Microorganisms and Microbiology

Lecture-1

“Microbesrun the world. It’s that simple.”

(Committee on Metagenomics, 2007)
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Microorganisms and Microbiology
• The diversity of microbial world
• The Historical Foundations of Microbiology
• Microbial taxonomy

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The diversity of microbial world

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 What Is Microbiology about and Why Is It Important?
• Microbiology is a specialized area of biology that deals with living things ordinarily too small
to be seen without magnification.
• Such microscopic organisms are collectively referred to as microorganisms, microbes, or other
terms depending on the kind of microbe or the purpose.
• There are several major groups of microorganisms.
• They are bacteria, viruses, protozoa, helminths (parasitic invertebrate animals such as
worms), and fungi.
• All of these are cellular organisms, except for the viruses.
• Viruses infect each of the cellular organisms, and are noncellular, parasitic, protein-coated genetic
elements that can cause harm to the host cell they infect.
• 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 4
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 What Is Microbiology about and Why Is It Important?
• 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.
• 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.

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 The General Characteristics of Microorganisms

• Microbial cells are living compartments that interact with their environment and with other cells
in dynamic ways.
• All cells have much in common and contain many of the same components.
• All cells have a permeability barrier called the cytoplasmic membrane that separates the
inside of the cell, the cytoplasm, from the outside.
• The cytoplasm is an aqueous mixture of macromolecules—proteins, lipids, nucleic acids, and
polysaccharides—small organic molecules (mainly precursors of macromolecules), various
inorganic ions, and ribosomes, the cell’s protein-synthesizing structures.
• The cell wall lends structural strength to a cell; it is a relatively permeable structure located
outside the membrane and is a much stronger layer than the membrane itself.
• Plant cells and most microorganisms have cell walls, whereas animal cells, with rare exceptions,
do not.

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 The General Characteristics of Microorganisms

• Examination of the internal structure of cells reveals two patterns, called prokaryote and
eukaryote.
• Prokaryotes include the Bacteria and the Archaea and consist of small and structurally
rather simple cells.
• Eukaryotes are typically much larger than prokaryotes and contain an assortment of
membrane enclosed cytoplasmic structures called organelles.
• These include, most prominently, the DNA-containing nucleus but also mitochondria and
chloroplasts, organelles that specialize in supplying the cell with energy, and various other
organelles.
• Eukaryotic microorganisms include algae, protozoa and other protists and the fungi.

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 The General Characteristics of Microorganisms
• The genomes of prokaryotes and eukaryotes are organized differently.
• In eukaryotes, DNA is present as linear molecules within the membrane-enclosed nucleus.
• By contrast, the genome of Bacteria and Archaea is a closed circular chromosome (a few
prokaryotes have linear chromosomes).
• The chromosome aggregates within the cell to form the nucleoid, a mass visible in the electron
microscope.
• Most prokaryotes have only a single chromosome, but many also contain one or more small
circles of DNA distinct from that of the chromosome, called plasmids.
• Plasmids typically contain genes that confer a special property on the cell (such as a unique
metabolism, or antibiotic resistance) rather than essential genes needed under all growth
conditions.
• This contrasts with genes on the chromosome, most of which are needed for basic survival.

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 The General Characteristics of Microorganisms
• The majority of microorganisms live a free existence in habitats such as soil and water, where
they are relatively harmless and often beneficial.
• A free-living organism can derive all required foods and other factors directly from the nonliving
environment.
• Some microorganisms require interactions with other organisms.
• Sometimes these microbes are termed parasites.
• They are harbored and nourished by other living organisms called hosts.
• A parasite’s actions cause damage to its host through infection and disease.
• Although parasites cause important diseases, they make up only a small proportion of microbes.
• The majority of microorganisms are single-celled (all bacteria and archaea and some
eukaryotes), but some consist of a few cells.
• Certain invertebrate animals—such as helminths (worms), many of which can be seen with the
naked eye—are also included in the study of infectious diseases because of the way they are
transmitted and the way the body responds to them, though they are not microorganisms.
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 Activities of Microbial Cells

• What activities do microbial cells carry out?

