PRELIMS-MICROPARA LECTURE
Lesson 1: Introduction to Microbiology
Indigenous Microbiota
Human microbiome
500 to 1000 different species of
microbes live on and in us
Inhibit the growth of pathogens
(occupying space, depleting food
supply, and secretting materials that
prevent growth.
Opportunistic pathogens
Ex. E. coli
Microbes produce oxygen via
photosynthesis
Some microbes are decomposers or
saprophytes
Some microbes are capable of
decomposing industrial wastes
(bioremediation)
Many microbes are involved in elemental
cycles
Algae and bacteria serve as food for tiny
animals
Some microbes live in the intestinal tracts if
animals, where they aid in the digestion of
food and produce substances that are of
value to the host animals
E. coli produce vitamin K and B12
Many microbes are essential in various food
and beverage industries
Some bacteria and fungi produce
antibiotics
Engineered bacteria and yeasts can
produce a variety of substances like insulin,
growth hormones, interferons, and
materials for use as vaccines
Microbes have been used as “cell models”
Infectious Disease
A pathogen colonizes a person’s body
The pathogen causes disease
Example
MRSA Infection
Gas gangrene
Microbial Intoxication
A pathogen produces a toxin in vitro
A person ingests the toxin
The toxin causes a disease
Example
Staphylococcal food poisoning
Foodborne botulism
Anton Van Leeuwenhoek (1632-1723)
First person to see live bacteria and
protozoa
“Father of Microbiology”
Not a trained scientist
Made more than 500 single lens
microscopes
Louis Pasteur (1822-1895)
French Chemist
His contributions are considered to be the
foundation of the science of microbiology
and cornerstone of modern medicine.
Discovered that different types of
microbes produce different fermentation
products.
Yeasts convert glucose in grapes to ethyl
alcohol
Introduces the terms aerobes and
anaerobes.
Pasteurization
Heating wine to 55 C and holding that
temperature for several minutes
63-65 C for 30 minutes or 73-75 C for
15 seconds
Does not kill all the microbes in liquid
just the pathogen
Robert Koch (1843-1910)
Contributed to the germ theory of disease
Koch’s Postulates
Discovered B. anthracis produces spores
Developed methods of fixing, staining, and
photographing bacteria
Developed methods of cultivating bacteria
on solid media
 Agar Can not be used to observe living
Pure culture- a condition in which only organisms as they are killed during the
one type of organism is growing on a specimen-processing procedures
solid culture medium or in a liquid Uses the electron beam as a source of
culture medium. illumination and magnets to focus the
Discovered M. Tuberculosis causes TB beam
Discovered Vibrio cholerae causes cholera Transmission Electron Microscope (TEM)
Tuberculin led to the development of a Has a tall column, at the top of which
skin test valuable in diagnosing TB. an electron gun fires a beam of
electrons downward
Koch’s Postulates Scanning Electron Microscope (SEM)
Established an experimental procedure to Has a shorter column
prove that a specific microbe is the cause Specimen is placed at the bottom of
of a specific infectious disease. the column after being coated with a
1. A particular microbe must be conductive metal
found in all cases of the disease
and must not be present in
healthy animals or humans.
2. The microbe 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 microbes from
the pure culture are inoculated
into healthy susceptible lab
animals.
4. The same microbe must be
recovered from the
experimentally infected animals
and grown again in pure culture.

