Guide to Microbiology

What is Microbiology

The science of microbiology is all about microorganisms and how they work, especially the bacteria, a very large group of very small cells that have enormous basic and practical importance.

Microbiology is also about diversity and evolution of microbial cells, about how different kinds of microorganisms arose and why. Microbiology embraces ecology, so it is also about where microorganisms live on Earth, how they associate and cooperate with each other, and what they do in the world at large, in soils and waters and in animals and plants.

The science of microbiology revolves around two interconnected themes:

(1) understanding the nature and functioning of the microbial world, and
(2) applying our understanding of the microbial world for the benefit of humankind and planet Earth.

As a basic biological science, microbiology uses microbial cells to probe the fundamental processes of life. In so doing, microbiologists have developed a sophisticated understanding of the chemical and physical basis of life and have learned that all cells share much in common. As an applied biological science, microbiology is at the forefront of many important breakthroughs in human and veterinary medicine, agriculture, and industry. From infectious diseases to soil fertility to the fuel you put in your automobile, microorganisms affect the everyday lives of humans in both beneficial and detrimental ways.

Microorganisms existed on Earth for billions of years before plants and animals appeared, and we will see later that the genetic and physiological diversity of microbial life dwarfs that of theplants and animals. Although microorganisms are the smallest forms of life, collectively they constitute the bulk of biomass on Earth and carry out many necessary chemical reactions for higher organisms. In the absence of microorganisms, higher life forms would never have appeared and could not be sustained. Indeed, the very oxygen we breathe is the result of past microbial activity. Moreover, humans, plants, and animals are intimately dependent on microbial activities for the recycling of key nutrients and for degrading organic matter. It is thus safe to say that no other life forms are as important as microorganisms for the support and maintenance of life on Earth.

History of Microbiology

Robert Hooke, an English natural philosopher (the term scientist was not coined until 1833), was one of the most inventive and ingenious minds in the history of science. As the Curator of Experiments for the Royal Society of London, Hooke was the first to take advantage of the magnification abilities of the compound microscope. Although these microscopes only magnified about 25 times (25X), Hooke made detailed studies of many small living objects.

In 1665, the Royal Society published his Micrographia, which contained descriptions of microscopes and stunning hand-drawn illustrations, including the anatomy of many insects and the structure of cork, where he used the word cella to describe the “great many little boxes” he observed and from which today we have the word “cell”.

Theory of Spontaneous Generation

There was a considerable controversy surrounding the origin of microbial pathogens. Some proposed that microorganisms originated from nonliving things by spontaneous generation even though larger organisms did not (theory of spontaneous generation). They pointed out that boiled extracts of hay or meat would give rise to microorganisms after sometime. Needham (1713–1781) on the basis of his experiments proposed that all organic matter contained a vital force that could confer the property of life to nonliving matter.

Louis Pasteur Cartoon

Louis Pasteur: Father of Microbiology

Louis Pasteur, French Microbiologist, is known as the father of medical microbiology for his immense contributions to the field of medical microbiology. He first coined the term “microbiology” for the study of organisms of microscopic size.

Joseph Lister: The Pioneer of Antiseptics

Indirect evidence that microorganisms are the agents of human disease came from the work of an English surgeon Joseph Lister (1827–1912) on the prevention of wound infections. Lister, impressed with Pasteur’s studies on the involvement of microorganisms in fermentation and putrefaction, developed a system of antiseptic surgery designed to prevent microorganisms from entering wounds. Instruments were heat sterilized and phenol was used on surgical dressings and at times sprayed over the surgical area. The approach was remarkably successful and transformed surgery after Lister published his findings in 1867. It also provided strong indirect evidence for the role of microorganisms in disease because phenol, which killed bacteria, also prevented wound infections.

Robert Koch: The Founder of Koch’s Postulates

The first direct demonstration of the role of bacteria in causing disease came from the study of anthrax by the German physician Robert Koch (1843–1910). Koch used the criteria proposed by his former teacher, Jacob Henle (1809–1885), to establish the relationship between B. anthracis and anthrax, and he published his findings in 1876 briefly describing the scientific method he followed. In this experiment, Koch injected healthy mice with a material from diseased animals, and the mice became ill. After transferring anthrax by inoculation through a series of 20 mice, he incubated a piece of spleen containing the anthrax bacillus in beef serum. The bacilli grew, reproduced, and produced spores. When the isolated bacilli or spores were injected into mice, anthrax developed.

During Koch’s studies on bacterial diseases, it became necessary to isolate suspected bacterial pathogens. His criteria for proving the causal relationship between a microorganism and a specific disease are known as Koch’s postulates.

Microbial Life Is Everywhere

As we embark on our journey to the microbial world, we will be astounded to learn where microorganisms live in nature. In brief, they live everywhere, including locations too harsh for macroorganisms.

For example, a research team studying the permanently ice-covered Lake Vida in the McMurdo Dry Valleys of Antarctica (top photo) found living bacteria immersed in a subfreezing salt solution at -13°C.

