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Microbiology:
The Science of
Microorganisms
What is Microbiology?
• Biology is the study of living organisms
• Microbiology is the study of very small living organisms
• Microorganisms are ubiquitous (they are everywhere!),
those living things that are too small to be seen with the
naked eye.
• Categories of microorganisms include:
– Viruses
– Bacteria
– Archaeans
– Protozoa
– Some algae and fungi
Type of
Organisms
Name of
Study
Characteristics of Organism
Microorganisms
Bacteria
Viruses
Simple, single-cell organisms.
Bacteriology
Grow in many environments.
Lack a true nucleus and most
organelles
Virology
Composed of nucleic acid (DNA
or RNA) and protein. Can
reproduce only within living
cells—obligate intracellular
parasites
Representative
Examples
Bacteria
Viruses
Very simple, nongreen, plantlike
organisms. Single-cell, globular Fungi
forms are yeasts; multicellular
filamentous forms are molds
Fungi
Mycology
Protozoa
Protozoology Single-cell, animal-like organisms Protozoa
What is Microbiology?
• Viruses are technically
infectious agents or particles
• “Germs” are the
microorganisms that cause
disease
• Disease-causing
microorganisms are
technically pathogens
• Microorganisms that do not
cause disease are nonpathogens
Disease
• Disease- abnormality of structure or function of a body
part, organ or system

May be felt or observed by others.

May have a known or unknown cause.

Severity of effects may be variable.
Where are Microbes?
• Soil
• Water
• Air
• Food
• Chemicals
• Sewage
Why Study Microbiology?
• Microorganisms live on and in
our bodies (indigenous
microflora)
• Microorganisms participate in
bioremediation and genetic
engineering
• Some microorganisms are
opportunistic pathogens
• Microorganism are involved
in elemental cycles
• Microorganisms are essential
for life on this planet
• Microorganisms are involved
in decomposition of dead
organisms and waste
(decomposers and
saprophytes)
• Algae and bacteria serve as
food for tiny animals
• Microorganisms aid in
digestion of food
• Microorganisms are used in
the food and beverage
industry
Why Study Microbiology?
• Some microorganisms produce antibiotics used to treat
diseases
• Microbes are essential in the field of genetic engineering
• Microbes are used as “cell models”
• Microorganisms cause two categories of disease:
– Infectious diseases-a pathogen inhabits the body and
subsequently causes disease
– Microbial intoxications- an individual ingests a toxin
(poisonous substance) that has been produced by a
pathogen outside the body
Benefits of Microorganisms
• Fertilizing the soil
• Aiding plant growth
• Returning nitrogen from the air into the soil
• Producing yeast (raised breads), cheeses, wine, beer, etc..
• Destruction of waste materials (paper, feces, biodegradable
substances)
• Purifying waste water.
Relevance in Healthcare
• Taking precautions to protect self
• Protecting patients and the community by preventing the
spread of pathogens
• Transferring harmful organisms
• Keeping surrounding areas clean
Types of Microbes
• Pathogenic-caused by disease causing microbe
–
virulence refers to the degree of damage caused by a microbe to its
host. The pathogenicity of an organism - its ability to cause disease - is
determined by its virulence factors
• Opportunistic-Microb with the potential to cause disease, but
doesn’t under normal circumstances
• Normal flora-population of microorganisms that normally grows on
body surfaces or cavities.
• Saprophytes-organisms that live on dead or decaying matter
(mushrooms)
• Nitrogen fixing- bacteria capable of converting nitrogen gas to
ammonia. Ex Clostridium
• Iron-utilizing-bacteria which utilize the oxidation of iron ions as an
essential component in their metabolic functioning (brown in color)
ex; Bordetella
Pioneers in the Science of Microbiology
Anton van Leeuwenhoek
(1632-1723)
– “Father of Microbiology”
– Not a trained scientist!
– Made many simple
single-lens microscopes
– He was first to describe
cells and bacteria
”animalcules” (bacteria
and protozoa), seen
through his microscopes
Pioneers in the Science of Microbiology
Louis Pasteur (1822-1895)
–
French chemist who made
numerous contributions to
microbiology
–
Investigated different
fermentation products
–
Developed the pasteurization
process
– Reduces the number of
microorganisms in foods such
as milk
–
Discovered life forms that
could exist without oxygen –
anaerobes
–
Developed several vaccines,
including rabies and anthrax
vaccines
Pioneers in the Science of Microbiology
Robert Koch (1843-1910)
–
German physician who
made numerous
contributions to
microbiology
–
Significant contribution to
germ theory of disease
–
Discovered that B. anthracis
produced spores
–
Developed method of fixing
and staining bacteria
–
Developed methods to
cultivate bacteria by
Assisted Julius Petri in
creating the Petri dish to
grow bacteria for study
Koch’s Postulates
1. A particular microorganism
must be found in all cases of
the disease and must not be
present in healthy animals or
humans.
