Chapter 1: Microbiology - The Science
What is Microbiology?
 Microbiology is the study of microbes.
Why study Microbiology?
 Studying microbiology is important because it
helps us understand the biology and behavior
of microscopic organisms, which play a crucial
role in many diseases and infections,
biotechnology and medicine, environmental
science, food and industrial processes, and
evolution and diversity. It provides insights into
the complex interactions between
microorganisms and their environment and
helps develop strategies to address many of the
world's health, environmental, and
technological challenges.
Define pathogen, nonpathogenic, and opportunistic
pathogen.
 Pathogens are disease-causing microorganisms.
 Non-pathogens are microbes that do not cause
disease.
 Opportunistic pathogens are microbes with the
potential to cause disease, but that does not do
so under ordinary circumstances.
Differentiate between acellular microbes and
microorganisms and list several examples of each.
 Acellular microbes are microbes that are not
composed of cells. Example: prions and viruses.
 Microorganisms are very small organisms and are
usually microscopic. Example: bacteria, archaea,
certain algae, protozoa, and certain fungi.
First Microorganisms on earth.
 The first microorganisms on Earth are archaeans and
cyanobacterias.
Earliest known infectious diseases.
 Some of the earliest known infectious diseases are
smallpox, the bubonic plague, malaria, tuberculosis,
cholera, yellow fever, measles, syphilis, and etc.
Contributions of the pioneers in the science of
Microbiology: Anton van Leeuwenhook, Louis Pasteur,
Robert Koch.
Anton van Leeuwenhoek:
 He was the first to observe bacteria, yeast, and
protozoa with a microscope.
 He described the structure and movement of
bacteria, contributing to the understanding of their
role in fermentation and decay.
Louis Pasteur:
 Demonstrated the existence of microorganisms and
their role in fermentation and spoilage.
 Established the concept of "germ theory", showing
that microorganisms can cause disease.
 Developed pasteurization, a heat treatment that
kills harmful microorganisms in food and beverages.
 Contributed to the development of vaccines for
rabies and anthrax.
Robert Koch:
 Discovered the causative agents of several major
diseases, including tuberculosis, cholera, and
anthrax.
 Developed Koch's postulates, a set of criteria used
to establish the relationship between a microbe and
a disease.
 Made significant contributions to the field of
bacteriology, including the development of
techniques for growing pure cultures of bacteria.
List several reasons why microbes are important.
 Microbes play a crucial role in maintaining the
balance of the ecosystem by breaking down organic
matter and recycling nutrients.
 They are the primary producers in many food chains
and provide food and nutrition to many species.
 They are used in many industrial processes, such as
the production of food, beverages, and
biodegradable plastics.
 They are important for human health, with some
microbes serving as beneficial probiotics and others
causing diseases.
 They are used in medical and biotechnological
applications, such as the production of vaccines,
antibiotics, and biopharmaceuticals.
 Microbes have unique properties, such as antibiotic
resistance and biodegradability, that have important
implications for environmental and human health.
 They play a key role in biogeochemical cycles, such
as the carbon cycle, and help regulate the Earth's
climate.
Explain the relationship between microbes and infectious
diseases.
 Microbes, such as bacteria, viruses, fungi, and
parasites, can cause infectious diseases by invading
the body and multiplying, leading to symptoms such
as fever, inflammation, and tissue damage.
 Microbes spread from one person to another
through direct or indirect contact, or through
contaminated food or water.
Differentiate between infectious diseases and microbial
intoxications.
 Infectious disease is a disease caused by a microbe
following colonization of the body by that microbe.
 Microbial intoxication is a disease that results from
ingestion of a toxin that was produced by pathogen
in vitro.
Differentiate between biogenesis and abiogenesis.
 Biogenesis is the theory that life originated only
from preexisting life and never from nonliving
matter.
 Abiogenesis is the theory that life can arise from
nonliving matter; also known as a spontaneous
generation.
Explain the germ theory of disease.
 The germ theory of disease states that many
diseases are caused by the presence and actions of
specific microorganisms, such as bacteria, viruses,
and fungi.
 The germ theory was first proposed by Girolamo
Fracastoro in the 16th century, but it was Louis
Pasteur who provided the experimental evidence
needed to support the theory. He showed that
microorganisms could cause spoilage in food and
wine, and that diseases such as chicken cholera and
anthrax were caused by specific microorganisms.
Outline Koch's Postulate and cite some circumstances in