Viewing the Microbial World

Simple Microscope
Containing only one magnifying lens
3 to 20 times larger than the actual size
Compound Microscope
Contains more than one magnifying
lens
Hans Jansen and son Zacharias
Magnify objects 1000 times
X4 scanning
X10 low-power
X40 high-power
X100 oil immersion
Lesson 2: Cell Structure and Taxonomy
Endoplasmic Reticulum
Highly convoluted system of
membranes that are interconnected and
arranged to form a transport network of
tubules and flattened sacs within the
cytoplasm
Rough ER- attached ribosomes
Smooth ER- no ribosomes
Ribosomes
Synthesis of proteins
2 subunits- 605 and 405
Subunits join together with an mRNA to
initiate protein synthesis
Most of the proteins produced are not
mature
Chromosomes
Single, ling, supercoiled, circular DNA
Suspended or embedded in the
cytoplasm
DNA-occupied space is called the
bacterial nucleoid
Plasmids may be present
Cell Wall
External structured that provide rigidity,
shape, and protection
Eukaryotic cell walls
Simpler
Contain cellulose, pectin, lignin,
chitin, and some mineral salts
Spores (Endospores)
Bacillus and Clostridium
Capable of forming thick-walled spores
as a means of survival when moisture or
nutrient supply is low
Sporulation- process of formation
Resistant to heat, cold, drying, and most
chemicals
Spore staining
Acellular microbes- infectious particles
Cellular microbes- microorganisms
Cell
Fundamental unit of any living organism
Obtains nutrients from that
environment to produce energy for
metabolism
Grow and reproduce
Respond to stimuli in its environment
Can mutate
Cytoplasmic Particles
Most are ribosomes occurring in
clusters called polyribosomes
70S and 30S subunits
Lysosomes
Small vesicles that originate at Golgi
complex
Contain lysozyme and other digestive
enzymes
Break down foreign material taken into
the cell by phagocytosis
Aid in breaking down worn out parts of
the cell or entire cell by a process
called called autolysis
Science of the classification of living
organisms
Classification
Arrangement of organisms into the
taxonomic groups on the basis of
similarities or relationships
Kingdom or domain, divisions or phyla,
orders, families, genera, and species
Nomenclature
Assignment of names to the various
taxa according to international rules
Identification
Process of determining whether an
isolate belongs to one of the
established, named taxa or represents
a previously unidentified species
Escherichia coli or Escherchia coli
Bacterial Cell
10x smaller
Reproduction is by binary fission
Cytoplasm is surrounded by a cell
membrane, cell wall, and sometimes a
capsule or slime layer
Golgi Complex
Connects or communicates with ER
 Stack of flattened, membrane sacs Prokaryotic vs Eukaryotic
Complete the transformation of newly Flagella and Cilia
synthesized proteins to mature, Flagella
functional ones Long thin structures
Packages them into small, membrane- Whip-like
enclosed vesicles for storage or export Cilia
Tend to be shorter
Peroxisomes More numerous
Membrane-bound vesicles in which Mitochondria
hydrogen peroxide is generated and Where most of the ATP are formed by
broken down cellular respiration
Contains catalase Number varies greatly depending on
Prominent in mammalian liver cells the activities required of that cell
Nucleus Prokaryotes
Command center of the cell Bacteria and Archaea
3 components Do not have the complex system of
Nucleoplasm- gelatinous matrix or membranes and organelles
base material of the nucleus Eukaryotes
Chromosomes- embedded in the Algae, protozoa, fungi, plants, animals,
nucleoplasm and humans
Membrane- skin around the nucleus True nucleus, and membrane bound
Genes are located along the DNA organelles
molecules Viruses
Contain the genetic information that Result of regressive or reverse
enables the cell to produce one or evolution
more gene products Composed of a few genes protected by
Plastids a protein coat
Energy-producing organelle Depend on the energy and metabolic
Sites of photosynthesis- converts machinery of a host cell to reproduce
carbon dioxide and water into Cytoplasm
carbohydrates and oxygen Semifluid, gelatinous, nutrient matrix
Chloroplasts Where most of the cell’s metabolic
One type of plastid that contains reactions occur
chlorophyll Semifluid portion minus the granules
Found in plants and algae and organelles—cytosol
Cell membrane Bacteria Cell Wall
Plasma, cytoplasmic, or cellular Rigid exterior
membrane Main constituent is a complex
Mosaic composed of large molecules of macromolecular polymer—
proteins and phospholipids peptidoglycan
“Skin” Gram-positive bacteria- thick layer of
Selectively permeable peptidoglycan
Cytoplasm Gram-negative bacteria- thin layer of
Consists of water enzymes, dissolved peptidoglycan
oxygen, waste products, essential Mycoplasma- no cell wall
nutrients, proteins, carbohydrates, and Archaea- do not contain peptidoglycan
lipids Cell Wall Deficient bacteria- CWD
 Glycocalyx
Slimy, gelatinous material produced by
the cell membrane and secreted outside
of the cell wall
Pseudomonas has a slime layer that
enable it to glide or slide along solid
surfaces and protect the bacteria from
antibiotics, and desiccation
Capsule-highly organized and firmly
attached to the cell wall
Useful in differentiating types of
bacteria within a particular species
H. influenzae, Klebsiella, Neisseria,
streptococcus
Can be detected using a capsule-
staining procedure (unstained halo)
Agar: smooth, mucoid, and glistening
Antiphagocytic function