2. The microorganism must be
isolated from the diseased
animal or human and grown in
pure culture in the laboratory.
3. The same disease must be
produced when
microorganisms from the pure
culture are inoculated into
healthy susceptible lab
animals.
4. The same microorganism must
be recovered from the
experimentally infected
animals and grown again in
pure culture.
Koch’s Postulates (continued)
• If an organism fulfills Koch’s postulates it is proven to be
the cause of that particular infectious disease.
• Koch’s Postulates helped to prove the germ theory of
disease
• Koch gave a tremendous boost to the development of
microbiology by stressing lab culture and identification of
microorganisms
• Circumstances do exist in which Koch’s Postulates cannot
be fulfilled.
Exceptions to Koch's Postulates
1. Some microbes are obligate intracellular parasites (like
chlamydia or viruses) and are very challenging, or even
impossible, to grow on artificial media.
2. Some diseases, such as tetanus, have variable signs
and symptoms between patients.
3. Some diseases, such as pneumonia & nephritis, may
be caused by a variety of microbes.
4. Some pathogens, such as S. pyogenes, cause several
different diseases.
5. Certain pathogens, such as HIV, cause disease in
humans only -- it is unethical to purposefully infect a
human.
Ignaz Semmelweis/Holmes
• Discovered the transmission of disease/microorganisms
to patients from cadaver studies
• Discovered the importance of handwashing to prevent
the spread of infection
John Tyndall
• Opposed to spontaneous generation of organisms
• Established “Tyndallization” or discontinuous heating with
steam as a sterilization technique.
Using the Metric System to Express the
Sizes of Microorganisms
• Metric units are used to express the sizes of
microorganisms.
• The basic unit of length in the metric system is the meter
(m); it is equivalent to 39.4 inches.
• The sizes of bacteria and protozoa are usually expressed
in terms of micrometers (µm).
• The sizes of microorganisms are measured using an
ocular micrometer.
Representations of Metric Units of
Measure and Numbers
Microscopes
• The human eye, a telescope, a pair of binoculars, a
magnifying glass and a microscope are various types of
optical instruments.
• A microscope is an optical instrument that is used to
observe tiny objects; those that cannot be seen with the
unaided human eye.
• Each optical instrument has a limit as to what can be
seen
– The limit is referred to as the resolving power or
resolution of the instrument.
Simple Microscopes
• A simple microscope is one that
contains only one magnifying lens.
• A magnifying glass could be
considered a simple microscope.
– With a magnifying glass,
images appear 3-20 times
larger than the object’s actual
size.
• Leeuwenhoek’s simple
microscopes had a maximum
magnifying power of about 300X
or 300 times.
Compound Microscopes
• A compound microscope
contains more than one
magnifying lens.
• Because visible light is the
source of illumination, the
compound microscope is
also referred to as a
compound light
microscope .
• Compound light
microscopes usually
magnify objects about
1000 times!
Electron Microscopes
• Electron microscopes enable us to see extremely small
infectious agents such as rabies and smallpox viruses.
• Living organisms cannot be seen with an electron
microscope – the processing procedures kill the
organisms.
• An electron beam is used as a source of illumination and
magnets are used to focus the beam.
• Electron microscopes have a much higher resolving
power than the compound light microscope.
• There are 2 types of electron microscopes - transmission
and scanning.
The Transmission Electron Microscope
• Uses an electron gun to fire
a beam of electrons through
an extremely thin specimen
(<1 µm thick).
• An image of the specimen is
produced on a phosphorcoated screen.
• Magnification is 1000 times
greater than the compound
light microscope.
The Scanning Electron Microscope
• Electrons are bounced off the
surface of a specimen and
the image appears on a
monitor.
• Used to observe the outer
surfaces of specimens.
• Resolving power not as high
as the transmission electron
microscope.
• Scanning and transmission
electron micrographs are
black and white images.
S. aureus
S. aureus and red blood
cells as seen by light
microscopy
S. aureus as seen by
transmission electron
microscopy (TEM)
S. aureus as seen by
Scanning electron
microscopy
Introduction: Cell Structure and Taxonomy
• A cell is the fundamental living unit of any living
organism because it exhibits the basic characteristics of
life.