• Microbial cells typically live in groups called microbial communities.
• All cells show some form of metabolism by taking up nutrients from the environment and
transforming them into new cell materials and waste products.
• During these transformations, energy is conserved that can be used by the cell to support
synthesis of new structures.
• Production of these new structures culminates in the division of the cell to form two cells.
• In microbiology, we use the word growth to refer to the increase in cell number as a result of cell
division.

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 Activities of Microbial Cells

• During metabolism and growth, both genetic and catalytic events occur in cells; biological
information flow is initiated and metabolic pathways are engaged.
• On the genetic side, the cell’s genome is replicated, and the proteins needed to support growth
under a given set of conditions are biosynthesized in the sequential processes of transcription and
translation.
• These events require that the cell’s catalytic machinery—its enzymes— carry out reactions that
supply the energy and precursors necessary for the biosynthesis of all cell components.
• Catalytic and genetic events in a microbial cell are coordinated and highly regulated to ensure
that new cell materials are made in the proper order and concentrations and that the cell remains
optimally tuned to its surroundings.

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 Activities of Microbial Cells

• Many microbial cells are capable of motility.

• Motility allows cells to move away from unfavorable conditions and to exploit new
resources or growth opportunities.
• Some microbial cells undergo differentiation, which may result in the formation of modified
cells specialized for growth, dispersal, or survival.
• Cells respond to chemical signals in their environment, including those produced by other
cells of either the same or different species, and these signals often trigger new cellular
activities.
• Microbial cells thus exhibit intercellular communication; they are “aware” of their neighbors
and can respond accordingly.
• Many prokaryotic cells can also transfer genes to or accept genes from neighboring cells,
either of the same species or of a different species, in the process of genetic exchange.

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 Activities of Microbial Cells

• Evolution is the process of descent with modification in which genetic variants (mutants) are
selected based on their reproductive fitness.
• Although evolution is a very slow process, evolution in microbial cells can be very rapid when
selective pressure is strong.
• For example, witness today how genes encoding antibiotic resistance in pathogenic (disease-
causing) bacteria have been selected and widely distributed by the indiscriminate use of
antibiotics in human and veterinary medicine.
• Genetic exchange between prokaryotic cells, which is independent of evolution, can also
significantly accelerate the adaptation of cells to new habitats or to rapidly changing conditions.

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 Members of the Microbial World
• Life on earth through the ages Earth is 4.6 billion years old and evidence shows that microbial cells
first appeared between 3.8 and 3.9 billion years ago.
• During the first 2 billion years of Earth’s existence, its atmosphere was anoxic (O2 was absent), and
only nitrogen (N2), carbon dioxide (CO2), and a few other gases were present.
• Only microorganisms capable of anaerobic metabolisms could survive under these conditions.
• The evolution of phototrophic microorganisms— organisms that harvest energy from sunlight—
occurred within 1 billion years of the formation of Earth.
• The first phototrophs were relatively simple ones, such as purple or green bacteria and other
anoxygenic (non-oxygen-evolving) phototrophs.
• Cyanobacteria (oxygen-evolving phototrophs) evolved from anoxygenic phototrophs nearly a
billion years later and began the slow process of oxygenating Earth’s atmosphere.
• Triggered by increases in O2 in the atmosphere, multicellular life forms eventually evolved and
continued to increase in complexity, culminating in the plants and animals we know today.
• But plants and animals have only existed for about half a billion years.
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 Members of the Microbial World
• Microorganisms were the first entities on Earth that showed
the properties we associate with life.
• How did microbial cells originate and how are extant
microbial cells related to one other?
• Because all cells are constructed in similar ways, it is thought
that all cells have descended from a common ancestral cell,
the last universal common ancestor (LUCA).
• After the first cells arose from nonliving materials, a
process that occurred over hundreds of millions of years, their Figure: The three domains of cellular organisms
subsequent growth formed cell populations and these began to are Bacteria, Archaea, and Eukarya. Archaea
interact with other cell populations to form microbial and Eukarya diverged long before nucleated
communities. cells with organelles (“modern eukaryotes” in
• Along the way, evolution and genetic exchange served up part a) appear in the fossil record. LUCA, last
variants that could be selected for improvements that made universal common ancestor.
their success and survival more probable.

