The document provides an overview of microbiology, focusing on the classification systems of living organisms proposed by Robert Whittaker and Carl Woese, as well as the characteristics and structures of bacteria. It elaborates on the differences between prokaryotic and eukaryotic cells, including their reproduction methods, chemical composition, cellular structures, and growth phases. Additionally, it discusses the role and structure of bacterial components such as flagella, pili, and the cell wall, highlighting their importance in bacterial survival and function.

1. Microbiology 1
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Definition of Microbiology
Classification of organisms
The five kingdom classification system was proposed by Robert Whittaker in 1969. This
system divides all living organisms into five kingdoms: Animalia. This system has been
widely accepted, and is still used today for the classification of living organisms.
Group Examples Cell
Animalia mammals, birds, fish, reptiles, and amphibians Multicelluar, Eukaryots
Plantae trees, shrubs, grasses, and flowers Multicelluar, Eukaryots, Plastid
Fungi mushrooms, yeasts, and molds Multicelluar, Eukaryots, no Plastid
Protista amoebas, protozoans, and algae Unicellular, Eukaryots
Monera bacteria and cyanobacteria Unicellular, prokaryots
In 1977, Carl Woese proposed a new classification system, known as the six-kingdom
system. This system divides all living organisms into six kingdoms: Animalia, Plantae,
Fungi, Protista, ArchaeaBacteria, and EuBacteria. This system is based on evolutionary
relationships, and is still used today for the classification of living organisms.
In 1977, Carl Woese proposed a new classification system, known as the three-domain
system. This system divides all living organisms into three domains: Archaea, Bacteria, and
Eukarya. Archaea and Bacteria are both prokaryotic organisms, while Eukarya consists of
all eukaryotic organisms, including plants, animals, fungi, and protists. This system is based
@February 4, 2023 10:02 AM

2. Microbiology 2
on evolutionary relationships, and is still used today for the classification of living
organisms.
Research the three-domain system proposed by Carl Woese in 1977.
Investigate the evolutionary relationships used in the three-domain system.
Examine the current uses of the three-domain system for the classification of living organisms.
Major groups of microbes
Muramic acid only present in Bacteria and Rickettsia.
Viruses, Rickettsiae, and Chlamydiae do not grow without a medium.
Viruses and Chlamydia are sensative to interferon
Viruses are insensitive to antibiotics.
Morphology of Bacteria
Defination of bacteria?
Bacteria are single-celled, prokaryotic microorganisms. They come in a variety of shapes,
sizes and types. Bacteria are found almost everywhere on Earth, living in soil, water, the
atmosphere, and even inside other organisms. Some bacteria are beneficial, such as
those that help us digest food, while others can cause disease. Bacteria reproduce
quickly, using a process called binary fission, where one cell divides into two.
Bacteria are defined as organisms that are microscopic, unicellular, independently
reproducing, and mostly free-living. Bacteria are ubiquitous in nature.
Identify the three domains of the three-domain system.
Compare and contrast prokaryotic and eukaryotic organisms.

3. Microbiology 3
Bacteria are single-celled organisms in the prokaryotic group. These organisms don't
have some organelles and a true nucleus.
Different shape of bacteria?
Bacteria come in a variety of shapes and sizes, including cocci (spherical), bacilli (rod-
shaped), vibrio (comma-shaped), and spirilla (spiral). Different shapes of bacteria may
help them survive in different environments and perform specific functions. Cocci, for
example, can survive in harsh environments, while vibrio are well-adapted for swimming
in water.
Spherical cocci: Cocci are classified based on their arrangement, such as diplococci,
streptococci, staphylococci, and tetrad. Diplococci are two cocci that are attached to each
other and typically found in pairs, while streptococci are arranged in chains.
Staphylococci are found in clusters, and tetrad are arranged in groups of four.
Rod-shaped-bacilli: Rod-shaped bacilli are classified based on their arrangement, such as
diplobacilli, streptobacilli, staphylobacilli, and palisade. Diplobacilli are two bacilli that are
attached to each other and typically found in pairs, while streptobacilli are arranged in
chains. Staphylobacilli are found in clusters, and palisade are arranged in groups of four.

4. Microbiology 4
Srtucture of a typical bacteria?
A typical bacterial cell consists of three main parts: a cell wall, a cell membrane and
cytoplasm. The cell wall provides protection and structure for the cell, while the cell
membrane regulates the passage of molecules in and out of the cell. The cytoplasm is the
gel-like material that contains the cell's genetic material, and also plays a role in protein
production and cell metabolism.
External Structures
External Structures of Bacteria: Bacteria possess several external structures that are
important for the survival of the organism. These include flagella, pili, and fimbriae.
Flagella are long, tail-like structures that allow bacteria to move in liquid environments,
while pili and fimbriae are short, thread-like structures that can help bacteria attach to
surfaces and other bacteria. In addition, some bacteria have a capsule, which is an
outer coating of polysaccharides that can help protect the cell from dehydration,
predation, and other environmental factors. Prostheceae and stalk. Sea sheaths.
Internal Structures
Internal Structures of Bacteria: Bacteria also contain several internal structures that are
important for the survival of the organism. These include ribosomes, which are
responsible for the production of proteins, and a plasma membrane, which regulates
the passage of molecules in and out of the cell. Additionally, bacteria contain a
nucleoid, which contains the cell's genetic material, and a cytoplasm, which is a gel-
like material that contains the cell's enzymes, ions, and other molecules. Finally, some
bacteria contain a storage granule, which can store extra nutrients for later use.

5. Microbiology 5
Chemical composition of bacteria?*
Bacteria are composed of a variety of chemicals, including carbohydrates, proteins,
lipids, and nucleic acids. Carbohydrates, such as polysaccharides and monosaccharides,
make up the cell wall of bacteria and provide it with structure. Proteins make up much of
the cell's machinery and are responsible for energy production, metabolism, and other
processes. Lipids, such as fatty acids and phospholipids, make up the cell membrane and
play a role in cell signaling and communication. Finally, nucleic acids, such as DNA and
RNA, are responsible for the storage and transmission of genetic information
Chemical Composition of Bacteria 20% solid
Chemical Function %
Carbohydrates/Polysaccharide Structure and energy storage 15%
Proteins Energy production and metabolism 40%
Lipids Cell membrane and cell signaling 15%
Nucleic acids
Storage and transmission of genetic
information
10%
Peptidoglycan 10%
Low molecular compound 10%
Flagella

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Chemical structure
Chemical Structure of Flagella
The flagella of bacteria are composed of several different chemicals, including
proteins, lipids, and carbohydrates. The most important component is the protein,
flagellin, which forms the core of the flagellum. Additionally, lipids, such as fatty acids,
are present in the flagellum and help to keep it flexible and mobile. Finally,
carbohydrates, such as polysaccharides, are present in the flagellum and help to
provide structure.
Structure of Flagellum
The structure of the bacterial flagellum is composed of three parts: the hook, the
filament, and the basal body. The hook is a curved structure made of protein that
attaches the filament to the basal body. The filament is a long, thin structure made of
protein that extends from the hook to the tip of the flagellum. The basal body is a
structure at the base of the flagellum that is responsible for its movement and rotation.
Function

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The function of the bacterial flagellum is to provide motility to the cell. This is
accomplished by the rotation of the filament, which creates a force that propels the cell
forward. Flagella are also important for bacterial navigation and can help the cell find
food, move away from unfavorable conditions, and even swarm with other bacteria.
Pili/Fimbriae
Pili/Fimbriae
Pili, also known as fimbriae, are short, thread-like structures that are found on the surface
of some bacteria. They are composed of proteins, such as pilin and fimbrillin, and help
bacteria attach to surfaces and other bacteria. Additionally, pili can also help bacteria
share genetic material, such as antibiotic resistance genes, with other bacteria. Present in
gram negative bacteria.
Glycocalyx or capsule
The glycocalyx, also known as the capsule, is a slime layer composed of polysaccharides
and proteins that surrounds the bacterial cell.
The capsule helps to protect the cell from dehydration and predation, as well as from the
actions of the immune system.
Additionally, the capsule can help bacteria attach to surfaces and other bacteria, and also
aid in the exchange of nutrients and other molecules.
Cell wall
The cell wall of bacteria is composed of peptidoglycan, a polymer made of two types of
sugar molecules: N-acetylglucosamine and N-acetylmuramic acid. The peptidoglycan is
made of alternating layers of these two sugars and is held together by peptide cross-
links.
The cell wall provides structural integrity
Protects the cell from its environment
Protects the cell from the action of the immune system
In addition, the cell wall also helps the cell resist osmotic pressure, as well as maintain
the cell's shape and integrity.
Difference between Gram Positive and Gram Negative Bacterial Cell Wall
Gram Positive Gram Negative
Cell wall composed of a single layer of peptidoglycan Cell wall composed of two layers of peptidoglycan
Layer of lipoteichoic acid outside the cell wall
Outer membrane composed of phospholipids and
lipopolysaccharides
More susceptible to antibiotics that target peptidoglycan More resistant to antibiotics due to outer membrane
Cell membrane
The cell membrane of bacteria is composed of a phospholipid bilayer, which is made up
of two layers of phospholipid molecules. The cell membrane helps regulate the passage
of molecules in and out of the cell, and also helps to maintain the cell's shape and
integrity. Additionally, the cell membrane is responsible for cell signaling and
communication, as well as energy production. Finally, the cell membrane also plays a role