Branches (Sub-Disciplines) of Microbiology

  1. General microbiology: broad range of microbiological questions
  2. Medical microbiology: microbes that cause human disease
  3. Public health and epidemiology: Studies and controls transmission, frequency, and distribution of disease
  4. Immunology: the immune system
  5. Agricultural microbiology: impact of microbes on agriculture
  6. Microbial ecology: relationships between microbes and their habitats. biogeochemical cycles – bioremediation to reduce pollution effects. Try to combat plant diseases that attack important food crops, work on methods to increase soil fertility and crop yields etc. Currently there is a great interest in using bacterial or viral insect pathogens as substitute for chemical pesticides.
  7. Food microbiology: Prevention of food-borne disease; microbes that make food and drink
  8. Industrial microbiology: commercial use of microbes to produce products. used to make products such as antibiotics, vaccines, steroids, alcohols and other solvents, vitamins, amino acids and enzymes.
  9. Biotechnology: manipulation of organisms to form useful products.
  10. Genetic engineering: arisen from work of microbial genetics and molecular biology. Engineered microorganisms are used to make hormones, antibiotics, vaccines and other products. New genes can be inserted into plants and animals.
  11. Microbial physiology and Biochemistry: study the synthesis of antibiotics and toxins, microbial energy production, microbial nitrogen fixation, effects of chemical and physical agents on microbial growth and survival etc.
  12. Microbial genetics and Molecular biology: nature of genetic information and how it regulated the development and function of cells and organisms. Development of new microbial strains that are more efficient in synthesizing useful products.

Future of microbiology

  • Future challenges such as finding new ways to combat disease, reduce pollution and feed the world’s population.
  • AIDS, hemorrhagic fevers and other infectious diseases.
  • Create new drugs, vaccines. Use the techniques in molecular biology and rDNA to solve the problems.
  • Host-pathogen relationships.
  • Study the role of microorganisms as.
  • Sources of high-quality food and other practical products such as enzymes for industrial application.
  • Degrade pollutants and toxic wastes.
  • Used as vectors to treat diseases and enhance agricultural productivity of Microbiology.

Medical Microbiology

Medical Microbiology Image

Medical microbiology is a branch of microbiology that deals with the study of microorganisms including bacteria, viruses, fungi, and parasites of medical importance that are capable of causing diseases in humans. It also includes the study of microbial pathogenesis, disease pathology, immunology, and epidemiology of diseases.

Medical microbiology is among the most widely studied branches of Microbiology. It has given mankind a chance to fight the organisms that, at one point of time, were pure nemesis to us. This has also provided an in-depth knowledge and in-detail understanding of the nature of pathogens that cause disease in humans. This field of microbiology has been the precursor to the wide gamut of immunological innovations in the field of medical science. This field not only has helped to develop vaccines against many invading organisms, it has also, in a more holistic way, given mankind a second shot at life.

Deadly and debilitating diseases like smallpox, polio, rabies, plague, etc. have been either eradicated or have become treatable now because of the efforts of scientists and researchers in the field of medical microbiology.


Bacteria can be of 2 types:

A. Typical bacteria:
Most bacteria have shapes that can be described as a rod, sphere, or corkscrew. Prokarytoic cells are smaller than eukaryotic cells. Nearly all bacteria, with the exception of the mycoplasma, have a rigid cell wall surrounding the cell membrane that determines the shape of the organism. The cell wall also determines whether the bacterium is classified as gram positive or gram negative. External to the cell wall may be flagella, pili, and/or a capsule. Bacterial cells divide by binary fission. However, many bacteria exchange genetic information carried on plasmids (small, specialized genetic elements capable of self-replication) including the information necessary for establishment of antibiotic resistance.

B. Atypical bacteria

Atypical bacteria include groups of organisms such as Mycoplasma, Chlamydia, and Rickettsia that, although prokaryotic, lack significant characteristic structural components or metabolic capabilities that separate them from the larger group of typical bacteria.


Fungi are non-photosynthetic, generally saprophytic, eukaryotic organisms. Some fungi are filamentous and are commonly called molds, whereas others (that is, the yeasts) are unicellular. Fungal reproduction may be asexual, sexual, or both, and all fungi produce spores. Pathogenic fungi can cause diseases, ranging from skin infections (superficial mycoses) to serious, systemic infections (deep mycoses).


Protozoa are single-celled, non-photosynthetic, eukaryotic organisms that come in various shapes and sizes. Many protozoa are free living, but others are among the most clinically important parasites of humans. Members of this group infect all major tissues and organs of the body. They can be intracellular parasites, or extracellular parasites in the blood, urogenital region, or intestine. Transmission is generally by ingestion of an infective stage of the parasite or by insect bite. Protozoa cause a variety of diseases.


Helminths are groups of worms that live as parasites. They are multicellular, eukaryotic organisms with complex body organization. They are divided into three main groups: tapeworms (cestodes), flukes (trematodes), and roundworms (nematodes). Helminths are parasitic, receiving nutrients by ingesting or absorbing digestive contents or ingesting or absorbing body fluids or tissues. Almost any organ in the body can be parasitized.