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 Members of the Microbial World

• Microorganisms are defined as those organisms too small to be seen clearly by the unaided eye
(figure 1.1).
• They are generally several micrometer or less in diameter.
• Although small size is an important characteristic of microbes, it alone is not sufficient to define
them.
• Some microbes, such as bread molds and filamentous photosynthetic microbes, are actually
visible without microscopes.
• These macroscopic microbes are often colonial, consisting of small aggregations of cells.

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• Some macroscopic microorganisms are multicellular.
• They are distinguished from other multicellular life forms such as plants and
animals by their lack of highly differentiated tissues.
• Most unicellular microbes are microscopic.
• In addition to microorganisms, microbiologists study a variety of acellular
biological entities (figure 1.1).
• These include viruses and subviral agents.
• Although the term “microorganism” is often applied only to cellular
microbes, some texts use both “microorganism” and “microbe” when
referring to these acellular agents.

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 Members of the Microbial World

• The diversity of microorganisms has always presented a challenge to microbial taxonomists.

• An important breakthrough in microbial taxonomy arose from studies of their cellular
architecture, when it was discovered that cells exhibited one of two possible “floor plans.”
• Cells that came to be called prokaryotic cells (Greek pro, before, and karyon, nut or kernel;
organisms with a primordial nucleus) have an open floor plan.
• That is, their contents are not divided into compartments (“rooms”) by membranes.
• The most obvious characteristic of these cells is that they lack the membrane-delimited
nucleus observed in eukaryotic cells (Greek eu, true, and karyon, nut or kernel).
• Eukaryotic cells not only have a nucleus but also many other membrane-bound organelles that
separate some cellular materials and processes from others.

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 Members of the Microbial World
• These observations eventually led to the development of a classification scheme that
divided organisms into five kingdoms: Monera, Protista, Fungi, Animalia, and Plantae.
• Microorganisms (except for viruses and other acellular infectious agents, which have
their own classification system) were placed in the first three kingdoms.
• In this scheme, all organisms with prokaryotic cell structure were placed in Monera.
• The five-kingdom system was an important development in microbial taxonomy, but it
is no longer accepted by microbiologists.

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 Members of the Microbial World
• Great progress has been made in three areas that profoundly affect microbial classification.
• First, much has been learned about the detailed structure of microbial cells from the use of electron
microscopy.
• Second, microbiologists have determined the biochemical and physiological characteristics of
many different microorganisms.
• Third, the sequences of nucleic acids and proteins from a wide variety of organisms have been
compared.
• The comparison of ribosomal RNA (rRNA), begun by Carl Woese (1928–2012) in the 1970s, was
instrumental in demonstrating that there are two very different groups of organisms with
prokaryotic cell architecture: Bacteria and Archaea.
• Later studies based on rRNA comparisons showed that Protista is not a cohesive taxonomic unit
(i.e., taxon) and that it should be divided into three or more kingdoms.
• These studies and others have led many taxonomists to reject the five-kingdom system in favor of
one that divides cellular organisms into three domains: Bacteria, Archaea, and Eukarya (all
eukaryotic organisms) 25
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 Bacteria

• Bacteria (singular: bacterium) are relatively simple, single-

celled (unicellular) organisms.
• The cells are described as prokaryotic because they lack a
nucleus (their genetic material is not enclosed in a special
nuclear membrane) bacterial cells are called prokaryotes, from
Greek words meaning prenucleus.
• Prokaryotes include both bacteria and archaea.
• Bacteria are abundant in soil, water, and air, including sites
that have extreme temperatures, pH, or salinity.
• Bacteria are also major inhabitants of our bodies, forming
the human microbiome.

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 Archaea
• They are prokaryotic cells
• Archaea or Archaebacteria differ from true bacteria by their
distinctive rRNA sequences, their cell wall structure and lack
peptidoglycans and have unique membrane lipids.
• Some have unusual metabolic characteristics, such as the
methanogens, which generate methane (natural) gas.
• They are found in extreme environmental conditions.
• The extreme halophiles (halo = salt; philic = loving) live in
extremely salty environments such as the Great Salt Lake and
the Dead Sea.
• The extreme thermophiles (therm = heat) live in hot sulfurous
water, such as hot springs at Yellowstone National Park.
• Archaea are not known to cause disease in humans.
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 Fungi
• Fungi (mushroom, molds, and yeasts) are eukaryotic cells (with
a true nucleus).
• Most fungi are multicellular and their cell wall is composed of
chitin.
• They obtain nutrients by absorbing organic material from
their environment (decomposers), through symbiotic
relationships with plants (symbionts), or harmful
relationships with a host (parasites).
• They form characteristic filamentous tubes called hyphae that
help absorb material.
• The collection of hyphae is called mycelium.
• Fungi reproduce by releasing spores.