8. Microbiology 8
in cell adhesion, or the ability of bacteria to attach to surfaces and other bacteria. 50%
lipid 50% protein.
Cytoplasm
The cytoplasm of bacteria is a gel-like material composed of water, ions, and other
molecules. It also contains the cell's genetic material, enzymes, and other proteins that
are important for cell metabolism, as well as energy production. The cytoplasm plays an
important role in the movement of molecules in and out of the cell, as well as in the
production of proteins and other cellular processes. 40% protein 35% RNA
Function of Cytoplasm:
The cytoplasm of bacteria plays an important role in cell metabolism and energy production.
It is responsible for the movement of molecules in and out of the cell, as well as the production of proteins and
other cellular processes.
The cytoplasm also contains the cell's genetic material, enzymes, and other proteins, which are important for cell
metabolism and energy production.
Additionally, the cytoplasm can store extra nutrients for later use.
Structure of bacteria
Difference between Prokaryotic and Eukaryotic Cells
Prokaryotes and eukaryotes are two types of cells that differ in size, structure, and
complexity. Prokaryotic cells are much smaller than eukaryotic cells and lack a true
nucleus. Prokaryotic cells also lack membrane-bound organelles, such as the
endoplasmic reticulum and Golgi apparatus, which are present in eukaryotic cells.
Additionally, prokaryotic cells contain a single chromosome, while eukaryotic cells
contain multiple chromosomes. Finally, prokaryotes typically reproduce through binary
fission, while eukaryotes typically reproduce through mitosis or meiosis.
Prokaryotes Eukaryotes
Smaller size Larger size
Lack a true nucleus Have a true nucleus
Lack membrane-bound organelles (ER, GC, mitocondria) Have membrane-bound organelles
Single chromosome Multiple chromosomes
Reproduce through binary fission Reproduce through mitosis or meiosis
No cell wall (execpt fungi) yes
80S Ribosome 70S Ribosome
Genome of Bacteria
The genome of bacteria is composed of a single, circular chromosome made of DNA.
This DNA is packaged into a structure called a nucleoid, which is located in the center
of the bacterial cell. In addition, bacteria may also contain other pieces of DNA, such as
plasmids, which are short, circular pieces of DNA that can be exchanged between
bacteria. Plasmids can contain genes that are beneficial to the bacteria, such as
antibiotic resistance genes.
Division of bacteria

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Cell Division of Eukaryotic Bacteria
Eukaryotic bacteria are capable of reproducing through binary fission, a process by
which a single cell divides into two daughter cells. During binary fission, the DNA of
the parent cell is replicated, and the replicated DNA is then separated into the two
daughter cells. The daughter cells then begin to grow and eventually separate from
each other. This process can occur relatively quickly, allowing for the rapid expansion
of bacterial populations.
Cell Division of Prokaryotic Bacteria
Prokaryotic bacteria also reproduce through binary fission, a process by which a
single cell divides into two daughter cells. During binary fission, the DNA of the parent
cell is replicated, and the replicated DNA is then separated into the two daughter cells.
The daughter cells then begin to grow and eventually separate from each other.
Additionally, prokaryotic cells can also reproduce through conjugation, a process by
which two cells exchange genetic material.
The bacterial endospores
The bacterial endospore is a specialized, dormant form of a bacterial cell which is
highly resistant to environmental stresses, such as extreme temperatures, radiation,
and chemicals. Endospores are formed by a process called sporulation, in which the
bacterial cell undergoes several changes in order to become dormant and resistant to
environmental stresses. Endospores are typically found in soil and water, and they can
remain dormant for long periods of time before being reactivated by the right
environmental conditions.
What is generation time?
Generation time is the time it takes for a bacterial population to double in size. It is
typically measured in the number of generations per unit of time, such as generations per
hour or generations per day. Generation time is affected by a variety of factors, such as
the growth rate of the bacteria, the availability of nutrients, and environmental conditions.
Factor responsible for growth and multiplication of Bacteria?
Factors Description

10. Microbiology 10
Factors Description
Temperature
Affects the rate of growth and multiplication of bacteria, as
some bacteria are able to grow and multiply more quickly at
higher temperatures, while others are able to grow and
multiply more quickly at lower temperatures. 20-45 or 37
pH
Affects bacterial growth and multiplication, as some bacteria
prefer acidic environments and others prefer alkaline
environments.
Nutrients
Availability of nutrients affects the growth and multiplication
of bacteria.
Other Bacteria
Presence of other bacteria can also affect the growth and
multiplication of bacteria.
Atmosphare and Some bacteria need oxygen, some don’t.
Moisture Bacteria need moisture to grow.
Radiation
Mechanical and sonic stress
Osmotic effects
Bacterial growth curve
Bacterial Growth Curve
The bacterial growth curve is a graphical representation of the growth of a bacterial
population over time. The curve is composed of four phases: the lag phase, the log phase,
the stationary phase, and the death phase. The lag phase is the period of time when the
population is adapting to its environment, while the log phase is the period of exponential
growth. The stationary phase is the period of time when the population has reached its
maximum growth and has stabilized, while the death phase is the period of time when the
population begins to decline.
Phase Description Metamorphosis Time
Lag Phase
Period of time when the
population is adapting to its
environment
The cells synthesise RNA,
growth factors and other
molecules required for cell
division.
Untill maximum size
Log Phase
Period of time of exponential
growth
The cells are the healthiest at
this stage. Small in size. Stain
uniformly.
Continues until there is
depletion of nutrients in the
setup.
Stationary Phase The rate of growth of the cells The rate of growth of the Until nutrion available
O2 CO2

11. Microbiology 11
becomes equal to its rate of
death.
bacterial cells is limited by
the accumulation of toxic
compounds. Stain
ununiformly
Death Phase
Period of time when the
population begins to decline
Lack of nutrients, physical
conditions or other injuries to
the cell leads to death of the
cells.
Understand the four phases of the microbial growth curve: lag phase, log phase, stationary phase, and death phase.
Determine the period of time for each phase of the microbial growth curve.
Identify when the population has reached its maximum growth and has stabilized.
Recognize when the population begins to decline.
Prokaryotes vs Eukaryotes
Prokaryotes and eukaryotes are two types of cells that differ in size, structure, and
complexity. Prokaryotic cells are much smaller than eukaryotic cells and lack a true nucleus.
Prokaryotic cells also lack membrane-bound organelles, such as the endoplasmic reticulum
and Golgi apparatus, which are present in eukaryotic cells. Additionally, prokaryotic cells
contain a single chromosome, while eukaryotic cells contain multiple chromosomes. Finally,
prokaryotes typically reproduce through binary fission, while eukaryotes typically reproduce
through mitosis or meiosis.
Prokaryotes Eukaryotes
Smaller size 0.2 to 2 µm Larger size 10-100 µm
Lack a true nucleus Have a true nucleus
Lack membrane-bound organelles (ER, GC, mitocondria) Have membrane-bound organelles
Single chromosome Multiple chromosomes
Reproduce through binary fission Reproduce through mitosis or meiosis
Cell wall No (execpt fungi)
80S Ribosome 70S Ribosome
Plasmid No Plasmid
PM without sterols PM without sterols
Bacterial Nutrients
Types of Bacterial Nutrients
Essential nutrients of bacteria: Essential for growth
Nutrient Function
Carbohydrates Provide energy and structural support
Proteins Important for the production of enzymes and other proteins
Lipids
Provide energy, maintain the cell membrane, and are
involved in cell signaling
Research the differences between prokaryotic and eukaryotic cells
Identify the components of a prokaryotic cell
Identify the components of a eukaryotic cell
Compare the reproduction methods of prokaryotes and eukaryotes

12. Microbiology 12
Nutrient Function
Vitamins and minerals Essential for a variety of metabolic processes
Trace elements Involved in enzyme reactions
Oxygen Required to produce energy
Accesory nutrients for bacteria:
Accessory Nutrients for Bacteria: Accessory nutrients are nutrients that are not essential
for bacterial growth but can be beneficial for the bacteria. These nutrients can provide
additional energy, as well as vitamins, minerals, and other essential compounds.
Examples of accessory nutrients include nitrogen, sulfur, phosphorus, iron, magnesium,
and potassium. Accessory nutrients can also help bacteria to survive in stressful
environments, and can increase the efficiency of nutrient uptake.
Types of bacteria based on Nutrition
Type of Bacteria Description Medical Importance
Autotrophic
Produce their own energy by using
light or inorganic compounds.
NO
Heterotrophic
Must obtain energy from organic
compounds. Unable to synthesize their
own metabolites.
YES (all pathogens)
Based on nutritional requirment
Phototrophs Chemotrophs Organotrophs Lithotrophs
Bacteria which derive their
energy from sunlight.
Bacteria which derive energy
from chemical reactions.
Require organic sources of
hydrogen
Require inorganic sources of
hydrogen like NH3, H2S
Identify sources of energy for bacteria
Learn about essential minerals for bacterial growth
Research the benefits of organic compounds for bacterial growth
Classification of bacteria
Based on morphology
Cocci
Diplococci Stephylococci Streptococci
Streptococcus pneumuniae Stephylococcus aureus Streptococcus pygenes
Bacilli
Organism Genus Species
Streptobacilli Bacillus anthracis
Based on temperature.
Classification of Bacteria Based on Temperature
Bacteria can be classified based on their optimal growth temperature. These three categories are psychrophiles,
mesophiles, and thermophiles. Psychrophiles are bacteria that can grow at temperatures below 20°C, mesophiles can
grow at temperatures between 20°C and 45°C, and thermophiles can grow at temperatures above 45°C. Additionally,
Understand the types of nutrients bacteria need to survive

