Chapter one

Introduction to microbiology
 Learning objective
At the end of this chapter students will be able to
• Define microbiology and microorganism
• Discuss Scope of microbiology
• Describe importance of microorganism
• Recognize History of microbiology
• Explain taxonomy and classification of
microorganisms
 Scope of microbiology

Expected Learning Outcomes

1. Define microbiology and
microorganisms
2. Identify the major organisms
included in the science of
microbiology.
3. Name and define the primary areas
included in microbiological studies
 Introduction
 Microbiology is a specialized area of biology that deals with tiny
life forms that are not readily observed without magnifi cation.
 Medical microbiology is the study of pathogens or medically
important microbes, the disease caused by them, and the body’s
defenses against disease.
 Microorganisms-simple in structure, and usually small in size,
that are generally considered to be neither plants nor animals
Where we can find microorganisms?
• To sum up the presence of microbes in
one word, they are ubiquitous.
• *They are found in all natural habitats
• Microbes exist deep beneath the polar
icecaps, in the ocean to a depth of 7
miles,
• in hot springs and thermal vents, in toxic
waste dumps, and even in the clouds
• The nature of microorganisms makes
them both easy and difficult to study.
• Easy, because they reproduce so
rapidly and can usually be grown in
large numbers in the laboratory.
• Difficult, because we can’t observe
or analyze them without special
techniques, especially the use of
microscopes
• Microbiology study every aspect of
microbes like
their genetics,
their physiology,
 characteristics that may be harmful or
beneficial,
the ways they interact with the
environment,
the ways they interact with other
organisms, and
 their uses in industry and agriculture.
• There are several major groups of
microorganisms that we will be
studying. They are
– Bacteria
– Viruses
– Fungi
– Protozoa
– Algae and
– Helminths (parasitic worms).
 Microbiology is highly versatile science that involved in every
aspects of our life. It involves
 geomicrobiologists, who focus on the roles of microbes in the
development of earth’s crust;
 marine microbiologists, who study the oceans and its smallest
inhabitants;
 medical technologists, who do the tests that help diagnose
pathogenic microbes and their diseases; nurse epidemiologists,
who analyze the occurrence of infectious diseases in hospitals;
 astrobiologists, who study the possibilities of organisms in
space
• Veterinary Microbiology- animal digestion and disease dx, pro-
biotics.
• Public Health Microbiology- in foods and beverages
• Industrial Microbiology –involve in production, bioremediation
• Pharmaceutical Microbiology – antibiotics production and test-
ing
• Agriculture Microbiology – natural fertilizers, decomposing
• Plant Microbiology – plant disease dx and elemental cycle
 A Sampling of Fields and
Occupations in Microbiology
A. Immunology
• This branch studies the complex web
of protective substances and
reactions caused by invading
microbes and other harmful entities.
• It includes such diverse areas as
blood testing, vaccination, and
allergy
B. Public Health Microbiology and Epidemiology
• These branches monitor and control the
spread of diseases in communities.
• Some of the institutions charged with this
task are the U.S. Public Health Service
(USPHS) and the Centers for Disease Control
and Prevention (CDC).
• The CDC collects information and statistics
on diseases from around the United States
and publishes it in a newsletter,
C. Biotechnology
• This branch is defined by any process
that harnesses the actions of living
things to arrive at a desired product,
ranging from beer to stem cells.
• It includes industrial microbiology, which
uses microbes to produce and harvest
large quantities of such substances as
vaccines, vitamins, drugs, and enzymes
D. Genetic Engineering and
Recombinant DNA Technology
• These interrelated fields involve
deliberate alterations of the genetic
makeup of organisms to create novel
microbes, plants, and animals with
unique behavior and physiology.
• This is a rapidly expanding field that
often complements biotechnology
E. Food Microbiology, Dairy Microbiology, and
Aquatic Microbiology
• These branches examine the ecological and
practical roles of microbes in food and water.
• Food microbiologists are concerned with the
effects of microbes, including such areas as
food spoilage, food-borne diseases, and
production.
• Aquatic microbiologists explore the ecology of
natural waters as well as the impact of
microbes on water purity and treatment.
F. Agricultural Microbiology
• This branch is concerned with the
relationships between microbes and
domesticated plants and animals.
• Plant specialists focus on plant diseases,
soil fertility, and nutritional interactions.
• Animal specialists work with infectious
diseases and other associations animals
have with microorganisms.
 Essence of microbiology
Food and Food Safety
• The natural processes of microorganisms impact food in both
positive and negative ways.
• Fermentation of wine and beer depend on microbial processes
• Bread rises because of the carbon dioxide released by yeast as
the yeast grows.
• The transformation of milk to cheese requires microbes.
Food-borne illnesses
• Food-borne illnesses can be caused by bacteria, viruses, para-
sites, natural toxins (often a byproduct of microorganism ac-
tivit) and environmental toxins.
• Food spoilage occurs when microorganisms decompose food.