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 Algae
• Algae (singular: alga) are photosynthetic eukaryotes with a wide variety
of shapes.
• Algae are photosynthetic.
• They, together with cyanobacteria, produce about 75% of the planet’s
oxygen and are the foundation of aquatic food chains.
• The algae of interest to microbiologists are usually unicellular.
• The cell walls of many algae are composed of a carbohydrate called
cellulose.
• Algae are abundant in freshwater and saltwater, in soil, and in
association with plants.
• As a result of photosynthesis, algae produce oxygen and carbohydrates that
are then utilized by other organisms, including animals.
• Thus, they play an important role in the balance of nature
• They live in water, damp soil, and rocks and produce oxygen and
carbohydrates used by other organisms.
• It is believed that cyanobacteria are the origins of green land plants. 30
 Protozoa

• Protozoa (singular: protozoan) are unicellular eukaryotic microbes, animal-like protists

• Protozoa move by pseudopods, flagella, or cilia.
• Amebae move by using extensions of their cytoplasm called pseudopods (false feet).
• Other protozoa have long flagella or numerous shorter appendages for locomotion called
cilia.
• Protozoa have a variety of shapes and live either as free entities or as parasites (organisms
that derive nutrients from living hosts) that absorb or ingest organic compounds from their
environment.
• Many free-living protozoa function as the principal hunters and grazers of the microbial
world.

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• They obtain nutrients by ingesting organic matter and other microbes.
• They can be found in many different environments, and some are normal
inhabitants of the intestinal tracts of animals, where they aid in digestion
of complex materials such as cellulose.
• Some protozoa, such as Euglena, are photosynthetic.
• They use light as a source of energy and carbon dioxide as their chief source
of carbon to produce sugars.

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 Multicellular Animal Parasites
• Although multicellular animal parasites are not strictly microorganisms, they are of
medical importance.
• Animal parasites are eukaryotes.
• The two major groups of parasitic worms are the flatworms and the roundworms,
collectively called helminths.
• During some stages of their life cycle, helminths are microscopic in size.
• Laboratory identification of these organisms includes many of the same techniques used
for identifying microbes.

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 Viruses

• The microbial world also includes numerous acellular

infectious agents.
• Viruses are very different from the other microbial groups
• They are so small that most can be seen only with an
electron microscope).
• Structurally very simple, a virus particle contains a core
made of only one type of nucleic acid, either DNA or
RNA.
• This core is surrounded by a protein coat, which is
sometimes encased by a lipid membrane called an
envelope.

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 Members of the Microbial World

• However, their small size belies their power: they cause many animal and plant diseases and have
caused epidemics that have shaped human history.
• Viral diseases include smallpox, rabies, influenza, AIDS, the common cold, and some cancers.
• Viruses also play important roles in aquatic environments, and their role in shaping aquatic
microbial communities is currently being explored.
• Viroids are infectious agents composed only of ribonucleic acid (RNA).
• They cause numerous plant diseases.
• Satellites are composed of a nucleic acid enclosed in a protein shell.
• They cause plant diseases and some important animal diseases such as hepatitis.
• Finally, prions, infectious agents composed only of protein, are responsible for causing a variety
of spongiform encephalopathies such as scrapie and “mad cow disease.”

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The Historical Foundations of Microbiology

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 Robert Hooke

• Robert Hooke (1635–1703), an English mathematician and natural historian, was also an
excellent microscopist.
• In 1665, after observing a thin slice of cork through a crude microscope
• Robert Hooke reported that life’s smallest structural units were “little boxes,” or “cells.”
• Using his improved microscope, Hooke later saw individual cells.
• To Hooke, thin sections of cork resembled“Honey-comb,”or “small Boxes
• Hook e’s discovery marked the beginning of the cell theory—the theory that all living things are
composed of cells.
• Described fruiting structures of molds in 1665
• First person to describe microorganisms

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Robert Hooke

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 Antoni van Leeuwenhoek (1632-1723)

 Dutch merchant and amateur scientist Anton van Leeuwenhoek was probably the first to
observe live microorganisms through the magnifying lenses of the more than 400 microscopes
he constructed.
 Between 1673 and 1723, he wrote about the “animalcules” he saw through his simple, single
lens microscopes.
 Van Leeuwenhoek made detailed drawings of organisms he found in rainwater, feces, and
material scraped from teeth.
 These drawings have since been identified as representations of bacteria and protozoa.