13. Microbiology 13
some bacteria are able to survive in extreme temperatures, such as the thermophilic bacteria that live in hot springs, or
the psychrophilic bacteria that live in the Arctic.
Category Temperature Range Example
Psychrophiles Below 20°C Flavobacterium spp
Mesophiles 20°C - 45°C Streptococcus spp
Thermophiles Above 45°C Bacillus sterothermophilus
Understand the three categories of bacteria based on temperature
Identify the optimal temperatures for psychrophiles, mesophiles, and thermophiles
Learn about bacteria that live in extreme temperatures
Research the benefits of temperature for bacterial growth
Based on Oxygen
Classification of Bacteria Based on Oxygen
Bacteria can be classified based on their oxygen requirements. These three categories are obligate aerobes, obligate
anaerobes, and facultative anaerobes. Obligate aerobes are bacteria that require oxygen in order to survive, while
obligate anaerobes are bacteria that can’t survive in the presence of oxygen. Facultative anaerobes are bacteria that
can survive with or without oxygen.
Category Oxygen Requirements Example
Obligate Aerobes Requires oxygen to survive Escherichia coli
Obligate Anaerobes Can't survive in the presence of oxygen Clostridium spp
Facultative Anaerobes Can survive with or without oxygen Staphylococcus aureus
Microaerophilic
Grow best in the presence of low
oxygen levels
Campylobacter spp
Aerotolerant anaerobic
Anaerobic, but tolerates exposure to
O2
Clostridium perfringens
Capnophilic organism requires high CO2 levels. Neisseria spp.
Understand the three categories of bacteria based on oxygen requirements
Identify the oxygen requirements for obligate aerobes, obligate anaerobes, and facultative anaerobes
Learn about bacteria that rely on oxygen for survival
Research the benefits of oxygen for bacterial growth
Bacterial spores
The bacterial endospore is a specialized, dormant form of a bacterial cell which is highly
resistant to environmental stresses, such as extreme temperatures, radiation, and
chemicals. Endospores are formed by a process called sporulation, in which the bacterial
cell undergoes several changes in order to become dormant and resistant to environmental
stresses. Endospores are typically found in soil and water, and they can remain dormant for
long periods of time before being reactivated by the right environmental conditions.
Sporulation Process

14. Microbiology 14
The process of sporulation begins when the bacterial cell begins to form a new cell wall,
called an exosporium.
The exosporium is composed of several layers, including a layer of peptidoglycan and an
outer layer of lipopolysaccharides.
Inside the exosporium, the bacterial cell begins to produce a thick, protective layer called
the cortex.
In addition, the bacterial cell also begins to produce a cork-like layer called the spore
coat, which helps to protect the endospore from environmental stress.
The endospore is then released from the parent cell and is ready to survive in the
environment.
Understand the definition of a bacterial endospore
Identify the process of sporulation
Recognize the environmental conditions in which endospores can be reactivated
Research the benefits of endospores for bacteria
History of Microbiology

15. Microbiology 15
Varo and Columella: Deseases are caused by some invisible species.
Fracstourious: Contagium vivum
Antonie van leewenhoek: First person to observe microorganisms. Father of microbiology.
Nicolas Appert: Father of canning
Golden age
Louis Pasteur(1822-1895): Louis Pasteur was a French chemist and microbiologist who is
best known for his contributions to the fields of microbiology and immunology. He is
credited with developing the process of pasteurization, which is used to prevent the
growth of bacteria in food and drinks. He also discovered the process of fermentation,
which is used to produce beer, wine, and other alcoholic beverages. In addition, Pasteur
is also credited with developing the first successful vaccine against rabies, which saved
the life of a young boy in 1885. Father of Bacteriology, immunology.
Louis Pasteur (1822-1895)
Contributions
Microbiology, Immunology, Pasteurization(1862),
Fermentation(1859), First successful rabies vaccine(1880).
Resolve the controversy of spontaneous generation.
Proposed the germ theory of disease
Known As Father of Bacteriology, experimental Immunology
John Tyndal (1820-1893): John Tyndal was a British physicist who is best known for his
contributions to the study of light and sound. He is credited with showing that light
travels in straight lines, and he was the first to measure the intensity of sunlight. He also
discovered that certain gases, such as carbon dioxide, have the ability to absorb infrared
radiation and are therefore important for regulating the Earth’s climate. Tyndal also
developed a device for measuring the concentration of various gases in air, which was
later used to measure air pollution. Discovery of endospore. Tyndallization. Blown out
spontaneous generation theory.
Name Work
John Tyndal (1820-1893) Discovery of endospore; Tyndallization; Blown out spontaneous generation theory
Robert Koch (1843-1910): Robert Koch was a German physician and microbiologist who
is best known for his contributions to the field of microbiology. He is credited with
developing the Koch Postulates, which are a set of criteria used to determine whether a
specific organism is the cause of a specific disease. He also developed the first
successful vaccine against tuberculosis, and he was the first to successfully isolate the
anthrax bacillus. Koch also developed methods for staining and viewing bacteria, which
allowed him to identify different types of bacteria and to observe their behavior. He also
developed methods for culturing bacteria, which allowed him to study them in a
controlled environment.
Koch's Postulates
Koch's postulates are a set of criteria proposed by German physician and microbiologist
Robert Koch in 1890, used to determine whether a specific organism is the cause of a
specific disease. The postulates state that a microorganism must be found in abundance
in a diseased organism, must be isolated and grown in pure culture, must cause disease
when introduced to a healthy organism, and must be re-isolated from the infected
organism. Koch's postulates have been used as the basis for determining the causation
of many diseases, including cholera, typhoid, tuberculosis, and many others.

16. Microbiology 16
Name Contributions
Name Contributions
Robert Koch
(1843-1910)
Developed Koch Postulates(1884), developed first successful vaccine against tuberculosis(1882), first to
isolate anthrax bacillus(1876), developed methods for staining and viewing bacteria, developed methods
for culturing bacteria.
Emil von Behring (1854-1917): Emil von Behring was a German physician and scientist
who is best known for his contributions to the field of immunology. He is credited with
developing the first successful vaccine against diphtheria, and he was awarded the Nobel
Prize in Medicine in 1901 for his discoveries. Von Behring also developed the diphtheria
antitoxin, which is used to treat the disease. He also developed the first serum therapy,
which involved the use of antibodies to treat bacterial infections. Von Behring also
developed methods for studying the immune response of animals, which helped to
further the understanding of immunology. Saviour of children.
Name Contribution
Emil von Behring(1854-1917)
Developed the first successful vaccine against diphtheria, the diphtheria antitoxin, and the
first serum therapy. Studied the immune response of animals.
Known as Helped to further the understanding of immunology. Saviour of children.
Fanne Eilshemius Hesse (1860-1940): Fanne Eilshemius Hesse was a German
bacteriologist and physician who is best known for her contributions to the field of
microbiology. She was the first woman to receive a doctorate in bacteriology in Germany,
and she was the first woman to be assigned to a laboratory at a German university. Hesse
is credited with isolating the causative agent of diphtheria, and she was the first to isolate
the bacterium that causes tuberculosis. In addition, she is credited with developing a
method for the detection of the typhoid bacillus, as well as a method for the detection of
the cholera bacillus. Hesse also developed a method for the production of antiserum,
which is used to treat bacterial infections.
Name Accomplishments
Fanne Eilshemius Hesse
(1860-1940)
First proposed the use of agar.
Richard Petri (1852-1931): Richard Petri was a German physician and bacteriologist who
is best known for his contributions to the field of microbiology. He is credited with
developing the Petri dish, which is a shallow, circular dish used for culturing
microorganisms. Petri is also credited with developing the method of streak plate
technique, which is used to isolate pure cultures of bacteria. He also developed the Gram
staining technique, which is used to differentiate between different types of bacteria. Petri
also developed methods for culturing and preserving bacteria, which allowed him to
study them in a controlled environment.
Name Contribution
Richard Petri(1852-
1921)
Developed Petri dish, developed method of streak plate technique, developed Gram staining
technique, developed methods for culturing and preserving bacteria
Paul Ehrlich (1854-1915) was a German physician and scientist who is best known for his
contributions to the fields of immunology and chemotherapy. He is credited with
developing the first effective treatment for syphilis, which was the first drug for treating a
bacterial infection. Ehrlich also developed the concept of chemotherapy, which is the use
of chemical agents to treat infections. He also developed the side-chain theory, which is
used to explain how the body recognizes antigens and how the immune system responds
to them. Lastly, Ehrlich is credited with developing the first successful vaccine against
tetanus.
Name Contributions