Cell Membrane
Similar in structure and function to the
eukaryotic cell membrane
Controls which substances may enter or
leave the cell
Flexible and thin
Mesosomes-inward folding of the cell
membrane where cellular respiration takes
place in the bacteria

Pili and Fimbriae

Hair-like structures found in Gm(-)
bacteria
Thin, rigid structures, and not
associated with motility
Fimbriae are present over the entire
surface of the bacterium-enable
attachment
Sex pilus-facilitates transfer of genetic
material from one bacterial cell to
another
Cytoskeleton
System of fibers
3 types
Microtubules
Microfilaments
Intermediate filaments
Strengthen, support, and stiffens the
cell
Lesson 3: Acellular and Prokaryotic Microbes
Viruses
Virions- complete virus particles
10 to 300 nm in diameter
Observed using the electron microscope
Infect humans, animals, plants, fungi,
protozoa, algae, and bacterial cells
Oncogenic- viruses/oncoviruses- cause
specific types of cancer
5 Specific Properties of Viruses
Possess either DNA or RNA
Unable to replicate on their own
Do not divide binary fission, mitosis, or
meiosis
Lack genes and enzymes necessary for
energy production
Depend on the ribosomes, enzymes, and
metabolites of the host cell for protein
and nucleic acid production
Classified by the ff characteristics
Type of genetic material (DNA or RNA)
Virus nucleic acid is the single-stranded
or double stranded
Virus nucleic acid is positive-sense or
negative-sense
Shape of the capsid
Number of capsomeres
Size of the capsid
Presence or absence of an envelope
Type of host it infects
Type of disease it produces
Target cell
Immunologic or antigenic properties
Viral Budding
Animal Viruses
Infect humans and animals
DNA or RNA viruses
Steps in Multiplication of Animal Viruses
1. Attachment- virus attaches to a protein or
receptor on the surface of a host cell
2. Penetration- entire virus enters the host
cell
3. Uncoating- viral nucleic acid escapes from
the capsid
4. Biosynthesis- viral genes are expressed;
many viral pieces are produced
5. Assembly- viral pieces or parts are
assembled to create complete virions 6.
Release- complete virions escape from the
host cell by lysis or budding
Inclusion Bodies
Remnants or collections of viruses
Often seen in infected cells
Used as diagnostic tool to identify
certain viral diseases
Negri bodies- rabies; cytoplasmic
inclusion bodies in nerve cells
Guarnieri bodies- smallpox
Latent Virus Infections
Herpes virus infections/cold sores
Shingles
Infected person is always harboring the
virus in nerve cells
Trigger: fever, stress, or excessive
sunlight
Limited by the body’s defense system
Oncogenic Viruses
Viruses that cause cancer
Epstein-Barr virus causes infectious
mononucleosis plus nasopharyngeal
carcinoma, Burkitt lymphoma, and B-
cell lymphoma
Kaposi sarcoma- caused by human
herpesvirus 8; found in AIDS patients
Hepatitis B and C- liver cancer
HPV- cervical cancer
Human Immunodeficiency Virus
AIDA
Enveloped- single-stranded RNA virus
Retrovirus- allows RNA to genome to
be replicated into a provirus DNA form
that can be integrated into the host cell
genome
Long Incubation period
Infect CD4+ T cells thus weakening the
immune system and making
opportunistic infections
Provirus Transmitted via insects, nematodes,
Viral genome infected seeds, mites, cuttings,
Allow the virus to cause latent contaminated tools
infections Transmissible spongiform
Replicated with the host cell genome encephalopathies
during cell division and can remain Viroids
latent through many host cell Consist of short, naked fragments of
generations single-stranded RNA
Ebola and Zika Viruses Interfere with the metabolism of plant
Ebola cells and stunt the growth of plants
High mortality Prions
Thread-shaped virus that is thought Small infectious proteins that cause
to cross over from bats to infect fatal neurologic diseases in animals
humans and humans
Zika Brain becomes riddled with holes
Cause serious birth defects Transmitted by consumption of
Transmitted by mosquitoes contaminated food
Untreatable and fatal
Antiviral Agents Kuru, Creutzfeldt-Jakob Disease,
Interfere with virus-specific enzymes Gerstmann-Straussler-Scheinker
and virus production Syndrome
Disrupting critical phase in viral Most resistant to destruction
replication cycles Destroyed by prolonged exposure to
Inhibiting the synthesis of viral DNA, sodium hydroxide
RNA, or proteins
Bacteriophages Bacteria
Bacteria infected by viruses Phenotypic categories
3 categories based on shape: Gram-negative and have a cell wall
icosahedron, filamentous, and complex Gram-positive and have a cell wall
Single or double-stranded Lack a cell wall
RNA or DNA phages
Virulent or temperate phages Cell morphology
Virulent bacteriophages Cocci- round
Cause the lytic cycle which ends Bacilli- rod shaped
with the destruction of the bacterial Spirilla- curved and spiral-shaped
cell Singly
Do not enter the host cell but rather Pairs- diplo
inject their nucleic acid into the cell Chains- strepto
Giant Viruses of Amebae Clusters- staphylo
2003 Four- tetrads
Extremely large double-stranded DNA Eight-octads
Recovered from amebas Pleomorphism- bacteria that can exist in a
Mimivirus variety of shapes
Plant Viruses
Diseases of citrus trees, rice, barley, Staining Procedure
tobacco, turnips, cauliflower, potatoes, Bacteria are smeared in a glass slide, air-
tomatoes dried, and then fixed
 Heat fixation- placing the slide on a slider warmer
Methanol fixation- flooding the smear with absolute methanol for 30 seconds
Fixation serves 3 purposes
Kills the organism
Preserves their morphology
Anchors the smear to the slide
Structural Staining Procedure- procedures used to observe bacterial capsules, spores, and
flagella