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Environment and Ecosystems
• Microorganisms fill many niches in environments.
• Microbes like the chemosynthetic bacteria at deep sea vents
and phytoplankton form the base of many aquatic food chains.
• Fungi, bacteria and protists perform the important task of de-
composition that releases nutrients back into the environment.
• A gram of soil contains an estimated one billion microorgan-
isms from possibly thousands of species.
• carbon, nitrogen, phosphorus and sulfur cycles.

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Health and Medicine
• Different studies showed that microbes had to have traveled
from place to place.
• Understanding vectors, those methods of transport, led to many
health practices, including washing one‘s hands before eating
and after using the bathroom.

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Research and Teaching
• Microbiology research provides answers (and questions) about
microorganisms.
– Pasteur‘s research into spoilage of beer and wine led to
health practices like pasteurization of beer, wine and, after
1886, milk.
• Pasteur's techniques led to the discovery of viruses by the
Russian microbiologist Dmitry Ivanovsky.
• Researchers test microorganisms to understand their behaviors
and interactions.
• Microbiology research has led to improved crop yields, bio
remediation of pollutants like oil and diesel and techniques to
cure diseases, reduce food-borne illnesses and prevent infec-
tions.

20
Probiotics: are mixtures of bacteria or yeast that upon ingestion
colonize and proliferate, even temporarily, the intestine.
• It believed that they act by rebalancing the microbiome and its
functions, such as enhancing digestion of food and modulating the
individual’s innate and immune response.
• The most common reason people use over-the counter probiotics
is to promote and maintain regular bowel function.
• Probiotics are commonly gram-positive bacteria (e.g., Bifidobac-
terium, Lactobacillus) and yeasts (e.g., Saccharomyces).

21
 General Characteristics of Microorganisms and
Their Roles in the Earth’s Environments

 Expected Learning Outcomes

Describe the basic characteristics of prokaryotic cells and

eukaryotic cells and their evolutionary origins.
State several ways that microbes are involved in the earth
ecosystems.
Describe the cellular makeup of microorganisms and their
ange, and indicate how viruses differ from cellular microbes.

22
 The Origins of
Microorganisms
• The fossil record dating from ancient
rocks and sediments points to
bacteria like cells that existed at
least 3.5 billion years ago
• These simple cells were the
dominant cells on earth for about 2
billion years.
• They were very small and lacked
complex internal structures.
• One of these structures was a 23
• About 1.8 billion years ago, there
appeared in the fossil record a more
complex cell, which contained a
nucleus and other complex internal
structures
• These types of cells and organisms
are defined as eukaryotic * in
reference to their “true” nucleus.
• The early eukaryotes, probably
similar to algae and protozoa, started
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 The Cellular Organization
of Microorganisms
• As a general rule, prokaryotic cells
are smaller than eukaryotic cells, and
in addition to lacking a nucleus, they
lack other complex internal
compartments called organelles.
• Organelles are structures in cells that
are bound by one or more
membranes.
• Examples such as mitochondria and
Golgi complex perform specific 25
• All prokaryotes are microorganisms
and include the bacteria and
archaeons
• Only some of the eukaryotes are
microorganisms: primarily algae,
protozoa, molds and yeasts (types of
fungi), and certain animals such as
arthropods and worms.