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 The Theory of Spontaneous Generation

 The Greek philosopher Aristotle (384–322 BC) was one of the

earliest recorded scholars to articulate the theory of
spontaneous generation, the notion that life can arise from
nonliving matter.
 Aristotle proposed that life arose from nonliving material if
the material contained pneuma (“vital heat”).
 As evidence, he noted several instances of the appearance of
animals from environments previously devoid of such animals,
such as the seemingly sudden appearance of fish in a new
puddle of water.

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 The theory of biogenesis

• In 1858 Rudolf Virchow challenged spontaneous

generation theory with the concept of biogenesis,the claim
that living things can arise only from preexisting living
cells
• Because he could offer no scientific proof, arguments about
spontaneous generation continued until 1861, when the
issue was finally resolved by the French scientist Louis
Pasteur.

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 Disproving Spontaneous Generation
Louis Pasteur (1822-1895)

• Though challenged in the 17th and 18th

centuries by the experiments of Francesco
Redi and Lazzaro Spallanzani, spontaneous
generation was not disproved until the work
of Louis Pasteur and John Tyndall in the mid-
19th century.
• By the middle of the 19th century, experiments by
Louis Pasteur and others refuted the
traditional theory of spontaneous generation
and supported biogenesis.

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 Pasteur’s Experiments
• Pasteur set up a series of experiments to test the hypothesis that “Life only arises from
other life”.
• Experiment 1A and 1B: Pasteur sterilized a meat broth in glass flasks by heating.
• He then either left the neck open to the air (A) or sealed the glass neck (B).
• Organisms only appeared (turned the broth cloudy) in the open flask.
• Experiment 2A and 2B: Pasteur sterilized a meat broth in swan-neck flasks (A), so
named because their S-shaped necks resembled a swan’s neck.
• No organisms appeared, even after many days.
• However, if the neck was snapped off or the broth tipped to come in contact with the neck
(B), organisms (cloudy broth) soon appeared.

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Pasteur’s Experiments

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 Disproving Spontaneous Generation

• Pasteur showed that microorganisms can be present in nonliving matter—on solids, in

liquids, and in the air.
• Furthermore, he demonstrated conclusively that microbial life can be destroyed by heat
and that methods can be devised to block the access of airborne microorganisms to
nutrient environments.
• These discoveries form the basis of aseptic techniques, procedures that prevent
contamination by unwanted microorganisms, which are now the standard practice in
laboratory and many medical procedures.
• Modern aseptic techniques are among the first and most important concepts that a
beginning microbiologist learns.

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 Fermentation and Pasteurization

• One of the key steps that established the relationship between microorganisms and disease
occurred when a group of French merchants asked Pasteur to find out why wine and beer
soured.
• At the time, many scientists believed that air converted the sugars in these fluids into alcohol.
• Pasteur found instead that microorganisms called yeasts convert the sugars to alcohol in the
absence of air. This process, called fermentation, is used to make wine and beer.
• Souring and spoilage are caused by different microorganisms, called bacteria.
• In the presence of air, bacteria change the alcohol into vinegar (acetic acid).
• Pasteur’s solution to the spoilage problem was to heat the beer and wine just enough to kill most
of the bacteria that caused the spoilage.
• The process, called pasteurization, is now commonly used to reduce spoilage and kill potentially
harmful bacteria in milk and other beverages as well as in some alcoholic beverages.