17. Microbiology 17
Name Contributions
Paul Ehrlich(1854-1915)
Developed first effective treatment for syphilis, concept of chemotherapy, side-chain theory,
and first successful vaccine against tetanus
Elie Metchnikoff (1845-1916) was a Russian scientist who is best known for his
contributions to the field of immunology. He is credited with discovering the process of
phagocytosis, which is the process by which certain white blood cells attack and destroy
invading pathogens. He also developed a theory of aging and longevity, which proposed
that aging is caused by the accumulation of toxic substances in the body. Metchnikoff is
also credited with discovering the process of cell-mediated immunity, which is the body’s
first line of defense against invading pathogens. Finally, Metchnikoff was the first to
recognize the beneficial properties of certain probiotic bacteria, which can help to boost
the immune system. Father of cellular immunology.
Father of Cellular Immunology Elie Metchnikoff (1845-1916)
Discovery Phagocytosis
Theory of Aging
Aging is caused by the accumulation of toxic substances in
the body
Cell-Mediated Immunity Body’s first line of defense against invading pathogens
Probiotic Bacteria Help to boost the immune system
Importnce of microbes in relation to food
What is food microbiology
The science that deals with the microorganism involve in the spoilage, contamination and
preservation of food is called Food microbiology.
Pathogenic microbes
Pathogenic bacteria can cause food-borne infections or intoxication, but they don't cause
food spoilage. You can't see or test their contamination.
Microbes Foodborne Illnesses Prevention
Pathogenic microbes Salmonellosis, Cholera
Proper food storage, handling,
cooking; good hygiene practices,
checking food temperature
The main factors that contribute to occurence of food borne diseases?
Factors
Improper food storage, handling, and cooking
Poor hygiene practices
Inadequate checking of food temperature
Contaminated water or soil
Cross contamination of food
Certain environmental factors, such as a warm climate
Certain medical conditions, such as weakened immune systems

18. Microbiology 18
Pathogenic bacteria in Food.
The following are some examples of pathogenic bacteria that can be found in food:
Salmonella spp.
Escherichia coli
Clostridium botulinum
Vibrio cholerae
Staphylococcus aureus
Listeria monocytogenes
Campylobacteria
Pathogenic voruses in food.
The following are some examples of pathogenic viruses that can be found in food:
Norovirus
Hepatitis A virus
Rotavirus
NIPAH Virus
Human adenovirus
Astrovirus
Pathogenic parasites in food.
The following are some examples of pathogenic parasites that can be found in food:
Trichinella spiralis
Giardia lamblia
Entamoeba histolytica
Food spoilage bacteria
It is the change of consistency, texture, colour, odor of foods due to contaminaton by
bacteria, yeasts and molds.
Lactic acid formation: Lactobacillus
Pigment formation: Flavobacterium
Gas formation: Lactobacillus
Slime formation: Streptococcus
Food spoilage molds
Food most risk for molds
Foods that are most at risk of being contaminated with molds include bread, fruits,
vegetables, dairy products, and processed meats. Mold growth can occur when foods
are stored in damp or humid conditions, or when they have been stored for too long. In

19. Microbiology 19
addition, foods that have been left out at room temperature for an extended period of
time are also more likely to become contaminated with molds.
Grain and grain product Many mycotoxin
Peanuts, nuts and pulses Aflatoxin
Fruits and vegetable Patulin
Milk and milk product Aflatoxin
Food borne infection and intoxication
Food Borne
Illness
Means of Exposure Symptoms Treatment
Incubation
Period
Communicable
Infection
Contaminated food with
pathogens
(Bacteria,Virus,parasite,protozoa)
Fever,
vomiting,
diarrhea,
abdominal pain
Antibiotics Hours to days Yes
Intoxication Contaminated food with toxins
Milder than
infection
Supportive
care - hydration
and electrolyte
replacement
Minutes to
houur
No
Practical
Study on sterilization and disinfection
What is sterilization
Sterilization refers to the process of killing or eliminating all forms of microbial life,
including bacteria, viruses, fungi, and spores, from a surface, object, or substance.
What is disinfection
Disinfection is the process of eliminating or reducing the number of harmful
(Pathogen) microorganisms, such as bacteria, viruses, and fungi, on a surface,
object, or substance. Unlike sterilization, disinfection does not necessarily kill all
types of microorganisms, but rather reduces their numbers to a level that is
considered safe for human health.
Sterilization Disinfection
Goal Eliminate all forms of microbial life
Reduce the number of harmful
microorganisms
Microbial reduction Complete elimination Partial reduction
Methods
Physical and chemical methods
(heat, radiation, chemical
disinfectants, filtration, etc.)
Chemical disinfectants, physical
methods (UV radiation, filtration, etc.)
Typical use
Healthcare facilities, medical
equipment production, etc.
Wider range of settings, including
healthcare, food processing, and
public settings
Outcome
A sterile surface, object, or
substance
A surface, object, or substance with
a reduced level of harmful
microorganisms
Importance
Critical for preventing infection and
contamination
Important for maintaining hygiene
and preventing the spread of disease
Properties of ideal disinfectant

20. Microbiology 20
1. Broad-spectrum activity: An ideal disinfectant should be able to kill a wide range of
microorganisms, including bacteria, viruses, fungi, and spores.
2. Fast-acting: The disinfectant should have a quick onset of action and work rapidly to eliminate
microorganisms.
3. Residual effect: An ideal disinfectant should have a residual effect, meaning it continues to provide
antimicrobial activity after application, preventing the growth of new microorganisms on the surface
or object.
4. Non-toxic: The disinfectant should not be toxic to humans or animals, and should not cause
irritation or allergic reactions.
5. Non-corrosive: The disinfectant should not damage or corrode the surfaces or objects being
disinfected.
6. Compatible: An ideal disinfectant should be compatible with a wide range of surfaces and materials
and not cause discoloration, staining or damage.
7. Easily available: An ideal disinfectant should be readily available and affordable for widespread use.
8. Environmentally safe: The disinfectant should not cause any harm to the environment and should
be easily biodegradable.
9. User-friendly: An ideal disinfectant should be easy to use, with clear instructions for application and
appropriate protective equipment.
Name of some disinfectant?
1. Chlorine-based disinfectants, such as bleach
2. Alcohol-based disinfectants, such as ethanol or isopropyl alcohol
3. Quaternary ammonium compounds (quats), such as benzalkonium chloride
4. Hydrogen peroxide-based disinfectants
5. Phenolic disinfectants, such as Lysol
6. Formaldehyde-based disinfectants
7. Glutaraldehyde-based disinfectants
8. Peracetic acid-based disinfectants
Types of disinfectant?
Types of heat sterilization
Dry heat
By flame, red heat, burning. This method involves exposing the objects or
surfaces to high temperatures ranging from 160°C to 250°C for a specified period
of time to achieve sterilization. This method is commonly used for heat-stable
objects, such as glassware, metal instruments, and surgical tools.
Moist heat
Boiling
Boiling water for at least 10 minutes is a simple and effective method for sterilizing heat-stable objects
such as glassware, plastic instruments, and some types of surgical instruments.
What is tyndalization

21. Microbiology 21
The process of tyndallization involves exposing the material to be sterilized
to steam for a short period of time, typically 30 minutes to an hour. This
initial exposure kills any vegetative cells that may be present, but does not
necessarily kill spores. The material is then allowed to incubate at room
temperature for a period of several hours, which allows any surviving spores
to germinate into vegetative cells. The material is then exposed to steam
again, and the process is repeated several times, typically over a period of
two to three days. The intermittent heating and incubation cycles gradually
kill off any spores that may have survived the initial exposure to steam,
resulting in sterilization of the material.
Autoclave
Steam with pressure 121℃and 15 psi for 20-30 minutes
Pasteurization
HTST/Flushing
High-temperature, short-time (HTST) pasteurization: This involves heating to
a temperature of 72°C (161°F) for 15 seconds
UHT
Ultra-high temperature (UHT) pasteurization: This involves heating milk to a
temperature of 135°C (275°F) for a few seconds, followed by rapid cooling.
UHT pasteurization kills all harmful bacteria in milk and extends its shelf life
for several months if packaged under sterile conditions. UHT milk does not
require refrigeration until it is opened.
LTHT/Holding
Low-temperature, long-time (LTHT) pasteurization is a method of
pasteurization that involves heating to a lower temperature for a longer
period of time than HTST pasteurization. The process is also sometimes
referred to as batch pasteurization or vat pasteurization. During LTHT
pasteurization, is typically heated to a temperature of 63°C (145°F) for 30
minutes or more. This slower heating process is designed to preserve the
taste and nutritional quality of milk while also killing harmful bacteria.
Study on method of sampling.
Types of food sample (by nature)
Solid sample
Liquid sample
Surface sample
Preparation for surface sample
By washing
One part of food is placed in 10 parts of sterilized dilutent.
By cutting the surface of the food