Viruses are obligate intracellular parasites that do not have a cellular structure. Rather, a virus consists of molecule(s) of DNA (DNA virus) or RNA (RNA virus), but not both, surrounded by a protein coat. A virus may also have an envelope derived from the plasma membrane of the host cell from which the virus is released. Viruses contain the genetic information necessary for directing their own replication but require the host’s cellular structures and enzymatic machinery to complete the process of their own reproduction. The fate of the host cell following viral infection ranges from rapid lysis and release of many progeny virions to gradual, prolonged release of viral particles.

Microbial Ecology

The study of microbial ecology encompasses topics ranging from individual cells to complex systems and includes many different microbial types. Not only is there a visual difference in examining pure cultures and unique microbial environments, but also there is a difference in study approach in each of the images. Microbial ecology has benefited from studies by scientists from many different scientific fields addressing environments throughout the globe. At this time there is considerable interest in understanding microbial community structure in the environment. To achieve this understanding, it is necessary to identify microbes present; this can be accomplished by using molecular methods even though the microbes have not been cultivated in the laboratory. Enzymatic activities of microorganisms and microbial adaptations to the environment are contributing to our knowledge of the physiological ecology of microorganisms.

Persistent questions about microorganisms in the environment include:

  • Which microbes are present?
  • What is the role of each species?
  • What interactions occur in the microbial environment?
  • How do microbes change the environment?

Viruses Bacteria and Other Microorganisms

Microorganisms in the Atmosphere

One of the most hostile environments for many micro-organisms is the atmosphere. Suspended in the air, the tiny microbial propagule may be subjected to desiccation, to the damaging effects of radiant energy from the sun, and the chemical activity of elemental gaseous oxygen (O2) to which it will be intimately exposed. Many microorganisms, especially Gram-negative bacteria, do indeed die very rapidly when suspended in air and yet, although none is able to grow and multiply in the atmosphere, a significant number of microbes are able to survive and use the turbulence of the air as a means of dispersal.

Airborne Bacteria

The bacterial flora can be shown to be dominated by Gram-positive rods and cocci unless there has been a very recent contamination of the air by an aerosol generated from an animal or human source, or from water. The pigmented colonies will often be of micrococci or corynebacteria and the large white-to-cream coloured colonies will frequently be of aerobic spore forming rods of the genus Bacillus. There may also be small raised, tough colonies of the filamentous bacteria belonging to Streptomyces or a related genus of actinomycetes.

Airborne Fungi

Spores of Penicillium and Aspergillus seem to get everywhere in this passive manner and species of these two genera are responsible for a great deal of food spoilage. The individual spores of Penicillium are only 2–3 mm in diameter, spherical to sub-globose (i.e. oval), and so are small and light enough to be efficiently dispersed in turbulent air.

Microorganisms of Soil

The soil environment is extremely complex and different soils have their own diverse flora of bacteria, fungi, protozoa and algae. The soil is such a rich reservoir of microorganisms that it has provided many of the strains used for the industrial production of antibiotics, enzymes, amino acids, vitamins and other products used in both the pharmaceutical and food industries.

The soil is also a very competitive environment and one in which the physico-chemical parameters can change very rapidly. In response to this, many soil bacteria and fungi produce resistant structures, such as the endospores of Bacillus and Clostridium, and chlamydospores and sclerotia of many fungi, which can withstand desiccation and a wide range of temperature fluctuations.

Microorganisms of Water

The aquatic environment represents in area and volume the largest part of the biosphere and both freshwater and the sea contain many species of microorganisms adapted to these particular habitats. The bacteria isolated from the waters of the open oceans often have a physiological requirement for salt, grow best at the relatively low temperatures of the oceans and are nutritionally adapted to the relatively low concentrations of available organic and nitrogenous compounds.

Fungi are also present in both marine and fresh waters but they do not have the same level of significance in food microbiology as other microorganisms.

Microorganisms of Plants

All plant surfaces have a natural flora of micro-organisms which may be sufficiently specialized to be referred to as the phylloplane flora, for that of the leaf surface, and the rhizoplane flora for the surface of the roots. The numbers of organisms on the surfaces of healthy, young plant leaves may be quite low but the species which do occur are well adapted for this highly specialized environment. Moulds such as Cladosporium and the so-called black yeast, Aureobasidium pullulans, are frequently present. There are frequently true yeasts of the genera Sporobolomyces and Bullera on plant leaf surfaces.

Microorganisms of Animal Origin

All healthy animals carry a complex microbial flora, part of which may be very specialized and adapted to growth and survival on its host, and part of which may be transient, reflecting the immediate interactions of the animal with its environment. From a topological point of view, the gut is also part of the external surface of an animal but it offers a very specialized environment.

The microorganisms are characteristic for each species of animal and, in humans, the normal skin flora is dominated by Gram-positive bacteria from the genera Staphylococcus, Corynebacterium and Propionibacterium.

The nose and throat with the mucous membranes which line them represent even more specialized environments and are colonized by a different group of microorganisms. Staphylococcus aureus is carried on the mucous membranes of the nose by a significant percentage of the human population and some strains of this species can produce a powerful toxin capable of eliciting a vomiting response.

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