• Metabolism -the chemical reactions that occur within a
cell.
• Bacterial cells do not have the complex system of
membranes and organelles found in the more advanced
cellular organisms.
Introduction (continued)
• Bacteria and Archaea are called procaryotes or
procaryotic cells because they do not have a true
nucleus.
• More complex cells that contain a true nucleus and many
membrane-bound organelles are called eucaryotes or
eucaryotic cells.
• Eucaryotes include algae, protozoa, fungi, plants, animals
and humans.
• Some microorganisms are procaryotic, some are
eucaryotic, and some are not cells at all.
Functions of Living Organisms

Metabolism
◦ Physical & chemical processes involved in maintaining
life





Growth
Ability to reproduce
Irritability (able to react to environment)
Motion – gliding, flagella, axial filaments
Protection
Acellular and Cellular Microbes
Viruses
• Composed of only a few genes protected by a protein
coat.
• Depend on the energy and metabolic machinery of a host
cell in order to reproduce.
• They are acellular, that is, they are not composed of
cells.
Eucaryotic Cell Structure
TEM of Yeast Cell
Nuclear pores
Vacuole
Nucleus
Cell membrane
Mitochondria
Eucaryotic Cell Structures
• Cell Membrane
– Mosaic of large molecules of proteins and
phospholipids.
– Regulates passage of nutrients, waste products and
secretions in and out of the cell.
– Has selective permeability.
The Nucleus
• The “command center” of the cell.
• 3 components: nucleoplasm, chromosomes, and nuclear
membrane.
• Chromosomes are embedded in the nucleoplasm.
• Eucaryotic chromosomes consist of linear DNA molecules
and proteins
– Genes are located along the DNA molecules.
– Each gene contains the information to produce a
gene product.
The Nucleus (continued)
• Most genes code for proteins but some code for 2 types
of ribonucleic acid (RNA)
– Ribosomal ribonucleic acid (rRNA)
– Transfer ribonucleic acid (tRNA)
• The organism’s complete collection of genes is the
organism’s genotype or genome.
• The number and composition of chromosomes and the
number of genes on each chromosome are characteristic
of the particular species of organism.
• Human diploid cells have 46 chromosomes or 23 pairs.
Eucaryotic Cell Structures (continued)
• Centrioles
–
Are near the nucleus, occurring
in pairs and involved in the
development of spindle fibers in
cell division (mitosis)
• Cytoplasm
–
A semi-fluid, gelatinous,
nutrient matrix.
–
Contains storage granules and
a variety of organelles.
–
Each organelle has a specific
function.
–
The cytoplasm is where most
metabolic reactions occur.
• Endoplasmic Reticulum
–
A highly convoluted system
of membranes arranged to
form a transport network
in the cytoplasm.
• Ribosomes
–
Mainly ribosomal RNA and
protein.
–
Important in the synthesis
of proteins.
Eucaryotic Cell Structures (continued)
• Golgi Complex
– Also Golgi apparatus or
Golgi body.
– Connects or
communicates with ER.
– Completes the
transformation of newly
synthesized proteins and
packages them for
storage or export.
• Lysosomes &
Peroxisomes
– Originate in the Golgi
complex.
– Lysosomes contain
lysozyme and other
digestive enzymes.
– Peroxisomes are
membrane bound
vesicles where H2O2 is
generated and broken
down.
Eucaryotic Cell Structures (continued)
• Mitochondria
– “Power plants,”
“powerhouses,” or
“energy factories” of the
eucaryotic cell.
– ATP molecules are
formed by cellular
respiration.
– Number of mitochondria
varies depending on
activities of cell.
• Plastids
– Membrane-bound
structures containing
photosynthetic pigments
– they are sites of
photosynthesis.
– Chloroplasts are a type
of plastid.
Eucaryotic Cell Structures (continued)
• Cytoskeleton
– A system of fibers
throughout the
cytoplasm.
– 3 types of fibers:
microtubules,
microfilaments and
intermediate filaments.
– Microtubules and
microfilaments essential
for a variety of
activities.
• Cell wall
– Some eucaryotic cells
contain cell walls – an
external structure to
provide shape,
protection and rigidity.
– Simpler than procaryotic
cell wall.
– Chitin found in cell wall
of fungi; cellulose in cell
wall of algae and plants.