which they may not apply.
Koch's Postulates
 Koch's postulates are a set of criteria developed by
Robert Koch in the late 19th century to establish the
relationship between a microbe and a disease. The
postulates are:
1.The microbe must be present in every case of the
disease.
2.The microbe must be isolated and grown in pure culture.
3.The disease must be produced when the pure culture is
introduced into a healthy, susceptible host.
4.The same microbe must be reisolated from the
experimentally infected host.
These postulates have been widely used for over a
century to identify the cause of infectious diseases.
However, there are circumstances in which they may not
apply:
a.Non-culturable microorganisms: Some microorganisms
are not easily grown in the laboratory, making it difficult to
fulfill the second postulate.
b.Latent infections: Some microbes can exist in a host
without causing disease, making it difficult to fulfill the first
postulate.
c.Complex interactions: Many diseases are caused by the
interactions between multiple factors, including host
genetics, environmental exposure, and the presence of
multiple pathogens. In these cases, Koch's postulates may
not apply.
d.Non-infectious diseases: Some diseases, such as cancer
or autoimmune disorders, are not caused by the presence
of specific microbes, so Koch's postulates do not apply.
Discuss two medically related fields of microbiology.
Medical Microbiology:
 This field of microbiology deals with the study of
pathogenic microorganisms, their interactions with
the host, and the mechanisms by which they cause
disease. Medical microbiologists use various
techniques to isolate, identify, and study disease-
causing microorganisms, and to develop diagnostic
tests, treatments, and vaccines. This field is essential
for the prevention, diagnosis, and treatment of
infectious diseases, and for the development of
public health policies.
Immunology:
 This field of microbiology focuses on the study of
the immune system, including how it recognizes and
responds to invading pathogens. It also explores the
mechanisms by which the immune system is able to
remember previous infections and respond more
effectively in the future.
 This knowledge is used to develop immunotherapies
for the treatment of infectious diseases, as well as
for autoimmune disorders and cancer. Advances in
this field have led to the development of vaccines,
immunoglobulin therapy, and other treatments that
help the body fight infection
CHAPTER 2 - Microscopy
Using the metric System to Express the Sizes of
Microorganism
 Microbiology uses metric units, specifically
micrometers and nanometers, to express the sizes
of microbes.
 Centimeters, millimeters, micrometers, and
nanometers are all metric system units used to
measure length. They are related to each other by a
factor of 10, which means that each unit is 10 times
smaller than the previous one:
1 .A centimeter (cm) is equal to 10 millimeters (mm). This
means that there are 10 millimeters in one centimeter.
2 .A millimeter (mm) is equal to 1,000 micrometers (µm).
This means that there are 1,000 micrometers in one
millimeter.
3.A micrometer (µm) is equal to 1,000 nanometers (nm).
This means that there are 1,000 nanometers in one
micrometer.
 Bacteria, protozoa, and viruses are all
microorganisms that differ significantly in size. The
metric units used to express their sizes are:
a.Bacteria: The size of bacteria is typically measured in
micrometers (µm), which is also known as a micron. The
size of bacteria can range from 0.2 µm to 10 µm in
diameter.
b.Protozoa: The size of protozoa can vary widely
depending on the species, but they are generally larger
than bacteria. The size of protozoa is also typically
measured in micrometers (µm). Protozoa can range in size
from 2 µm to 1 mm in length.
c.Viruses: The size of viruses is much smaller than bacteria
and protozoa. The size of viruses is typically measured in
nanometers (nm), which is 1,000 times smaller than a
micrometer. Viruses can range in size from 20 nm to 300
nm in diameter.
Microscopes
 Microscopes are tools used to magnify small objects
or structures beyond the capabilities of the human
eye. There are several types of microscopes:
Simple Microscopes:
 Simple microscopes are the oldest type of
microscopes and use only one lens to magnify an
object. They are often referred to as magnifying
glasses and are commonly used for examining small
insects, minerals, and other objects. They have a
limited magnification range, typically ranging from
10x to 50x, and are generally low-cost and easy to
use.
Compound Light Microscopes:
 Compound light microscopes use two or more
lenses to magnify an object. They use visible light to
produce an image of the object and are commonly
used in biology, medicine, and other fields to view
living and non-living specimens.
 Compound light microscopes can magnify up to
2000x, which is sufficient for observing the structure
of cells, bacteria, and other small organisms.
 Compound light microscopes are also equipped with