Thick layer of peptidoglycan in the cell walls of Gram-positive bacteria makes it difficult to
remove crystal violet-iodine complex during the decolorization step
Thin layer of peptidoglycan in the cell walls of Gram-negative bacteria makes it easier to
remove the crystal violet-iodine complex during the decolorization step
Decolorizer dissolves the lipid in the cell walls of gram negative bacteria

Acid Fast Staining

Mycobacterium species- high lipid content in their cell wall
Red bacilli against a blue or green background
Colony Morphology
Contains millions of organism
Appearance of the colony
Size, color, overall shape, elevation, and
the appearance of the edge or margin of
the colony
Size is determined by the organism’s
rate of growth
Results of enzyme activity on various
types of culture media
Atmospheric Requirements
Obligate aerobes- require an
atmosphere containing molecular
oxygen in room air
Microaerophilic aerobes- require oxygen
but in lower concentrations
Facultative anaerobes- capable of
surviving in either the presence or
absence of oxygen
Aerotolerant anaerobes- does not
require oxygen, grows better in the
absence of oxygen, can survive in
atmospheres containing molecular
oxygen
Obligate anaerobes- grow only in
environments with 0 oxygen
Temperature Requirements
Some can grow in freezing pr extremely
high temperatures
Pathogenic bacteria are limited to
grown and are only adapted to human
body temperature
Nutritional requirements
Some have specific vitamin
requirements
Some need organic substances secreted
by other living organisms
Biochemical and Metabolic Activities
Some bacteria can be identified by the
enzymes they secrete
Some bacteria are characterized by the
production of certain gases
Pathogenicity
Ability to cause disease
Capsules, fimbriae, or endotoxins
Secrete exotoxins, and exoenzymes that
damage cells and tissues
Unique Bacteria
Small and difficult to isolate
Rickettsias
Gram-negative-type cell wall
Obligate intracellular- must live
within the host cell
Inoculated onto embryonated
chicken eggs, lab animals, or cell
cultures
Arthropod borne
Chlamydia
Energy parasites
Preferentially use the ATP of their
host cells
Obligate intracellular pathogens
Transferred via inhalation of
aerosols or direct contact between
hosts
Mycoplasma
Smallest of the cellular microbes
Lack cell walls
Assume many shapes
In humans, causes atypical pneumonia
and genitourinary infections
Resistant to penicillin
Produce “fried egg” colonies
Photosynthetic Bacteria
Do not all carry out photosynthesis in
the same way
Purple and green bacteria- do not
produce oxygen
Cyanobacteria- produce oxygen
Oxygenic photosynthesis-
photosynthesis that produce oxygen
Anoxygenic photosynthesis-
photosynthesis that does not produce
oxygen
Cyanobacteria
Photosynthesis takes place on
intracellular membranes known as
thylakoids where phycobilisomes
are attached (harvests lights)
Create a water boom or pond scum
Some produce toxins
Archaea
Many are extremophiles
Acidophiles
Alkaliphiles
Thermophiles
 Psychrophiles
Halophiles
Piezophiles

Differences Between Viruses and Bacteria

Viruses
Not composed of cells
Not considered to be living
Simpler in structure
Contain either DNA or RNA
Must enter a host cell to reproduce

