Chapter 1: Microbiology - The Science Earliest known infectious diseases. List several reasons why microbes are important.

What is Microbiology?  Some of the earliest known infectious diseases are  Microbes play a crucial role in maintaining the
smallpox, the bubonic plague, malaria, tuberculosis, balance of the ecosystem by breaking down organic
 Microbiology is the study of microbes. cholera, yellow fever, measles, syphilis, and etc. matter and recycling nutrients.

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

Archaea: This domain includes a diverse group of  Acellular infectious agents are biological particles Cell morphology: This refers to the physical shape and size
unicellular, prokaryotic organisms with a unique cell that lack a cellular structure and cannot replicate on of a bacterium. Bacteria can be spherical (cocci), rod-
membrane structure and genetic makeup that differs their own. They require a host cell to reproduce and shaped (bacilli), or spiral-shaped (spirilla) and can vary in
significantly from both bacteria and eukaryotes. Many spread. These agents are usually composed of size from less than 1 micron to several microns in length.
archaea are extremophiles, meaning they can live in nucleic acid (DNA or RNA) surrounded by a protein
coat or envelope. Acellular infectious agents include Staining reactions: Staining is used to differentiate
extreme environments such as high temperature, high
viruses, viroids, and prions. bacteria based on their ability to take up certain dyes. The
pressure, and high acidity.
most commonly used stains are Gram stain and acid-fast
Eukarya: This domain includes all organisms with Viruses: Viruses are the most common type of acellular stain, which can help identify bacteria as Gram-positive or
eukaryotic cells, which have a membrane-bound nucleus infectious agents. They are composed of a protein coat, Gram-negative, or acid-fast or non-acid-fast, respectively.
and other complex membrane-bound organelles. This called a capsid, which contains the viral genome (DNA or
RNA). Some viruses also have an envelope made up of Motility: Bacteria can be motile or non-motile. Motility can
includes animals, plants, fungi, and protists.
lipids and proteins. Examples of viruses include the be observed under a microscope or by observing the
Determining Relatedness Among Organisms common cold, influenza, measles, HIV, and Ebola. ability of bacteria to move across a surface or through a
liquid medium. Motility can be an important characteristic
 rRNA sequencing is a technique used to determine Viroids: Viroids are small, circular pieces of RNA that cause for identifying certain bacterial species.
the genetic sequence of ribosomal RNA (rRNA) disease in plants. They are different from viruses in that
molecules found in cells. they do not have a protein coat. Viroids are able to Colony morphology: This refers to the visible
replicate within the plant cell and interfere with the plant's characteristics of bacterial colonies that grow on agar
 Ribosomal RNA is a component of the ribosome, normal cellular processes. They can cause diseases such as plates. Different bacterial species have distinct colony
which is the cellular machinery responsible for potato spindle tuber viroid and citrus exocortis viroid. shapes, colors, and textures, which can help in their
protein synthesis. Because rRNA is present in all identification.
cells and evolves at a relatively slow rate, it can be Prions: Prions are infectious proteins that cause a variety
used to infer evolutionary relationships among of neurodegenerative diseases in humans and animals, Atmospheric requirements: Bacteria can be classified as
organisms. such as Creutzfeldt-Jakob disease and mad cow disease. aerobes, anaerobes, or facultative anaerobes based on
Unlike viruses and viroids, prions do not contain nucleic their need for oxygen to grow. Some bacteria require high
acid. Instead, they are composed of misfolded proteins levels of oxygen, while others cannot grow in the presence
that are able to convert normal proteins into the of oxygen.
CHAPTER 4 — Diversity of Microorganisms, Part 1
abnormal, disease-causing form.
Nutritional requirements: Bacteria have specific
Acellular and Procaryotic Microbes nutritional requirements for growth, including the need for
certain nutrients such as carbon, nitrogen, and minerals.
 Acellular microbes are microscopic organisms that
The Domain Bacteria Some bacteria require complex organic compounds while
lack a cellular structure. They do not have a cell
others can use simpler compounds.
membrane, organelles, or a nucleus. Examples of Domain bacteria contains organisms that are broadly
acellular microbes include viruses, viroids, and divided into three categories:
prions.
a.Gram-negative and have a cell wall.
 Prokaryotic microbes, on the other hand, are
microscopic organisms that have a simple cellular b.Gram-positive and have a cell wall. Biochemical and metabolic activities: Bacteria have
structure. They do not have a nucleus, and their distinct metabolic pathways that can be used to identify
them. These pathways can be observed through  Archaea were first discovered in extreme
biochemical tests that measure the presence or absence of environments such as hot springs, salt flats, and
specific enzymes or metabolic products. hydrothermal vents, but they have since been found
in a wide range of environments, including the
Pathogenicity: Some bacteria are pathogenic, meaning human gut.
they can cause disease in humans or animals. Identifying
pathogenic bacteria is important for controlling and Archaea are divided into several groups based on their
preventing the spread of infectious diseases. 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

a.Cyanobacteria

b.Chlorobi

c.Chloroflexi.

The Domain Archaea

 Archaea, also known as archaebacteria, are a group