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Eduard Buchner’s (1860 –1917) Experiments on Acellular Fermentation
Showed, in 1897, that fermentation does not require the actual presence of living
cells, but only cell-produced proteins called enzymes.
Buchner’s work begin the field of biochemistry and the study of metabolism (all
chemical reactions within an organism)

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 First Golden Age of Microbiology
• The period from 1857 to 1914 has been appropriately named the First Golden
Age of Microbiology.
• Rapid advances, spearheaded mainly by Pasteur and Robert Koch, led to the
establishment of microbiology.
 Discoveries during this period:
• Agents of diseases
• Role of immunity in the prevention and cure of disease
• Chemical activities of microorganisms
• Improved microscopy
• Culturing microorganisms
• Development of vaccines
• Surgical techniques

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 The Germ Theory of Disease
 For centuries, disease was believed to be punishment for an individual’s crimes or misdeeds.
 When the inhabitants of an entire village became ill, people often blamed the disease on demons
appearing as foul odors from sewage or on poisonous vapors from swamps.
 The realization that yeasts play a crucial role in fermentation was the first link between the
activity of a microorganism and physical and chemical changes in organic materials.
 This discovery alerted scientists to the possibility that microorganisms might have similar
relationships with plants and animals—specifically, that microorganisms might cause disease.
 This idea was known as the germ theory of disease.
 Agostino Bassi (1773–1856) demonstrated in 1835 that a silkworm disease was due to a
fungal infection.
 He also suggested that many diseases were due to microbial infections.
 In 1845 M. J. Berkeley (1803–1889) proved that the great potato blight of Ireland was
caused by a water mold (then thought to be a fungus), and in 1853 Heinrich de Bary (1831–
1888) showed that smut and rust fungi caused cereal crop diseases.
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 The Germ Theory of Disease

• In the 1860s, Joseph Lister, an English surgeon, applied the germ theory to medical
procedures.
• Lister had also heard of Pasteur’s work connecting microbes to animal diseases.
• Disinfectants were not used at the time, but Lister knew that phenol (carbolic acid) kills
bacteria, so he began treating surgical wounds with a phenol solution.
• The practice so reduced the incidence of infections and deaths that other surgeons quickly
adopted it.
• His findings proved that microorganisms cause surgical wound infections.

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 Robert Koch (1843–1910)

 The first proof that bacteria actually cause disease came from Robert Koch, a German physician
in 1876.
 Anthrax, a disease that was destroying cattle and sheep in Europe.
 Koch discovered rod shaped bacteria now known as Bacillus anthracis in the blood of cattle
that had died of anthrax.
 He cultured the bacteria on nutrients and then injected samples of the culture into healthy
animals.
 When these animals became sick and died, Koch isolated the bacteria in their blood and
compared them with the originally isolated bacteria.
 He found that the two sets of blood cultures contained the same bacteria.
 Koch thus established Koch’s postulates, a sequence of experimental steps for directly relating
a specific microbe to a specific disease
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 Koch’s postulates
• Koch’s research provides a framework for the study of the etiology of any infectious
disease. Today, we refer to Koch’s experimental requirements as Koch’s postulates
• Koch’s postulates state the following:
1. The disease-causing organism must always be present in animals suffering from the
disease but not in healthy animals.
2. The organism must be cultivated in a pure culture away from the animal body.
3. The isolated organism must cause the disease when inoculated into healthy susceptible
animals.
4. The organism must be isolated from the newly infected animals and cultured again in
the laboratory, after which it should be seen to be the same as the original organism

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 Robert Koch (1843–1910)

• After completing his anthrax studies, Koch fully

outlined his postulates in his work on the cause of
tuberculosis.
• In 1884 he reported that this disease was caused by
the rod-shaped bacterium Mycobacterium
tuberculosis
• 1905 he was awarded the Nobel Prize in Physiology
or Medicine.
• Koch’s postulates were quickly adopted by others and
used to connect many diseases to their causative
agent.

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 Work Toward Controlling Infections
• Two nineteenth-century physicians, Ignaz Philipp Semmelweis of Austria and Joseph Lister
of England, were convinced that microorganisms caused infections.
• In 1865, Lister, who had read of Pasteur’s work on pasteurization and Semmelweis’s work on
improving sanitation, initiated the use of dilute carbolic acid on bandages and instruments
to reduce infection.
• His methods, the first aseptic techniques, were proven effective by the decrease in surgical
wound infections in his surgical wards.
• He is considered the father of antiseptic surgery.