a variety of features such as adjustable
magnification, fine focus, and built-in lighting.
However, their resolution is limited by the
wavelength of visible light, making it difficult to
observe smaller structures such as viruses and other
subcellular components.
Electron Microscopes:
 Electron microscopes use a beam of electrons
instead of visible light to magnify an object. The
electron beam is focused using electromagnetic
lenses, and the resulting image is displayed on a
screen.
 Electron microscopes are commonly used in fields
such as materials science, nanotechnology, and
biology to view subcellular structures and other
small particles.
 Electron microscopes have a much higher
magnification range, up to 10 million times, and
higher resolution than compound light microscopes.
However, they are much more expensive, require
specialized training to operate, and cannot be used
to view living specimens.
There are two types of electron microscopes:
a.transmission electron microscopes (TEM) - TEMs are
used to examine thin slices of specimens, such as cells or
tissue
b.scanning electron microscopes (SEM) - SEMs are used
to produce 3D images of the specimen's surface.
CHAPTER 3 - Cell Structure and Taxonomy
Eukaryotic Cell Structure
 Eukaryotic cells are cells containing a true nucleus;
organisms possessing such cells are referred to as
eukaryotes.
Cell structure:
Cell membrane: The cell membrane is a thin, flexible, and
selectively permeable layer that surrounds the cell and
separates its internal environment from the external one.
It serves as a barrier to protect the cell from the outside
environment, while also allowing the passage of essential
molecules such as nutrients and waste products.
Nucleus: The nucleus is a membrane-bound organelle that
houses the cell's genetic material and controls cellular
activities such as DNA replication, transcription, and
regulation of gene expression.
Cytoplasm: The cytoplasm is a gel-like substance that fills
the cell and contains various organelles, proteins, and
other molecules. It serves as a medium for biochemical
reactions and intracellular transport.
Endoplasmic reticulum: The endoplasmic reticulum (ER) is
a network of interconnected membrane-bound tubules
and sacs that is involved in protein and lipid synthesis,
folding, and modification.
Ribosomes: Ribosomes are small, non-membrane-bound
organelles that are involved in protein synthesis. They read
messenger RNA and use the genetic code to assemble
amino acids into protein chains.
Golgi complex: The Golgi complex is a stack of flattened
membranes that sorts, modifies, and packages proteins
and lipids for transport to their final destination inside or
outside the cell.
Lysosomes: Lysosomes are membrane-bound organelles
that contain enzymes responsible for breaking down and
digesting cellular waste, foreign particles, and even entire
organelles that are no longer functional.
Peroxisome: Peroxisomes are membrane-bound
organelles that contain enzymes that break down fatty
acids and amino acids, as well as detoxify harmful
substances such as hydrogen peroxide.
Mitochondria: Mitochondria are membrane-bound
organelles that generate energy for the cell in the form of
ATP through the process of cellular respiration.
Plastids: Plastids are a diverse group of organelles found in
photosynthetic eukaryotes, such as plants and algae.
They are involved in various functions, such as
photosynthesis, pigmentation, and storage of nutrients.
Cytoskeleton: The cytoskeleton is a network of protein
fibers that maintains the cell's shape and provides
structural support, as well as facilitates intracellular
transport, cell division, and movement.
Cell wall: The cell wall is a rigid, protective layer found in
plant cells, fungi, and some bacteria. It provides
mechanical support and protection, as well as regulates
the exchange of materials between the cell and its
environment.
Flagella: Flagella are long, whip-like appendages that
protrude from the cell surface and are involved in cell
movement and fluid propulsion. They are found in a
variety of eukaryotic and prokaryotic organisms.
Prokaryotic Cell Structure
 Prokaryotic cells are cells lacking a true nucleus;
organisms consisting of such cells are referred to as
prokaryotes.
Cell structure:
Cell membrane: The cell membrane in prokaryotic cells is a
thin, semi-permeable layer that separates the interior of
the cell from the external environment. It helps maintain
the internal environment of the cell, controls the
movement of molecules in and out of the cell, and is
involved in cell signaling.
Chromosome: Prokaryotic cells typically have a single
circular chromosome that contains their genetic
information. This chromosome is responsible for
controlling the cell's activities, growth, and reproduction.
Cytoplasm: The cytoplasm is a gel-like substance that fills
the cell and contains various organelles, proteins, and
other molecules. It serves as a medium for biochemical
reactions and intracellular transport.
Cytoplasmic particles: Prokaryotic cells contain various