Bacteria
Composed of cells
Living organisms
More complex
Contain both DNA and RNA
Capable of reproducing on their own
Lesson 4: Eukaryotic Microbes Malaria, Ciard (?), African Sleeping
Sickness, and amoebic dysentery
1. Algae Symbiotic relationship- both organisms
Characteristics and Classification benefit
Photosynthetic, eukaryotic Termite and intestinal protozoa-
Phycology-study of algae protozoa digest the wood eaten by the
Cytoplasm, cell wall, cell membrane, termite
nucleus, plastids, ribosomes, mitochondria,
and Golgi bodies Classification and Medical Significance
Pellicle-thickened cell membrane Amebae
Stigma-light-sensing organelle; eyespot Move via pseudopodia
Lack true roots, stems, and leaves Ameboid movement
Contain cellulose Feed via phagocytosis
Classified as green, golden, brown, or red Drink via pinocytosis
Diatoms Entamoeba histolytica
Tiny, unicellular algae that live in both Amebic dysentery and
freshwater and seawater extraintestinal amebic abscesses
Used as filtration aid and mild abrasive Naegleria fowleri
in products such as metal polishes and Primary amebic
toothpaste meningoenceiphalitis
Dinoflagellates Acanthamoeba spp
Microscopic, unicellular, flagellated Eye infections
often photosynthetic algae Ciliates
Produces much of the earth’s oxygen Move by means of large numbers of
“Red tide” hairlike cilia on their surface
Important source of food, iodine, and other Balantidium coli
minerals, fertilizers, emulsifiers for pudding, Dysentery
stabilizers for ice cream and salad dressings Transmitted to humans by drinking
Gelling agent for jams water contaminated by swine feces
Agar for nutrient media Flagellates
Damage to water systems Move by whiplike flagella
Trypanosoma cruzi- Chaga’s disease
2. Protozoa Trichomonas vaginalis-STD
Characteristics Giardia lamblia- persistent diarrhea
Unicellular, free-living
More animal-like 3. Fungi
No chlorophyll Characteristics
Pellicle-protection Saprophytes
Cytostome-primitive mouth opening Main source of food: decaying matter
Paramecium spp-contractile vacuole: Decompose material into absorbable
pumps water out of the cell nutrients
Life cycle Not photosynthetic
Trophozoite stage- motile, feeding, Contain chitin
dividing stage Other grow filaments- hyphae
Cyst stage- non-motile, dormant, Some have septate or aseptate hyphae
survival stage
Some are parasitic
Reproduction
Budding, hyphal extension, or the
formation of spores
Sexual spores
Fusion of 2 gametes
Asexual spores
If formed within sac-like structure-
sporangiospore
If it arises from a fungal component-
conidiophore
Resistant to heat, cold, acids, bases,
and many chemicals
Yeasts
Eukaryotic, unicellular that lack mycelia Microsporidia
Blastospores or blastoconidia-
individual yeast cells
Reproduce by budding or by a type of
spore formation
Pseudohyphae-string of elongated buds
Chlamydospores- thick-walled, sporelike