22. Microbiology 22
A slice of sample is transfered to a suitable buffer and homoginized.
Ten-cate agar sausage
Collect in sterilized agar
Impression plate
Contact slide
Sampling for anaerobic bacteria
Stuarts transport media
Reinforced clostridial media
Robertson’s cooked meat media
Study on microbial load determination on food sample.
Methods of counting total number of micro organisms in food
Standard Plate count method/ total viable count
This is the most widely used method for counting microorganisms in a sample. In
this method, the sample is diluted and spread onto a solid growth medium in a
petri dish. The plates are then incubated under appropriate conditions to allow the
microorganisms to grow, and the colonies that develop are counted. Viable cells
Most probable number (MPN) method
The MPN method is a statistical method used for counting microorganisms in
samples that contain low numbers of microorganisms. In this method, the sample
is serially diluted and inoculated into a series of tubes containing a liquid growth
medium. The tubes are then incubated under appropriate conditions, and the
number of positive tubes at each dilution level is recorded. The MPN is then
calculated based on the number of positive tubes and the dilution factor.
Direct microscopic count method
In this method, a known volume of the sample is placed on a microscope slide,
stained with a suitable dye, and examined under a microscope. The
microorganisms in the sample are then counted directly.
Dye reduction
Name of some food borne pathogen
1. Salmonella: This bacterium is commonly found in raw or undercooked poultry, eggs, and meat, as well as in
contaminated fruits and vegetables.
1. E. coli: This bacterium is commonly found in undercooked beef and other meats, as well as in contaminated
produce and water.
1. Staphylococcus aureus: This bacterium can produce toxins in food, and is commonly found in food that has
been handled improperly.

23. Microbiology 23
1. Clostridium botulinum: This bacterium produces a deadly toxin that can cause botulism, and is commonly
found in improperly canned or preserved food.
1. Bacillus cereus: This bacterium is commonly found in rice dishes, pasta dishes, and other starchy foods that
have been cooked and then left at room temperature for too long.
Metabolic
Enterotoxin
Botulinum
Mycotoxin
Indicator bacteria in food
Coliform (lactose farmented bacteria)
Enterococci
Study on preparation of cultural media.
Classification of cultural media
Based on consistency
• Solid media: These media have a solid consistency and are used for the
cultivation of microorganisms that require a solid surface to grow on. Examples
include agar plates and slants. Agar melts at 95℃and solidifies at 42℃it is used
as a concentration of 1.3% to make solid agar
• Liquid media: These media are in liquid form and are used for the cultivation of
microorganisms that can grow in suspension. Examples include broth and
thioglycollate medium. Sugar broth
• Semi-solid media: These media have a gel-like consistency and are used for the
cultivation of microorganisms that require a semi-solid surface to grow on.
Examples include motility agar and soft agar. 0.2 to 0.5% agar in liquid media.
Used for demonstration of bacterial motility and separation of mortile bacteria
from non mortile bacteria. Stuart’s and Amies media, Manitol mortile media.
• Biphasic medium is a type of culture medium that consists of two phases: a
solid agar phase and a liquid broth phase. The agar phase provides a solid
surface for the growth of microorganisms, while the broth phase provides a liquid
environment for the growth of microorganisms in suspension. Custaneda system
for blood culture.
Based of functional use
• Basal media: These media are designed for the cultivation of a wide range of non
festidious microorganisms. Nutrient broth, nutrient agar
• Enrichment media: These media are used to increase the numbers of a specific
type of microorganism in a mixed culture. Examples include selenite broth and
thiosulfate-citrate-bile-sucrose agar (TCBS). Blood agar, Chocolate agar.
• Differential media: These media are designed to differentiate between different
types of microorganisms based on their biochemical characteristics. Examples
include blood agar and MacConkey agar

24. Microbiology 24
MacConkey agar
Used to differentiate lactose fermentor from non lactose fermentor.
Manitol salt agar
Xylose lysine deoxylate agar
• Selective media: These media are designed to promote the growth of certain
types of microorganisms while inhibiting the growth of others. Examples include
Sabouraud agar Eosin Methylene Blue agar.
Eosin Methylene Blue agar.
Salmonella-Shigella agar (5-5)
Brilliant green agar
salmonella
Brucella agar
Stephylococcus medium
Gene transfer and mutation in bacteria
Gene transfer and mutation are two important mechanisms that contribute to genetic
diversity in bacteria. Gene transfer can occur through several mechanisms, including
conjugation, transformation, and transduction.
Conjugation
Conjugation is a process of gene transfer between bacteria that involves direct cell-to-cell
contact. In conjugation, a donor bacterium transfers a plasmid (a small, circular piece of
DNA) to a recipient bacterium through a structure called a pilus.
The steps involved in conjugation are as follows:
1. The donor bacterium synthesizes a conjugative pilus, which is a long, hair-like structure that extends from
the bacterial cell surface.
2. The pilus attaches to a recipient bacterium and retracts, bringing the two cells into close contact.
3. The donor bacterium then transfers a copy of the plasmid to the recipient bacterium through the pilus. The
plasmid is replicated within the recipient bacterium, resulting in the transfer of genetic material from the
donor to the recipient.
4. Once the plasmid has been transferred, the pilus is disassembled and the two bacteria separate.
The plasmid that is transferred during conjugation can carry a variety of genes, including
antibiotic resistance genes, virulence factors, and genes involved in metabolic pathways.
Conjugation is an important mechanism for the spread of antibiotic resistance genes
among bacteria and can contribute to the emergence of antibiotic-resistant strains.
Transformation
Transformation is a process of gene transfer between bacteria that involves the uptake
and incorporation of free DNA from the environment. The steps involved in
transformation are as follows:

25. Microbiology 25
1. A donor bacterium releases DNA into the surrounding environment through lysis or other means.
2. The DNA is taken up by a recipient bacterium through a process called competence, which involves the
binding and uptake of the DNA by specific proteins on the bacterial cell surface.
3. Once inside the recipient bacterium, the DNA may integrate into the genome or exist as a separate,
extrachromosomal element known as a plasmid.
4. If the DNA integrates into the genome, it can be passed on to daughter cells during cell division, resulting
in the transfer of genetic material from the donor to the recipient.
Transformation can occur naturally in some bacteria, but it can also be induced through
laboratory methods that make the recipient bacteria more competent for DNA uptake.
Transformation is an important mechanism for the spread of antibiotic resistance genes
and virulence factors among bacteria and can contribute to the emergence of pathogenic
strains.
Transduction
Transduction is a process of gene transfer between bacteria that involves the transfer of
DNA by a bacteriophage (a virus that infects bacteria). The steps involved in transduction
are as follows:
1. A bacteriophage infects a donor bacterium and begins to replicate inside the cell.
2. During the replication process, some of the phage particles may package fragments of the donor
bacterium's DNA instead of the phage DNA.
3. When the phage particles are released from the donor bacterium, they can infect a recipient bacterium.
4. If the phage particle containing the donor DNA infects a compatible recipient bacterium, the donor DNA
can integrate into the recipient's genome through recombination.
5. Once integrated, the donor DNA can be passed on to daughter cells during cell division, resulting in the
transfer of genetic material from the donor to the recipient.
Transduction can occur through two mechanisms: generalized transduction, in which any
part of the donor DNA can be packaged into the phage particle, and specialized
transduction, in which only specific regions of the donor DNA are packaged into the
phage particle. Transduction is an important mechanism for the spread of antibiotic
resistance genes and virulence factors among bacteria and can contribute to the
emergence of pathogenic strains.
A mutation is a change in the DNA sequence of a gene, which may changes the protein or
RNA product encoded by that gene. A cell or an organism which shows the effect of a
mutation is called a mutant. There are two ways of mutation:
Spontaneous mutation
Spontaneous mutations are genetic changes that occur naturally, without any external or
induced mutagenic agents. These mutations can arise due to errors in DNA replication,
recombination, or repair processes. The rate of spontaneous mutation can vary
depending on the specific bacterial species and environmental factors.
Induced mutation
Induced mutations are genetic changes that are caused by exposure to mutagenic agents
such as chemicals, radiation, or certain types of viruses. These agents can cause DNA
damage, leading to changes in the nucleotide sequence of the DNA. Unlike spontaneous
mutations, which occur naturally, induced mutations are deliberately introduced to study
the effects of specific genetic changes on bacterial phenotypes.