Eucaryotic Cell Structures (continued)
• Flagella and Cilia
– Some eucaryotic cells (e.g.,
spermatozoa) possess long
thin structures called flagella.
– Organelles of locomotion;
may be one or more flagella
on a cell.
– Cilia are also organelles of
locomotion but are shorter,
thinner and more numerous;
hair-like.
– Cilia can be found on some
species of protozoa and
certain types of cells in our
bodies (e.g., respiratory
tract).
Cell with numerous cilia
Procaryotic Cell Structure
• Procaryotic cells are about 10 times smaller than
eucaryotic cells.
• Procaryotic cells are simple compared to eucaryotic
cells.
• Procaryotic cells reproduce by binary fission.
• All bacteria are procaryotes as are archaeans.
• Unlike eucaryotic cells, the cytoplasm of procaryotic cells
is not filled with internal membranes.
• Cytoplasm of procaryotic cell surrounded by cell
membrane, a cell wall (usually) and sometimes a capsule
or slime layer.
Procaryotic Cell
Procaryotic Cell Structure (continued)
• Cell membrane
– Similar in structure and
function to the
eucaryotic cell
membrane.
– Selectively permeable.
– Many enzymes are
attached to the cell
membrane and
metabolic reactions take
place there.
• Chromosome
– Procaryotic chromosome
usually consists of a
single, long,
supercoiled, circular
DNA molecule – serves
as control center of cell.
– Plasmids are small
circular molecules of
DNA that are not part of
the chromosome.
Procaryotic Cell Structure (continued)
• Cytoplasm
– Semi-liquid that consists of water, enzymes, waste
products, nutrients, proteins, carbohydrates and
lipids – required for metabolic functions of the cell.
• Cytoplasmic particles
– Most are ribosomes occurring in clusters.
– Eucaryotic ribosomes are smaller than procaryotic
ribosomes, but function is the same
protein
synthesis.
Procaryotic Cell Structure (continued)
• Bacterial Cell Wall
– Rigid exterior that defines the shape of bacterial cells
– chemically complex.
– Main constituent of most bacterial cell walls is
peptidoglycan (only found in bacteria).
– Gram-positive bacteria have a thick layer of
peptidoglycan; Gram-negative bacteria have a
much thinner layer.
– Mycoplasma spp. do not have a cell wall.
Gram-negative and Gram-positive Cell Walls
Gram-negative bacterium
Gram-positive bacterium
Procaryotic Cell Structure (continued)
• Glycocalyx (Slime Layers and Capsules)
– Some bacteria possess a thick layer of glycocalyx
outside their cell wall.
– Glycocalyx is a slimy, gelatinous material produced
by the cell membrane and secreted outside the cell
wall which is loose and allow for bacteria to slide
along solid surfaces.
– 2 types of glycocalyx – slime layer and capsule.
– The capsule is more highly organized and more
firmly attached to the cell wall than the slime layer.
• Pseudomonas produces a slime layer.
• K. pneumoniae, N. meningitidis and S. pneumoniae
possess a capsule.
Capsule Stain
(Example of a negative staining technique)
Procaryotic Cell Structure (continued)
• Flagella
–
Flagella are threadlike, protein
appendages that enable bacteria to
move.
–
Number and arrangement of flagella
are characteristic of a particular
species:
–
Peritrichous bacteria – flagella over
entire surface
–
Lophotrichous bacteria – flagella at
one end
–
Amphitrichous bacteria – flagella at
both ends
–
Monotrichous bacteria – single polar
flagellum
A Peritrichous Salmonella Cell
Procaryotic Cell Structure (continued)
• Pili -Hair-like structures, most often observed on Gramnegative bacteria.
– Composed of polymerized protein molecules called
pilin.
– Pili are thinner than flagella, have a rigid structure
and are not associated with motility.
– Pili enable bacteria to anchor themselves to surfaces.
– Some bacteria possess a sex pilus for conjugation.
Proteus vulgaris cell, showing pili and several flagella
Pili
Flagella
Procaryotic Cell Structure (continued)
Spores (Endospores)
• A few genera (e.g., Bacillus and Clostridium) are capable of forming thick-walled
spores as a means of survival.
• The process of spore formation is called sporulation – it is not reproduction.
• Spores have been shown to survive for many years and are resistant to heat, cold
drying and most chemicals.
• Usually one spore is produced in a bacterial cell and generates into one vegetative
bacterium.
• Endospores can be visualized with a spore stain.
Recap of Structural Differences Between
Procaryotic and Eucaryotic Cells
• Eucaryotic cells contain a true nucleus; procaryotic cells
do not.