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 Work Toward Controlling Infections

• Ignaz Semmelweis was a Hungarian obstetrician who was shocked by

the numbers of pregnant women in his hospital who were dying of
puerperal fever (a type of blood poisoning also called childbed
fever) during labor.
• He determined the disease was more prevalent in the ward handled by
medical students (29% deaths) than in the ward run by midwifery
students (3% deaths).
• This comparative study suggested to Semmelweis that the mode of
transmission must involve his medical students.
• He deduced that the source of contagion must be from cadavers on
which the medical students previously had been performing
autopsies because midwifery students did not work on cadavers.
• So, in 1847, Semmelweis directed his staff to wash their hands in
chlorinated lime water before and after examining the patients.
• Deaths from childbed fever dropped, showing that disease spread
could be interrupted.
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 Work Toward Controlling Infections
• In 1854, a cholera epidemic hit London, including the Soho district.
• With residents dying, English surgeon John Snow set out to discover the reason for
cholera’s spread.
• He carried out one of the first thorough epidemiological studies by interviewing sick and
healthy Londoners and plotting the location of each cholera case on a district map.
• The results indicated most cholera cases clustered to a sewage-contaminated street
pump from which local residents obtained their drinking water.
• Snow then instituted the first known example of a public health measure to interrupt
disease transmission—he requested the parish Board of Guardians to remove the street
pump handle!
• He asserted that “organized particles” caused cholera—an educated guess that proved to
be correct even though the causative agent would not be identified for another 29 years

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 John Snow (inset) produced
a map plotting all the
cholera cases in the London
Soho district and observed a
cluster near to the Broad
Street pump (circle).
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 Vaccination

Edward Jenner, a young British physician, embarked on an experiment to find a way to protect
people from smallpox.
When a young milkmaid informed Jenner that she couldn’t get smallpox because she already had
been sick from cowpox— a much milder disease—he decided to put the girl’s story to the test.
First Jenner collected scrapings from cowpox blisters. He inoculated his own son with fluid from a
cowpox blister.
He later similarly inoculated an 8-year-old with the cowpox material and subsequently inoculated
the same child with smallpox.
 In a few days, the volunteer became mildly sick but recovered and never again contracted either
cowpox or smallpox.
The protection from disease provided by vaccination (or by recovery from the disease itself) is called
immunity. The word vaccinia (vacca, the Latin name for “cow”) gave rise both to the name of the
virus that causes cowpox and to the word vaccine.
Pasteur prepared vaccines against chicken cholera, anthrax and rabies. 63
 The First Synthetic Drugs

• Paul Ehrlich, a medical student, speculated about a “magic bullet” that could hunt down and destroy a
pathogen without harming the infected host.
• In 1910, after testing hundreds of substances, he found a chemotherapeutic agent called salvarsan, an
arsenic derivative effective against syphilis.
• Before this discovery, the only known chemical in Europe’s medical arsenal was an extract from the bark
of a South American tree, quinine, which had been used by Spanish conquistadors to treat malaria.
• By the late 1930s, researchers had developed several other synthetic drugs that could destroy
microorganisms.
• In addition, sulfonamides (sulfa drugs) were synthesized at about the same time

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 The Birth of Modern Chemotherapy

• 1928: Alexander Fleming discovered the first antibiotic.

• He observed that Penicillium fungus made an antibiotic,
penicillin, that killed S. aureus.
• 1940s: Penicillin was tested clinically and mass
produced.

65
Figure 1.5
Microbial taxonomy

66
 Classification of Microorganisms
• Taxonomy (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or
govern) is defined as the science of biological classification.
• In a broader sense it consists of three separate but interrelated parts: classification,
nomenclature, and identification.
• Once a classification scheme is selected, it is used to arrange organisms into groups called
taxa (s., taxon) based on mutual similarity.
• Nomenclature is the branch of taxonomy concerned with the assignment of names to
taxonomic groups in agreement with published rules.
• Identification is the practical side of taxonomy, the process of determining if a
particular isolate belongs to a recognized taxon.

67
 Classification of Microorganisms
Importance of Taxonomy:
•The objective of taxonomy is to classify living organisms - that is, to establish the relationships
between one group of organisms and another and to differentiate them.
•There may be as many as 100 million different living organisms, but fewer than 10% have been
discovered, much less classified and identified.
•Taxonomy also provides a common reference for identifying organisms already classified.
•To classify living organisms-that is to establish the relationships between one group of
microorganisms and another and to differentiate between them.
•To identify a previously unknown organism and then group or classify it with other organisms that
have similar characteristics.
•To provide a common reference for identifying organisms already classified.
•This is a basic and necessary tool for scientists,as it provides a universal language of
communication.