26. Microbiology 26
Two common types of mutation are
Point Mutations
Point mutations are the change in a single nucleotide base in the DNA sequence. These
mutations can occur spontaneously during DNA replication or can be induced by
mutagenic agents such as chemicals or radiation. Point mutations can be classified into
three types based on their effects on the encoded protein or RNA molecule
1. Silent mutations: These mutations do not result in any change to the amino acid sequence of the protein
product, as the substituted nucleotide codes for the same amino acid as the original nucleotide. (most
amino acids are coded for by several alternative codons)
2. Missense mutations: These mutations result in a change to the amino acid sequence of the protein
product, as the substituted nucleotide codes for a different amino acid than the original nucleotide.
3. Nonsense mutations: These mutations result in the premature termination of protein synthesis, as the
substituted nucleotide codes for a stop codon instead of an amino acid.
Frameshift mutation
Frameshift mutations are genetic changes that involve the insertion or deletion of one or
more nucleotides in the DNA sequence, which can alter the reading frame of the mRNA
molecule and ultimately result in a completely different amino acid sequence. Frameshift
mutations can be classified into two types:
1. Insertions: These mutations occur when one or more nucleotides are added to the DNA sequence,
causing a shift in the reading frame.
2. Deletions: These mutations occur when one or more nucleotides are removed from the DNA sequence,
causing a shift in the reading frame.
Plasmid and DNA Replication
What is plasmid?
Plasmid is an extra chromosomal, circular and always double stranded DNA molecules
that can replicate independently within a cell.
Properies of plasmid?
There are 1 copy to several dozens copy of plasmid can be in a cell.
1. Small size: Plasmids are usually much smaller than the host cell's chromosomal
DNA(0.1% to 10%), typically ranging in size from a few thousand to a few hundred
thousand base pairs (1000 bp (1 kbp) to 1000 kbp). This makes them easy to manipulate
and study in the laboratory.
2. Replication: Plasmids can replicate independently of the host cell's chromosomal DNA.
They typically carry their own replication origin, which allows them to initiate replication
and produce multiple copies within the cell.
3. Mobility: Plasmids can be transferred between cells through various mechanisms,
including conjugation, transformation, and transduction. This allows genes carried on
plasmids to spread rapidly through a population of bacteria or other organisms.
4. Selectable markers: Plasmids often carry genes that provide some type of selective
advantage to the host cell, such as antibiotic resistance, metabolic capabilities, or
virulence factors.

27. Microbiology 27
5. Ubiquitous: Almost all bacterial cells isolated in nature carry plasmids, often more than
one kind.
Example of plasmid gene
Antibiotic resistance genes: (produce enzymes that modify or degrade antibiotics).
plasmids with these genes are called R factors.
Conjugation genes (Regulate the fertility transfer). plasmids with these genes are called F
factors.
Bacteriocins producing genes (colicin - proteins toxic to other bacteria) plasmids with
these genes are called C factors.
Growth on unusual substrates gene (produce enzymes for hydrocarbon degradation)
What is DNA replication?
DNA replication is the process of making an identical copy of DNA within cell. DNA
replication occurs during the S phage of cell cycle.
Stage of DNA replication?
Initiation
Initiation stage started when initiator protein bind at a specific site in the DNA
molecule. The site is called the origin of replication. The double stranded DNA helix
separate from each other. SSB protein kept the two strands apart from each other
preventing reanneling. Helicase enzyme move for forward and unwind the DNA helix.
Elongation
Primase enzyme synthesize a short RNA sequence called primers which acts as a
starting point for DNA polymerase III enzyme to start the replication process.
Replication always occurs in 5’→3’ (5’ phosphate group 3’ OH group) direction. In one
stand the replication is continuous(leading strand) and other the replication occurs in
fragments (lagging strand). The gap between each fragments is known Okazaki gap.
DNA polymerase I remove the primer and replace it with proper base in the lagging
strand then The enzyme DNA ligase catalyses the formation of a phosphodiester
linkage between the DNA synthesized by DNA polymerase III and the small fragments
of DNA produced by DNA polymerase I. DNA gyrase: Restricts the supercoiling of the
DNA helix during the course of replication.
Termination
Termination is the final stage of DNA replication, which occurs when the replication
fork reaches the end of the DNA molecule.
Bacterial Pathogenicity
Bacterial pathogenicity refers to the ability of bacteria to cause disease in a host organism.
What is infection?
An infection is a condition caused by the invasion and multiplication of micro-organisms
within the host. Multiplication of natural bacteria which are part of our body is not
considered as infection.

28. Microbiology 28
What is pathogenicity?
Pathogenicity refers to the ability of a microorganism, such as a bacterium, virus, fungus,
or parasite, to cause disease or harm to a host organism.
What is virulence?
Virulence refers to the degree of pathogenicity of a microorganism, such as a bacterium,
virus, fungus, or parasite. A microorganism's virulence is determined by its ability to
cause disease in a host organism and the severity of the resulting illness.
what is toxigenicity?
Toxigenicity refers to the ability of a microorganism, such as a bacterium, to produce
toxins that cause disease or harm to a host organism.
what is invasion?
Invasion refers to the ability of a pathogenic microorganism, such as a bacterium, virus,
fungus, or parasite, to enter and replicate within host cells or tissues
Name of invasins
Virulence factor
Attachment (via adhesins)
Adhesins: Proteins or carbohydrates on the surface of bacteria that allow them to
adhere to host cells or tissues. Adhesins can be specific to certain types of host
tissues, allowing bacteria to target and colonize specific organs or tissues. Fimbrie,
Bacterial cell wall, capsule help bacteria to attach to the host cell.
Colonization
Colonization occurs when bacteria successfully establish themselves in a host
organism, typically by adhering to host tissues or by evading host defenses.
Pathogens usually colonize host tissues that are in contact with the external
environment.
Invasiveness
Invasiveness is the ability of a pathogenic microorganism, such as a bacterium, virus,
fungus, or parasite, to enter and replicate within host cells or tissues, leading to the
spread of the infection to other parts of the body.
mechanisms for colonization (adherence and initial multiplication),
production of extracellular substances ("invasins"), that promote the immediate
invasion of tissues
ability to bypass or overcome host defense mechanisms which facilitate the actual
invasive process.
Toxins and Enzymes
1. Toxins: Biological molecules that can damage host cells or tissues, disrupt normal
physiological processes, and trigger an immune response. Types of toxin
(Neurotoxins, Enterotoxins, Cytotoxins)

29. Microbiology 29
2. Enzymes: Molecules that can break down host tissues, allowing bacteria to invade
and colonize host tissues. There are virulence determinant enzymes that dissolve the
glue between cells, thus allowing the bacteria to spread rapidly through the tissue.
Inhibition of phagocytosis
Ability of pathogens to avoid or overcome phagocytes or inhibit the phagocytic
engulfment.
Immunology
Immunology concerns the study of the host responses to the introduction of the foreign
substances into the tissue and the methods by which body tries to eliminate these
substances and protect itself against any further invasion by them.
Seroology The branch of science dealing with the measurement and characterization of
antibodies, antigens and other immunological substances in body fluids (particularly in
serum) or even plants that are infected
Importance of immunology and serology#
To apply the knowledge in the vaccine production
To know the immune status of animal and poultry
For better production of livestock and poultry by improving immune status
To know the consequences of immune responses
The knowledge of immunology and serology is applied in the microbiology, patholgy,
physiology, medicine and even surgery.
Serological tests may be performed for diagnostic purposes when an infection is
suspected, in rheumatic illnesses, and in many other situations, such as checking an
individual's blood type. Serology blood tests help to diagnose patients with certain
immune deficiencies associated with the lack of antibodies, such as X-linked
agammaglobulinemia. In such cases, tests for antibodies will be consistently negative.
History of immunology
Edward Jenner is the father of immunology. Edward Jenner discovered that inoculating
people with cowpox could protect them against smallpox, leading to the development of
the first vaccine.

30. Microbiology 30
Louis Pasteur became the first experimental immunologist.
The field of immunology gained momentum in the late 19th and early 20th centuries with
the discovery of antibodies by Paul Ehrlich and the recognition of cellular immunity by
Elie Metchnikoff.
What is immunity
Immunity refers to the ability of an organism to resist or defend against potentially
harmful substances or pathogens.
Classification of immunity.
Natural/ Innate/ Non-specific immunity and
Innate immunity - this is the body's natural defense system that works immediately
when it detects a foreign invader like bacteria or virus. It includes physical and
chemical barriers like skin and stomach acid, as well as cells like phagocytes and
natural killer cells.
Acquired/ Adaptive/ Specific immunity
Adaptive immunity - this is a more specific and targeted response that develops after
exposure to a specific pathogen. It involves cells like B cells and T cells that can
recognize and remember specific antigens and mount a tailored response to eliminate
them. Adaptive immunity also provides immunological memory, which allows the body
to respond quickly and efficiently to future exposures to the same pathogen.
Active immunity
Active immunity is a type of immunity that develops when the body's immune
system produces its own antibodies in response to exposure to a specific pathogen
or antigen. This can occur naturally, when a person gets infected with a disease, or
artificially, when a person receives a vaccine.
When a pathogen enters the body, the immune system recognizes it as foreign and
activates B cells and T cells to produce antibodies that can recognize and eliminate
the pathogen. These antibodies then circulate in the bloodstream, providing
protection against future infections by the same pathogen. This process is called the
primary immune response.
After the initial exposure, the body also develops immunological memory, which
allows the immune system to mount a faster and stronger response upon
subsequent exposures to the same pathogen. This is called the secondary immune
response and is the basis for the long-lasting protection provided by vaccines.
types
Humoral immunity - B cells produce antibodies that recognize and neutralize
specific pathogens like bacteria and viruses in the bloodstream.
Cell-mediated immunity - T cells detect and kill infected or abnormal cells directly,
or help other immune cells to recognize and eliminate pathogens that have
invaded host cells.
Difference between Humoral and Cell mediated immunity***