structures
Saccharomyces cerevisiae- baker’s
yeast
Colonies look like bacterial colonies
Wet mount
Moulds
Seen in water, soil, and food
Grown in the form of cytoplasmic
filaments or hyphae that make up the
mycelium of the mould
Aerial hyphae- extend above the surface Fungal Infections of Humans
Vegetative hyphae- beneath the surface
Reproduction is by spore formation
Phytophthora infestans- potato blight
mould that caused famine in Ireland in
mid 19th century
Penicillium and Acremonium- antibiotic-
producing moulds
Produce large quantities of enzymes
such as amylase, citric acid, and organic
acids
Blue cheese, Roquefort, camembert,
and limburger—cheese with mould
Dimorphic fungi
Live either as yeast or mould
When growing in the body or
temperature of 37C–exists as
unicellular yeasts and produce yeast
colonies
When growing in the environment or
room temperature of 25C–exists as
moulds producing mould colonies
Histoplasma capsulatum
Sporothrix schenckii
Coccidioides immitis
Coccidioides posadasii
Blastomyces dermatitidis
Obligate intracellular parasitic fungi
Polar filament
Unique organelle
When it infects another cell, it extrudes
the polar filament which penetrates
the recipient cell
Spore injects its genetic material called
sporoplasm
Infection of the GIT or eye
Fleshy Fungi
Mushrooms, toadstools, puffballs, and
bracket fungi
True fungi
Network of filaments and strands plus a
fruiting body
Superficial and Cutaneous Mycoses
Hair, fingernails, toenails, and
epidermis–superficial
Dermis-cutaneous
Dermatophytes- group of moulds that
cause tinea infections (ringworms)
Tinea pedis- athlete’s foot
Tinea unguium- fingernails and
toenails
Tinea capitis- scalp
Tinea barbae- face and neck
Tinea corporis- trunk of body
Tinea cruris- groin area
Candida albicans- oral thrush, yeast
vaginitis
Page 30 (got skipped)
Systematic
Affecting 2 or more different organ systems
simultaneously
Conidia of some pathogenic fungi may be
inhaled from contaminated soil, bird/bat
feces, or may enter through wounds
Blastomycosis, and histoplasmosis
Bread moulds–Rhizopus or Mucor

Laboratory Diagnosis of Fungal Infections

Yeasts are identified up to the species level
Inoculating them into a series of
biochemical tests
Determine which substrates the yeast is
able to use as nutrients
Moulds are identified by:
Macroscopic- color, texture, and
topography of mould colony
Microscopic- type of structures on
which or within which spores or conidia
are produced

4. Lichens
Colored, circular patches on tree trunks,
and rocks
Combination of algae, filamentous fungus,
and yeast
Symbionts
Not associated with human disease but
some have shown antibacterial properties

5. Slime Moulds
Found in soil and rotting logs
Fungal and protozoal characteristics
Starting as ameba but progressing into a
multicellular organism
Does not cause human disease