particles in the cytoplasm, including ribosomes that are
involved in protein synthesis, and storage granules that
store nutrients such as starch, glycogen, or lipids.
Bacterial cell wall: The bacterial cell wall is a protective
layer that provides structural support and shape to the
cell, and also helps regulate the exchange of materials
between the cell and its environment. The cell wall is
made of peptidoglycan, a unique polymer that is found
only in bacteria.
Glycocalyx (slime layers and capsules): The glycocalyx is a
layer of polysaccharides that surrounds the cell wall in
some prokaryotic cells. It helps protect the cell from
environmental stress, such as desiccation, and may also be
involved in cell adhesion and biofilm formation.
Flagella: Flagella are long, whip-like structures that
protrude from the cell surface and are involved in cell
movement. They work like propellers, using energy to
rotate and propel the cell forward.
Pili and fimbriae: Pili and fimbriae are hair-like structures
that extend from the cell surface and are involved in cell
adhesion and conjugation, which is the transfer of genetic
material between cells.
Spores (endospores): Some prokaryotic cells can form
spores, which are highly resistant structures that protect
the cell from harsh environmental conditions. Endospores
are a form of spore that can survive for long periods of
time, and they are formed by some species of bacteria
such as Bacillus and Clostridium.
Structural Differences Between Prokaryotic and
Eukaryotic Cells
 Prokaryotic cells and eukaryotic cells have several
structural differences. Prokaryotic cells are smaller
and lack a true nucleus, membrane-bound
organelles, and a complex cell wall. They typically
have a single, long flagellum and smaller ribosomes.
 Eukaryotic cells, on the other hand, are larger and
have a true nucleus enclosed in a nuclear
membrane, membrane-bound organelles, and a less
prominent cell wall. They may have multiple shorter
flagella or cilia and larger ribosomes.
Taxonomy
 Taxonomy is the science of identifying, naming, and
classifying living organisms based on their
characteristics and relationships to other organisms.
It involves the use of various techniques, such as
morphology, genetics, and ecology, to categorize
living things into groups that reflect their
evolutionary history and biological characteristics.
 The most commonly used system of taxonomy is the
Linnaean classification system, developed by
Swedish botanist Carl Linnaeus in the 18th century.
This system organizes living organisms into a
hierarchical classification scheme, with each level of
classification becoming increasingly specific.
The levels of classification in the Linnaean system, from
most general to most specific, are:
1.Kingdom
2.Phylum (or Division, for plants)
3.Class
4.Order
5.Family
6.Genus
The three-domain system of classification is a biological
classification system that divides all living organisms into
three domains: Bacteria, Archaea, and Eukarya. This
system was proposed by Carl Woese and George Fox in
the late 1970s based on studies of ribosomal RNA (rRNA)
sequences.
 The three domains are differentiated based on
fundamental differences in their cellular structure,
biochemistry, and molecular biology:
Bacteria: This domain includes all known types of bacteria,
which are unicellular, prokaryotic organisms with a simple
cell structure and lack a membrane-bound nucleus. They
can be found in a wide range of environments, from soil to
water to living organisms.
Archaea: This domain includes a diverse group of
unicellular, prokaryotic organisms with a unique cell
membrane structure and genetic makeup that differs
significantly from both bacteria and eukaryotes. Many
archaea are extremophiles, meaning they can live in
extreme environments such as high temperature, high
pressure, and high acidity.
Eukarya: This domain includes all organisms with
eukaryotic cells, which have a membrane-bound nucleus
and other complex membrane-bound organelles. This
includes animals, plants, fungi, and protists.
Determining Relatedness Among Organisms
 rRNA sequencing is a technique used to determine
the genetic sequence of ribosomal RNA (rRNA)
molecules found in cells.
 Ribosomal RNA is a component of the ribosome,
which is the cellular machinery responsible for
protein synthesis. Because rRNA is present in all
cells and evolves at a relatively slow rate, it can be
used to infer evolutionary relationships among
organisms.
CHAPTER 4 — Diversity of Microorganisms, Part 1
Acellular and Procaryotic Microbes
 Acellular microbes are microscopic organisms that
lack a cellular structure. They do not have a cell
membrane, organelles, or a nucleus. Examples of
acellular microbes include viruses, viroids, and
prions.
 Prokaryotic microbes, on the other hand, are
microscopic organisms that have a simple cellular
structure. They do not have a nucleus, and their
genetic material is located in a single circular
chromosome. Prokaryotes include bacteria and
archaea.
Acellular Infectious Agents
