks of anthrax. Koch published his findings in 1876 and was rewarded with a job at the Imperial Health Office in Berlin in 1880. In 1881, he urged for the sterilization of surgical instruments using heat.

Probably as important as his work on tuberculosis, for which he was awarded a Nobel Prize in 1905, are Koch’s postulates. These postulates stated that to establish that an organism is the cause of a disease, it must be found in all cases of the disease examined. Additionally, it must be absent in healthy organisms prepared and maintained in a pure culture capable of producing the original infection, even after several generations in culture retrievable from an inoculated animal and cultured again. By using his methods, Koch’s pupils found the organisms responsible for diphtheria, typhoid, pneumonia, gonorrhoea, cerebrospinal meningitis, leprosy, bubonic plague, tetanus, and syphilis.

Perhaps the key method Koch developed was the ability to isolate pure cultures, explained in brief here. Pure cultures of multicellular organisms are often more easily isolated by simply picking out a single individual to initiate a culture. This is a useful technique for pure culture of fungi, multicellular algae, and small metazoa. Developing pure culture techniques is crucial to the observation of the specimen in question. The most common method to isolate individual microbes and produce a pure culture is to prepare a streak plate. The streak plate method is a way to physically separate the microbial population and is done by spreading the inoculate back and forth with an inoculating loop over the solid agar plate. Upon incubation, colonies will arise and single cells will have been isolated from the biomass.