31. Microbiology 31
Here is a table summarizing the differences between humoral and cell-mediated
immunity:
Feature Humoral Immunity Cell-Mediated Immunity
Effector cells B cells T cells
Type of antigen recognition
Extracellular pathogens or foreign
substances
Intracellular pathogens or
abnormal cells
Mechanisms of action
Antibodies can neutralize or
opsonize pathogens or foreign
substances, mark them for
destruction by other cells, and
activate complement
T cells can directly kill infected or
abnormal cells, or secrete
cytokines that stimulate other
cells to attack and eliminate the
targets
Duration of response
Short-term (several weeks to a few
months)
Long-term (memory T cells can
persist for years or even decades
after initial exposure
Passive immunity
Passive immunity is a type of immunity that is acquired from outside the body, rather
than being produced by the body's own immune system. In passive immunity, pre-
formed antibodies are transferred to an individual to provide immediate protection
against a specific pathogen or toxin. Passive immunity can occur naturally or
artificially.
Naturally acquired passive immunity occurs when a baby receives antibodies from
its mother through the placenta during pregnancy or through breast milk after birth.
This provides the baby with immediate protection against certain infections until its
own immune system can develop fully.
Artificially acquired passive immunity occurs when pre-formed antibodies are
administered to an individual, such as through injection of immunoglobulins or
antitoxins. This can provide immediate protection against specific pathogens, such
as in the case of rabies or tetanus exposure.
Difference between active and passive immunity***
Feature Active Immunity Passive Immunity
How immunity is acquired
Produced by person's own immune
system in response to pathogen or
antigen exposure
Transferred from another source, pre-
formed antibodies
Duration of protection
Long-lasting (immunological
memory)
Temporary (no immunological
memory)
Speed of protection Takes time to develop Immediate
Mechanism of action
Production of antibodies by B cells
and activation of T cells
Transfer of pre-formed antibodies
Types of immunity
Natural (resulting from exposure to
pathogen) or artificial (resulting from
vaccination)
Natural (such as maternal antibodies)
or artificial (such as through injection
of immunoglobulins)
Difference between innate and adaptive immunity***
Sure, here is a table summarizing the differences between innate immunity and
adaptive immunity:
Feature Innate Immunity Adaptive Immunity
Specificity Non-specific Highly specific
Memory No memory Immunological memory

32. Microbiology 32
Timing Immediate Takes time to develop
Cell types Phagocytes, natural killer cells, others B cells, T cells
Mechanisms
Physical barriers, chemical and
cellular components
Antibody production, T cell activation,
direct cell killing
Activation speed Rapid Slow
First line of defense Yes No
Diversity of receptors Limited Vast
Response to same pathogen Same every time Improved over time
Primary target
Pathogen-associated molecular
patterns (PAMPs)
Specific antigens
Effectors Various types of cells and proteins B cells, T cells
Lymphoid organs.
Lymphoid organs are specialized tissues of the immune system that are responsible for
the development, maturation, and activation of lymphocytes (white blood cells) and the
production of antibodies.
Primary lymphoid organs
The primary lymphoid organs are specialized tissues where lymphocytes (white blood
cells) develop, differentiate and mature. These organs include the bone marrow and
thymus gland. All these organs arise early in the fetal life
1. Bone marrow: The bone marrow is a soft, spongy tissue found inside bones, where
hematopoiesis (the formation of blood cells) occurs. In the bone marrow,
hematopoietic stem cells (HSCs) differentiate into all types of blood cells, including
lymphocytes. B cells, a type of lymphocyte, mature in the bone marrow.
2. Thymus gland: The thymus gland is a small gland located in the chest behind the
sternum. It is the site of T cell development and maturation. T cells are a type of
lymphocyte that play a crucial role in cell-mediated immunity, which is the immune
response that involves the destruction of infected or cancerous cells.
Secondary lymphoid organs
Secondary lymphoid organs are specialized tissues in the body that filter and trap
foreign substances, such as pathogens, and activate the immune response. These
organs include lymph nodes, spleen, tonsils, and Peyer's patches in the gut. The
secondary lymphoid organs arise late in fetal life and persist through adult life. They
respond to antigenic stimulation and are poorly developed in germ-free animals. These
organs are rich in macrophages and dendritic cells that trap and process antigens
Comparison between primary and secondary lymphoid organs***
Characteristics Primary Lymphoid Organs Secondary Lymphoid Organs
Function Develop and mature lymphocytes
Activate immune responses to
specific antigens
Location
Specific areas of the body (bone
marrow, thymus)
Located throughout the body (lymph
nodes, spleen, tonsils, Peyer's
patches)
Composition
Developing and maturing
lymphocytes, specialized supporting
cells
Mature lymphocytes, dendritic cells,
macrophages, B cells

33. Microbiology 33
Characteristics Primary Lymphoid Organs Secondary Lymphoid Organs
Immune response
Involved in the development of
adaptive immunity
Involved in the activation of adaptive
immune responses
Antigen response Unresponsive Fully responsive
Time of development Arise early in the fetal life late in fetal life
Origin Endoderm Mesoderm
Question
What is immunology?What are the two types of immunity?What is the difference between innate and adaptive
immunity?What is active immunity and how is it acquired?What is passive immunity and how is it acquired?
Name some primary lymphoid organs.Name some secondary lymphoid organs.What is the function of primary
lymphoid organs?What is the function of secondary lymphoid organs?What is the difference between primary
and secondary lymphoid organs?
Function of cells of immune response
Here are some functions of the cells involved in immune responses:
1. B cells: produce antibodies that recognize and bind to specific antigens, marking them for destruction by
other cells in the immune system.
2. T cells: recognize and destroy cells that have been infected with a pathogen or cancer cells, and help
regulate the immune response.
3. Natural Killer (NK) cells: identify and destroy cells that are abnormal or infected, such as virus-infected
cells or tumor cells.
4. Dendritic cells: capture and present antigens to T cells, activating the adaptive immune response.
5. Macrophages: engulf and digest foreign substances and cellular debris, and present antigens to T cells to
activate the adaptive immune response.
6. Neutrophils: are the first cells to respond to infection or inflammation, and phagocytose and kill
pathogens.
7. Eosinophils: are involved in the immune response against parasites and are important in allergic
reactions.
8. Basophils: are involved in allergic reactions and release histamine and other mediators.
9. Mast cells: release histamine and other mediators in response to allergens or injury, triggering
inflammation.
10. Monocytes: can differentiate into macrophages or dendritic cells and are involved in phagocytosis and
antigen presentation.
What are the basic feature of immune response***
The basic features of the immune response include:
Specificity: The immune system is able to recognize and respond to specific pathogens
or foreign substances, while ignoring self-components of the body.
Diversity: The immune system is able to recognize and respond to a wide variety of
pathogens or foreign substances, including bacteria, viruses, fungi, parasites, and toxins.
Memory: The immune system is able to "remember" previous exposures to pathogens or
foreign substances and respond more rapidly and effectively to subsequent exposures.

34. Microbiology 34
Self-tolerance: The immune system is able to distinguish between self-components of the
body and non-self-components, and avoid attacking normal, healthy tissues.
Regulation: The immune system is able to regulate the magnitude and duration of
immune responses to prevent excessive or inappropriate responses that could cause
tissue damage or autoimmunity.
Amplification: The immune system is able to amplify and coordinate immune responses
through signaling molecules and cytokines, to ensure effective elimination of pathogens
or foreign substances.
Primary and Secondary Immune responses
Here are some key differences between the primary and secondary immune responses:
Feature Primary Immune Response Secondary Immune Response
Time to onset Several days to a week Within hours
Strength of response Weaker Stronger
Duration of response Short-lived Long-lasting
Involvement of memory cells No memory cells Memory B and T cells
Efficiency of response Less efficient More efficient
Antigen
What is antigen
An antigen is a substance that triggers an immune response in the body. It is typically a
molecule or a part of a molecule that is foreign to the body, such as a protein on the
surface of a virus or bacteria.
Classification of antigen
Microbial antigen
Microbial antigens are antigens that come from microorganisms such as bacteria,
viruses, fungi, and parasites. Examples of microbial antigens include bacterial cell wall
components, viral capsid proteins, and fungal cell wall components.
Bacterial antigen
Bacterial antigens are substances that come from bacteria and can cause an
immune response in the body. They are typically composed of molecules found on
the surface of the bacterial cell, such as proteins or carbohydrates.
The cell wall of gram positive bacteria is largely composed of peptidoglycans and
the cell wall of gram negative bacteria is a polysaccharide – lipid – protein structure.
The cell wall is “O” antigen.
Bacterial capsules may be either polysaccharides or proteins. Capsular antigens
collectively known as “K” antigen.
Bacterial flagella consists of single protein called flagellin and this antigens are
known as “H” antigen.