 Acellular infectious agents are biological particles
that lack a cellular structure and cannot replicate on
their own. They require a host cell to reproduce and
spread. These agents are usually composed of
nucleic acid (DNA or RNA) surrounded by a protein
coat or envelope. Acellular infectious agents include
viruses, viroids, and prions.
Viruses: Viruses are the most common type of acellular
infectious agents. They are composed of a protein coat,
called a capsid, which contains the viral genome (DNA or
RNA). Some viruses also have an envelope made up of
lipids and proteins. Examples of viruses include the
common cold, influenza, measles, HIV, and Ebola.
Viroids: Viroids are small, circular pieces of RNA that cause
disease in plants. They are different from viruses in that
they do not have a protein coat. Viroids are able to
replicate within the plant cell and interfere with the plant's
normal cellular processes. They can cause diseases such as
potato spindle tuber viroid and citrus exocortis viroid.
Prions: Prions are infectious proteins that cause a variety
of neurodegenerative diseases in humans and animals,
such as Creutzfeldt-Jakob disease and mad cow disease.
Unlike viruses and viroids, prions do not contain nucleic
acid. Instead, they are composed of misfolded proteins
that are able to convert normal proteins into the
abnormal, disease-causing form.
The Domain Bacteria
Domain bacteria contains organisms that are broadly
divided into three categories:
a.Gram-negative and have a cell wall.
b.Gram-positive and have a cell wall.
c.Lack cell wall.
Many characteristics of bacteria are examined to provide
data for identification and classification. These
characteristics include:
Cell morphology: This refers to the physical shape and size
of a bacterium. Bacteria can be spherical (cocci), rod-
shaped (bacilli), or spiral-shaped (spirilla) and can vary in
size from less than 1 micron to several microns in length.
Staining reactions: Staining is used to differentiate
bacteria based on their ability to take up certain dyes. The
most commonly used stains are Gram stain and acid-fast
stain, which can help identify bacteria as Gram-positive or
Gram-negative, or acid-fast or non-acid-fast, respectively.
Motility: Bacteria can be motile or non-motile. Motility can
be observed under a microscope or by observing the
ability of bacteria to move across a surface or through a
liquid medium. Motility can be an important characteristic
for identifying certain bacterial species.
Colony morphology: This refers to the visible
characteristics of bacterial colonies that grow on agar
plates. Different bacterial species have distinct colony
shapes, colors, and textures, which can help in their
identification.
Atmospheric requirements: Bacteria can be classified as
aerobes, anaerobes, or facultative anaerobes based on
their need for oxygen to grow. Some bacteria require high
levels of oxygen, while others cannot grow in the presence
of oxygen.
Nutritional requirements: Bacteria have specific
nutritional requirements for growth, including the need for
certain nutrients such as carbon, nitrogen, and minerals.
Some bacteria require complex organic compounds while
others can use simpler compounds.
Biochemical and metabolic activities: Bacteria have
distinct metabolic pathways that can be used to identify
them. These pathways can be observed through
biochemical tests that measure the presence or absence of
specific enzymes or metabolic products.
Pathogenicity: Some bacteria are pathogenic, meaning
they can cause disease in humans or animals. Identifying
pathogenic bacteria is important for controlling and
preventing the spread of infectious diseases.
 Archaea were first discovered in extreme
environments such as hot springs, salt flats, and
hydrothermal vents, but they have since been found
in a wide range of environments, including the
human gut.
Archaea are divided into several groups based on their
habitat and metabolism:

Genetic composition: Bacteria have unique genetic a.Methanogens, which produce methane as a byproduct of
compositions that can be used to identify them. These their metabolism;
include the presence or absence of specific genes or DNA
sequences, which can be analyzed using techniques such b.Halophiles, which live in high-salt environments;
as polymerase chain reaction (PCR) or whole-genome
c.Thermophiles, which thrive in high-temperature
sequencing.
environments.
Unique bacteria: Have distinct characteristics that set
them apart from other types of bacteria. Examples
include:

a.Thermus aquaticus

b.Deinococcus radiodurans

c.Acidithiobacillus ferrooxidans

Photosynthetic bacteria: Can use light as a source of

energy for photosynthesis. Produce their own food using
energy from the sun and carbon dioxide from the air.
Examples include:

a.Cyanobacteria

b.Chlorobi

c.Chloroflexi.

The Domain Archaea

 Archaea, also known as archaebacteria, are a group

of single-celled microorganisms that are similar in
size and shape to bacteria but differ from them in
their genetic and biochemical characteristics.