26
27
28
 Microbial Dimensions: How
Small Is Small?
• The dimensions of macroscopic
organisms are usually given in
centimeters (cm) and meters (m),
• whereas those of most
microorganisms fall within the range
of micrometers (μm) and,
sometimes, nanometers (nm) and
millimeters (mm).
• The size range of most microbes
extends from the smallest viruses, 29
The Historical Foundations of Microbiology

Expected Learning Outcomes

• Outline the major events in the
history of microbiology, including
• the major contributors to the early
development of microscopy,
• medical advances,
• aseptic techniques, and
• the germ theory of disease.
The Historical Foundations of Microbiology

 Man kind has always been affected by diseases which were orig-
inally believed to be visitations by the gods and meant to punish
evil doers.
 Hippocratus, father of medicine, observed that ill health resulted
due to changes in air, winds, water, climate, food, nature of soil
and habits of people.
 But the causes of such phenomena were vague and obscure be-
cause the technology to study them was lacking
Varro (117-126 BC)
 theory that disease was caused by animated
particles invisible to naked eye but which were
carried in the air through the mouth and nose
in to the body.
Fracastorius (1500 G.C.)
 proposed that the agents of communicable dis-
ease were living germs, that could be transmitted
by direct contact with humans and animals, and
indirectly by objects ;
 but no proof because of lacking experimental
evidence.
The Development of the Microscope:
“Seeing Is Believing”
• True awareness of the widespread
distribution of microorganisms and
some of their characteristics was
finally made possible by the
development of the first
microscopes.
• These devices revealed microbes as
discrete entities sharing many of the
characteristics of larger, visible
plants and animals.
• Several early scientists fashioned
magnifying lenses, but their
microscopes lacked the optical clarity
needed for examining bacteria and
other small, single-celled organ-isms.
• Antony Van Leeuwenhoek (1632-1723 G.C.), a
Dutch linen merchant and self-made
microbiologist
• observed “animalcules” using simple
microscope with one lens.
• He took rainwater from a clay pot, smeared it
on his specimen holder, and peered at it
through his finest lens.
• He found “animals appearing to me ten
thousand times than those which may be
perceived in the water with the naked eye.
• He didn’t stop there.
• He scraped plaque from his teeth, and from the teeth
of some volunteers who had never cleaned their teeth
in their lives, and took a close look at that.
• He recorded: “In the said matter there were many
very little living animalcules, very prettily a-
moving. . . . Moreover, the other animalcules were in
such enor-mous numbers, that all the water . . .
seemed to be alive.
• ” Leeuwen-hoek started sending his observations to
the Royal Society of London, and eventually he was
recognized as a scientist of great merit.
• Leeuwenhoek constructed more than 250 small, powerful mi-
croscopes that could magnify up to 300 times
• Considering that he had no formal training in science and that
he was the first person ever to faithfully record this strange
new world, his descriptions of bacteria and protozoa (which he
called “animalcules”) were astute and precise.
• Because of Leeuwenhoek’s extraordinary contributions to
microbiology,
• he is sometimes considered the father of bacteriology and
protozoology.
 He was the first who properly described the differ-
ent shapes of bacteria.
 Although he was not concerned about the origin of
microorganism;
 many other scientists were searching for an expla-
nation for spontaneous appearance of living things
from
 decaying meat,
 stagnating ponds,
 fermenting grain and
 infected wounds.
On the bases of this observation, two major theories
were formulated.
 Theory of Abiogenesis
 Theory of Biogenesis
 Theory of Abiogenesis deals with the theory of
spontaneous generation;
 stating that living things originated from non-living
things.
 Spontaneous Generation
 The belief that life could originate from non-living or
decomposing matter
 Supported by:
 Aristotle (322-384 BC) –The founder of a theory
spontaneous generation.
 He observed spontaneous existence of fishes from
dried ponds, when the pond was filled with rain.
 John Needham (1713-1781) – Boiled mutton broth,
then sealed and still observed growth after a period of
time
 Lazarro Spallanzani (1729-1799) -No growth in
sealed flask after boiling
– proposed that air was needed for growth of organ-
isms
 Felix Pouchet (1859) – Proved growth without
contamination from air
 Disproved by:
 Francesco Redi (1626-1697) – maggot unable to
grown on meat if meat was covered with gauze
 He put the meat in a bottle and covered it with
a gauze,
 He observed that the flies laid eggs from which
the maggots developed,
 He said maggots did not developed from meat
but from flies egg.
 Schwann, Friedrich
Schroder and von Dusch
(1830s) –
- Air allowed to enter flask but
only after passing through a
heated tube or sterile wool
 John Tyndall (1820-1893) –
 Omission of dust  no growth.
Demonstrated heat resistant
forms of bacteria (endospores)
 Louis Pasteur (1822 - 1895)
 trapped airborne organisms in cotton;
 he also heated the necks of flasks, drawing them out in to
long curves, sterilized the media, and left the flasks open
to the air;
 no growth was observed because dust particles carrying
organisms did not reach the medium,
 instead they were trapped in the neck of the flask;
 if the necks were broken, dust would settle and the or-
ganisms would grow;
 in this way Pasteur disproved the theory of spontaneous
generation and supported germ theory
illustration of the Swan-necked bottle used in
Pasteur‘s experiments to disprove spontaneous
generation
 Theory of Biogenesis states that life comes from
pre-existing life.
 Louis Pasteur (1822-1895 GC) was the scientist
who disproved the theory of abiogenesis.
Major contribution of Louis Pasteur
 Microbial theory of fermentation
 Principles and practice of sterilization and pas-
teurization
 Control of diseases of silk worms
 Development of vaccines against anthrax and
rabies.
 Discovery of streptococci
The germ theory of disease
 The complete establishment of the germ theory of
disease depended on the work of Robert Koch
(1843-1910).
Role of Microorganisms in Disease