35. Microbiology 35
Pili are short projections that covers the surface and are classified as “Fork”
antigen.
Viral antigen
The protein layer is termed as capsid and the sub units are called capsomares. The
capsid proteins are good antigens. They are typically composed of molecules found
on the surface of the virus, such as viral proteins or glycoproteins.
Non-microbial antigen
Non-microbial antigens are substances that are not derived from microorganisms, but
can still trigger an immune response in the body. They can come from a variety of
sources, including environmental substances and the body's own cells.
Nature of good antigen
Generally large molecule i.e. high molecular weight > 10,000 daltons.
Foreign (non-self) to the body.
Things that induce immune system to produce an immune response and/or materials that
react with antibodies or immune cells.
Structurally complex (proteins and polysaccharides are good antigens.
Accessible i.e. the immune system must be able to contact the molecule
Antigens and immunogenicity
Antigens are substances that can trigger an immune response in the body.
Immunogenicity is the ability of an antigen to stimulate an immune response, leading to
the production of antibodies and activation of immune cells.
Not all antigens can stimulate or induce an immune response and those that do are said
to be antigenic and immunogenic.
Immunogens both stimulate an antibody response and bind to the antibodies
Factors significantly influence antigenicity
Contribution of the Immunogen
Immunogens are a subset of antigens that are specifically able to induce an immune
response in the body. They play a critical role in the body's immune response, as they
are responsible for triggering the production of antibodies and activation of immune
cells.
1. Foreignness: The degree to which an antigen is foreign or non-self to the body is an important factor in
determining its antigenicity. Antigens that are foreign to the body are more likely to be recognized as
"non-self" and trigger an immune response.
2. Size and complexity: The size and complexity of an antigen can affect its antigenicity. Larger and more
complex antigens are often more effective at triggering an immune response.
3. Structure: The three-dimensional structure of an antigen can significantly influence its antigenicity.
Antigens with a unique or complex structure are more likely to be recognized by the immune system
and trigger an immune response.

36. Microbiology 36
4. Solubility: The solubility of an antigen can also influence its antigenicity. Soluble antigens are often
more effective at triggering an immune response than insoluble ones.
Contribution of the Biological System
Biological systems play a critical role in the body's immune response, and contribute
to both the recognition and elimination of foreign substances, including antigens and
immunogens.
1. Genetic Factors: Some substances are immunogenic in one species but not in another. Similarly, some
substances are immunogenic in one individual but not in others (i.e. responders and non-responders).
The species or individuals may lack or have altered genes that code for the receptors for antigen on B
cells and T cells or they may not have the appropriate genes needed for the APC to present antigen to
the helper T cells.
2. Age: Age can also influence immunogenicity. Usually the very young and the very old have a
diminished ability to mount and immune response in response to an immunogen
Method of Administration
The method of administration is an important aspect of how antigens and immunogens
are delivered to the body.
1. Dose: The dose of administration of an immunogen can influence its immunogenicity. There is a dose
of antigen above or below which the immune response will not be optimal.
2. Route: Generally the subcutaneous route is better than the intravenous or intragastric routes. The
route of antigen administration can also alter the nature of the response
3. Adjuvants: Substances that can enhance the immune response to an immunogen
Epitope or Antigenic Determinant
Epitope or Antigenic determinant is a specific part of an antigen that is recognized by the
immune system and can trigger an immune response. Epitopes are usually small peptide
sequences, ranging from 5 to 25 amino acids in length, that are exposed on the surface of
the antigen. The immune system can recognize different epitopes on the same antigen,
and different antigens may share common epitopes.
Hapten
Hapten is a small molecule that can bind to a larger molecule, such as a protein, but
cannot elicit an immune response on its own. However, when a hapten binds to a larger
carrier molecule, it can create a new molecule, called a hapten-carrier conjugate, which
can then trigger an immune response. The immune system recognizes the hapten as a
foreign substance and mounts an immune response against it.
Heterophilic antigen
Heterophilic antigens are antigens that share some structural similarities with host (self)
antigens. This structural similarity can cause the immune system to mistakenly recognize
the host antigens as foreign and mount an immune response against them. This is known
as an autoimmune response, where the immune system attacks and damages host
tissues.
Superantigen
Superantigens are a class of antigens that are capable of triggering an excessive and
potentially dangerous immune response by activating a large number of T cells
indiscriminately. Unlike conventional antigens, which are presented to T cells by antigen-

37. Microbiology 37
presenting cells, superantigens directly bind to the T cell receptor and major
histocompatibility complex (MHC) molecules, causing a massive activation of T cells.
Upto 25%.
Summery
Antigens are substances that can elicit an immune response, while immunogens are antigens that can induce an
immune response on their own.
Antigens can be classified into microbial and non-microbial antigens, with microbial antigens including bacterial
and viral antigens.
The factors that significantly influence antigenicity include size, complexity, and foreignness.
A good antigen should be foreign, large, complex, and stable.
The biological system, including genetics, age, and health status, can influence the immune response to antigens.
The method of administration can impact the immune response to antigens and immunogens, with different
methods leading to different types and magnitudes of immune responses.
The different methods of administration include injection, oral, nasal, topical, and intravenous.
A mind map is a helpful tool for summarizing the important concepts related to antigens and immunogens.
Mind map
Title: Concepts related to antigens and immunogens
Main branches:
Antigens
Definition
Classification
Microbial antigens
Bacterial antigens
Viral antigens
Non-microbial antigens
Factors that influence antigenicity
Size
Complexity
Foreignness
Nature of a good antigen
Foreign
Large
Complex
Stable
Immunogens
Definition
Contribution to immune response
Differences from antigens
Immune response
Biological system

38. Microbiology 38
Genetics
Age
Health status
Method of administration
Injection
Oral
Nasal
Topical
Intravenous
Antibody
What is antibody
Antibody is a protein substance produced by the immune system in response to antigen.
Antibodies, also known as Immunoglobins, are designed to recognise and bind with
specific antigens.
Structure of an antibody
Antibodies are Y-shaped proteins consisting of four polypeptide chains, two heavy
chains, and two light chains, connected by disulfide bonds.
The two arms of the Y-shaped molecule are called the Fab regions (fragment antigen-
binding), and they contain the variable regions that are specific to the antigen-binding
site.
The stem of the Y-shaped molecule is called the Fc region (fragment crystallizable), and it
determines the biological activity of the antibody.
Classification of antibody

39. Microbiology 39
Function of antibody
Toxic Neutralization: Antibodies can directly neutralize the activity of toxins, such as viral
or bacterial toxin, by binding to the toxin molecules and preventing it from interacting
with host cells.
Opsonization: Antibodies can mark pathogens for destruction by immune cells, such as
macrophages or neutrophils, through a process called opsonization. Antibodies bind to
the surface of the pathogen, which facilitates its uptake and destruction by these cells.
Complement activation: Antibodies can activate the complement system, which is a
group of proteins that can directly destroy pathogens or facilitate their uptake by immune
cells. Antibodies can activate the complement system by binding to the complement
protein C1q, which triggers a cascade of reactions that ultimately lead to the formation of
a membrane attack complex (MAC) that can directly destroy pathogens.
ADCC (antibody-dependent cell-mediated cytotoxicity): In this process, antibodies bind to
the surface of a target cell, such as a cancer cell or an infected cell, and recruit immune
cells, such as natural killer (NK) cells or macrophages, to destroy the target cell.
Agglutination and precipitation: Antibodies combine with the surfaces of microorganisms
or soluble antigens and cause them to agglutinate or precipitate
Steric hindrance: Antibodies combine with the surfaces of microorganisms and may
block or prevent their attachment to susceptible cells or mucosal surfaces
Phagocytosis
Phagocytosis is the process of engulfment and digestion of pathogens or cellular debris
by cirtain cell such macrophages.
Steps of phagocytosis
1. Chemotaxis: In response to chemical signals, phagocytic cells are attracted to the site of infection or
injury.
2. Recognition and attachment: The phagocytic cell recognizes and binds to the surface of the pathogen
or debris through receptors, such as complement receptors or scavenger receptors.
3. Engulfment and formation of phagosome: The phagocytic cell extends its membrane around the
pathogen, forming a phagosome. The phagosome then seals off from the extracellular environment.

40. Microbiology 40
4. Formation of phagolysosome: The phagosome fuses with lysosomes, which contain enzymes and
reactive oxygen species, to form a phagolysosome.
5. Destruction: The contents of the phagolysosome, including the enzymes and reactive oxygen species,
digest and destroy the pathogen or debris.
6. Elimination: The remaining waste material is either released from the cell or stored within it until it can
be eliminated from the body.
Opsonization
Opsonization (also, opsonisation) is the molecular mechanism whereby molecules,
microbes, or apoptotic cells are chemically modified to have a stronger attraction to the
cell surface receptors on phagocytes and NK cells
An opsonin (from the Greek opsōneîn, to prepare for eating) is any molecule that
enhances phagocytosis by marking an antigen for an immune response or marking dead
cells for recycling. Opson (ancient Greece) referred to the delicious side-dish of any meal
Summery
We discussed the immune system and its components, including antibodies, phagocytic cells, and opsonins.

41. Microbiology 41
We talked about the structure of antibodies, which are Y-shaped proteins consisting of two heavy chains and two
light chains.
We covered the classification of antibodies based on their structure, which includes IgA, IgD, IgE, IgG, and IgM.
We also discussed the functions of antibodies, which include neutralizing pathogens, activating complement, and
facilitating opsonization.
Finally, we talked about the steps of phagocytosis, including chemotaxis, recognition and attachment, engulfment,
formation of phagolysosome, destruction, and elimination.
Mycotoxin
What is mycotoxin?
Mycotoxins are fungal metabolites which are secreted by fungas during their growth.
What is mycotoxicosis?
Mycotoxicosis is a disease or illness caused by the ingestion or exposure to mycotoxins