68
 Classification of Microorganisms
What is Classification?
•Classification is the organization of organisms into progressively more inclusive groups on the
basis of either phenotypic similarity or evolutionary relationship.
•Living organisms are grouped according to similar characteristics (classification), and each
organism is assigned a unique scientific name.
The Taxonomic Hierarchy:
•The classification of microbes involves placing them within hierarchical taxonomic levels.
•The highest rank is the domain, and all prokaryotes belong to either the Bacteria or the Archaea.
Within each domain, each microbe is assigned (in descending order) to a phylum, class, order,
family, genus, and species
•Just as a number of species make up a genus, related genera make up a family.
•A group of similar families constitutes an order, and a group of similar orders makes up a
class. Related classes, in turn, make up a phylum. All phyla that are related to each other make
up a kingdom, and related kingdoms are grouped into a domain.
69
70
71
72
 Methods of Classifying and identifying Microorganisms
•  Once an organism is identified, it can be placed into a previously devised classification scheme.
• Microorganisms are identified for practical purposes—for example, to determine an appropriate treatment
for an infection.
• Many different approaches are used in classifying and identifying microorganisms that have been isolated
and grown in pure culture.
• For clarity, we divide them into two groups: classical and molecular. The most durable identifications
are those that are based on a combination of approaches.
• Classical Characteristics: Classical approaches to taxonomy make use of morphological,
physiological, biochemical, and ecological characteristics. These characteristics have been employed
in microbial taxonomy for many years and form the basis for phenetic (phenotypic) classification. When
used in combination, they are quite useful in routine identification of well-characterized microbes.
• Molecular Characteristics: The study of DNA, RNA, and proteins has advanced our understanding of
microbial evolution and taxonomy.

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 Scientific Nomenclature
• Nomenclature is the actual naming of organisms and follows the binomial system of
nomenclature devised by the Swedish medical doctor and botanist, Carl Linnaeus, and
used throughout biology; organisms are given genus names and species epithets.
• Binomials are used by scientists worldwide.
• These names are the genus name and specific epithet (species), and both names are
printed underlined or italicized.
• The genus name is always capitalized and is always a noun.
• The species name is lowercase and is usually an adjective.
• Genus name is capitalized and may be abbreviated.
• Species name is never abbreviated
• A genus name may be used alone to indicate a genus group; species name is never used
alone eg: Bacillus subtilis (B. subtilis)

74
 Scientific Nomenclature
• Common or descriptive names (trivial names): Names for organisms that may be in common
usage, but are not taxonomic names.eg: tubercle bacillus  (Mycobacterium tuberculosis);
meningococcus (Neiserria meningitidis);Group A streptococcus (Streptococcus pyogenes)
• When writing a bacterial name, the first time you use the name it is spelled out in full.
• Every time after that, the genus name is abbreviated to (usually) one letter with a period and
the species name is spelled out in full (all are italicized)
– Escherichia coli or E. coli
– Clostridium perfringens or C. perfringens
• As well as taxonomically correct names, there are trivial names e.g., staphylococci or
corynebacteria.
• These names are never italicized or capitalized (unless at the beginning of a sentence):
– Some staphylococci are pathogenic for humans
– Staphylococci are often human pathogens
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 Scientific Nomenclature
• The species name is stable. In contrast, a generic name can change if the organism is assigned to
another genus.
• For example, some members of the genus Streptococcus were placed into two new genera,
Enterococcus and Lactococcus, based on rRNA analysis and other characteristics. Thus
Streptococcus faecalis is now Enterococcus faecalis.
• Rules for assigning names for protozoa and parasitic worms are published in the International
Code of Zoological Nomenclature.
• Rules for assigning names for fungi and algae are published in the International Code of
Botanical Nomenclature.
• Rules for naming newly classified prokaryotes and for assigning prokaryotes to taxa are
established by the International Committee on Systematics of Prokaryotes and are published in
the Bacteriological Code.
• Descriptions of prokaryotes and evidence for their classifications are published in the
International Journal of Systematic and Evolutionary Microbiology before being incorporated
into a reference called Bergey’s Manual. 76