 Robert Koch established that microbes can cause dis-

ease
 Robert Koch (1843 - 1910),
 using criteria he established the relation-
ship between Bacillus anthracis and
anthrax;
 his criteria became known as Koch’s Postu-
lates and are still used to establish the link
between a particular microorganism and a
particular disease:
 Koch’s Postulates

1. The causative (etiological) agent must be present in all

affected organisms but absent in healthy individuals
2. The agent must be capable of being isolated and cultured
in pure form
3. When the cultured agent is introduced to a healthy organ-
ism, the same disease must occur
4. The same causative agent must be isolated again from the
affected host
 Now a days additional postulate is mentioned i.e.
 Specific antibody to the bacterium should be de-
tectable in the serum during the course of the dis-
ease.
 Demonstrations that micoorganisms cause disease

 Joseph Lister (1827 - 1912)

 developed a system of surgery designed to
prevent microorganisms from entering
wounds – phenol sprayed in air
around surgical incision
 Decreased number of post-operative infec-
tions in patients
 Charles Chamberland (1851 - 1908)
 identified viruses as disease-causing agents –
Tobacco Mosaic Virus
 Edward Jenner (ca. 1798)
 used a vaccination procedure to protect indi-
viduals from smallpox
 Louis Pasteur
 developed other vaccines including those for
chicken cholera, anthrax, and rabies
Exceptions to Koch’s postulates
 Many healthy people carry pathogens but do not
exhibit symptoms of the disease.
 Some microbes are very difficult or impossible to
grow in vitro(in the laboratory) in artificial me-
dia. Eg. Treponema pallidum
 Many species are species specific. Eg. Brucella
abortus cause abortion in animals but no report in
humans.
 Certain diseases develop only when an oppor-
tunistic pathogen invades immunocompromised
host.
• Taxonomy/classification of
microorganisms
Taxonomy
• is the science of classifying and naming organisms.
• all members of any given taxon share certain common features,
• Taxonomy consists of three components:
 Classification -allows the orderly grouping of microorganisms
 Nomenclature- concerns the naming of these organisms and
requires agreement so that the same name is used unambiguously
by everyone.
 Identification-which is the practical science of determining that
an isolated individual or population belongs to a particular taxon.
 Basis of Taxonomy
Phenetic Classification System -groups organisms
based on mutual similarity of phenotypic
characteristics.
Phylogenetic Classification System -evolutionary
history of group of organisms
– Groups reflect genetic similarity and evolutionary relatedness

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 Level of Classifying microorganism :