• Eucaryotic cells are divided into plant and animal types
– Animal cells do not have a cell wall, plant cells have a
simple cell wall.
• Eucaryotic cells contain membranous structures and
many membrane bound organelles; procaryotic cells
possess no membranes other than the cell membrane
that encloses the cytoplasm
Reproduction of Organisms and Their Cells
• Procaryotic Cell
Reproduction
– Procaryotic cells reproduce
by a process known as
binary fission – one cell
splits in half to become two
daughter cells.
• Before a procaryotic cell
divides in half, the
chromosome must be
duplicated.
Taxonomy
• Taxonomy is the science of classification of living
organisms.
• Taxonomy consists of classification, nomenclature and
identification.
• Classification is the arrangement of organisms into
taxonomic groups (known as taxa).
• Tool for remembering the sequence of Taxa
– “King David Came Over for Good Spaghetti”
KDCOFGS, K for Kingdom, D for Division, C for Class,
O for Order, F for Family, G for Genus and S for
species.
Microbial Classification
• The science of taxonomy was established on the binomial
system of nomenclature.
• In the binomial system, each organism is given 2
names – genus and the specific epithet. Taken
together, both names constitute the species.
– For example, Escherichia coli; Escherichia is the
genus and coli is the specific epithet.
– The genus is frequently abbreviated with just a single
letter, (e.g., E for Escherichia).
• The abbreviation “sp.” is used to designate a single
species and “spp.” for more than one species.
Microbial Classification
• Organisms are categorized into larger groups based on
their similarities and differences.
• The Five-Kingdom System of Classification
1. Bacteria and archaeans – Kingdom Procaryotae
2. Algae and protozoa – Kingdom Protista
3. Fungi – Kingdom Fungi
4. Plants – Kingdom Plantae
5. Animals – Kingdom Animalia
• Viruses are not included because they are acellular.
• Other systems of classification do exist.
Microbial Classification (continued)
• The Three-Domain System of Classification
1. Archaea (procaryotic)
2. Bacteria (procaryotic)
3. Eucarya (all eucaryotic organisms)
The Domain Bacteria
Characteristics
• Bacteria are divided into 3 major phenotypic
categories:
– Those that are Gram-negative and have a cell wall.
– Those that are Gram-positive and have a cell wall.
– Those that lack a cell wall.
• Characteristics of bacteria used in classification and
identification include: cell morphology, staining reactions,
motility, colony morphology, atmospheric requirements,
nutritional requirements, biochemical and metabolic
activities, enzymes that the organism produces,
pathogenicity and genetic composition.
The Domain Bacteria
Cell Morphology
• There are 3 basic shapes of bacteria:
– Cocci (round bacteria)
– Bacilli (rod-shaped bacteria)
– Curved and spiral-shaped bacteria
• Cocci may be seen singly or in pairs (diplococci), chains
(streptococci), clusters (staphylococci), packets of 4
(tetrads), or packets of 8 (octads).
• The average coccus is about 1 µm in diameter.
• Some cocci have “coccus” in their name.
The Domain Bacteria
Cell Morphology (continued)
• Bacilli
– Often referred to as rods; may be short or long, thick
or thin, and pointed or with curved or blunt ends.
– They may occur singly, in pairs (diplobacilli), in
chains (streptobacilli), in long filaments, or branched.
– An average sized bacillus is 1 x 3 µm.
– Examples of medically important bacilli:
Escherichia, Klebsiella, and Proteus spp.
Pseudomonas, Haemophilus, and Bacillus spp.
The Domain Bacteria
Cell Morphology (continued)
• Curved and Spiral-Shaped Bacteria
– Examples of curved bacteria:
• Vibrio spp.
• Campylobacter spp.
• Helicobacter spp.
– Examples of spiral-shaped bacteria:
• Treponema spp.
• Borrelia spp.
Borrelia
hermsii in
stained blood
smear; a cause
of relapsing
fever.
Factors Influencing Growth of
Microorganisms

Light
◦ Amount
◦ Type





Temperature
Moisture
Food Availability
Atmosphere-Gas-Oxygen supply
pH
Naming Bacteria
• Genus name: Capitalized and italic
• species name: lowercase and italic
• EXAMPLE: Escherichia coli or E. coli
Species Clostridium
• Clostridium difficile
• Clostridium botulinum
• Clostridium sodellii
• Clostridium tetani
• Clostridium perfringens
• These 5 are the most commonly seen but there are
many others in this species…….