• The hierarchical;
– Carolus Linnaeus (mid-1700’)s was a Swedish biologist
who established a simple system for classifying and naming
organisms.
– He developed a Hierarchy (a ranking system) for classifying
organisms that is the Basis for Modern Taxonomy.
– For this reason, he is considered to be “father” of modern
taxonomy.
 Taxonomic hierarchy
• The hierarchy consist the following taxa
– Kingdom or domains
– Phylum or division
– Class
– Order
– Family
– Genus
– Species
• Strain

The taxonomic hierarchy shows evolutionary, or phylogenetic, relationships

among organisms
Classification below Species Level
 are also designated as groups or types on the basis of
 common serologic test
 biochemical reactions
 phage or bacteriocin sensitivity
 pathogenicity, or other characteristics
 some of the names given for strains below species level include:
 serotype
 phage type
 colicin type
 biotype
 bioserotype and
 pathotype
METHODS FOR TAXONOMIC CLASSIFICATION

• For determination of the genus and species of a newly

discovered prokaryote is based on the following taxonomic
approach.
• This approach includes
1. The Intuitive Method

2. Dichotimous Key

3. Numerical Approach

4. Genetic & molecular analysis

5. Polyphasic Approach
• The Intuitive Method
– In this method a microbiologist who is thoroughly
familiar with the properties of the organisms
decides that a particular organism represent a
species or genus
 Dichotomous Key

• Dichotomous keys are widely used for identification

of organisms.
• They are based on successive questions that each
have two possible answers
 Numeric

• In this method of taxonomy many (100 to 200)

characteristics for each bacterial strain is determined, giving
each characteristic equal weight.

• characteristics includes
– biochemical, morphological, and cultural characteristics, as well
as susceptibilities to antibiotics and inorganic compounds, are
used to determine the degree of similarity between organisms.
– calculate the coefficient of similarity or percentage
of similarity between strains
– Then percentage similarity (%S) of each strain to
every other known strain is calculated by the
formula:
• %S = ND/NS +ND
– where,
• NS= number of characteristics that are same (positive or
negative) for the two strains,
• ND = number of characteristics that are different.
• strains having a higher %S to each other are placed into
same group
 Genotypic
• Most reliable method of classification
• The standard reference is bergey’s manual of systematic bacteriology

• based on the degree of genetic relatedness between

organisms
– relies upon analysis of
• G+C content/ratio
• DNA homology
• Ribotyping: rRNA sequencing
• Plasimd
• DNA fingerprinting or Chromosomal DNA fragement analysis

12/14/2024 Bacteriology 69
Polyphasic Approach
 Has 3 steps
1. phenotypic grouping of strains by morphological ,biochemical and
any other characteristics of interest.
2. Then testing for DNA relatedness to determine whether the
observed phenotypic homogeneity (or heterogeneity) is reflected
by phylogenetic homogeneity or heterogeneity.
3. Re-examination of the biochemical characteristics of the DNA
relatedness groups.
This allows determination of the biochemical borders of each group and
determination of reactions of diagnostic value for the group.
 Nomenclature
• Nomenclature is the assignment of names to the various
taxa according to international rules.
• Linnaeus introduced the system of scientific nomenclature
– According to scientific nomenclature each organism is assigned
two name
– The method of assigning a scientific two part name is called the
binomial system of nomenclature
– Rules for the assignment of names to bacteria are established by
the International Committee on Systematic Bacteriology

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• In the binomial system of nomenclature organisms name is
always a combination of the genus(plural: genera) name
followed by the species name.
 International rules in Binomial nomenclature
includes:
– Genus name + species name
– Genus comes before species (e.g., Escherichia coli)
– Genus name is always capitalized (e.g., Escherichia)
– Species name is never capitalized (e.g., coli
– The genus name may be used alone, but not the species
name (i.e saying or writing “Escherichia “ alone is
legitimate while saying or writing “ coli” is not)
–
 BINOMIAL NOMENCLATURE…….

i. The two-part name of an organism is sometimes

abbreviated to save space, as in S. aureus, but
only if the genus name has already been stated.
ii. Both (Genus and species ) name should be
italicized (or underlined if using handwriting), as
follows:
Staphylococcus aureus

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• 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)