Microbiology and Parasitology
Study of important microorganisms and
parasites.
Microbiology
-study of microbes
-derived from Greek words mikros ("small") bios
("life”) and logia or logos ("study of")
Microbes-microscopic organisms that are too
small to be seen with the naked eye but visible
under microscopes.
-microbes are said to be ubiquitous.
2 major categories of microbes:
1. Acellular (nonliving) - microbes that is not
composed of cells.
- Also called infectious particles not made up of
cells. - - areas in body where most of the
viruses, viroid and prions small infectious aren't
the replication. e.g.; virus (HIV, AIDS)
2. Cellular- microbes that composed of cells.
Can be:
A. unicellular- single cell
B. multicellular- many cells
Also it can be:
A. prokaryotes- nucleus
B. eukaryotes- no nucleus
 Non pathogens -good health, do not
cause disease
-normal skin flora
A. skin micro biota
B. lactobacillus - promotes healthy
digestive
 Pathogens -can cause disease
- Infectious agents- biological agent that
causes disease or illness
-Disease- causing microorganisms
Example;
1. bacteria- diarrhea, ear and eye
infectious
2. algae- poisoning
3. fungi- allergies, pneumonia, vaginitis
4. protozoa- amebic, trichomoniasis
5. viruses- AIDS, hepatitis, meningitis
 Opportunist pathogens -microbes that
usually do not cause disease
- Normally inhabits intestinal tract
without causing a disease
- If gains access to curinary bladder,
blood stream or wound can cause disease
 Indigenous micro biota
indigenous microbes insides;
1. Ears and eyes
2. Mouth
3. Skin
4. GL tract
5. Genitourinary tract (vagina, urethra)
How can microbes benefit us?
1. In energy - microbes are essential in life
2. In waste and water treatment- microbes are
involved in decomposition of dead organism
and waste products of living organisms.
decomposition- process by which
substances are broken down into simpler form
of matter.
saprophytes- organisms that live on dead
or decaying organic matter.
3. In agriculture- microbes involved in elements
cycle (carbon,nitrogen,sulfur and phosphorus
cycles)
- farmers- crop rotation to replenish nutrients
in their field.
4. In food- algae and bacteria serve as food for
tiny animals
-microbes are essential in food and
beverage industries that through the process by
biotechnology.
5. in preventing disease- microbes lives in the
human intestinal tract that produce vitamin k
and B.
-Antibiotic- produced by a microbe that is
killing or inhibiting
6. in environment- capable of decomposing
industrial wastes (oil spills) using
bioremediation.
Evolution of Microbiology
1. Anton Von Leeuwenhoek (1632-1723)
- 1670 first to see live bacteria and
protozoa
- He used his self-made single lens
microscope to view organism
-"father of microbiology"
2. Louis Pasteur (1822-1895)
-French scientist, microbiologist, and
chemist
- He discovered microbial fermentation
- Fermentation- he discovered that
different microbes produces different
fermentation products
He introduced the term:
"Aerobes" organism that require oxygen
"Anaerobes" organism that don't require
oxygen
- He developed the process of
pasteurization
- "pasteurization" killing of bacteria
- Develop vaccines -substance used to
stimulate the production of antibiotics
- To prevent rabies in dogs and used the
vaccine to treat human rabies
-he attempt to prove the germ theory of
disease; theory that specific microbes cause
specific infectious
3. Robert Koch (1843-1910)
-introduced "Koch postulates" and the
concept that disease is caused by single
organism
- German physician and microbiology
- He discovered bacillus anthracis-
causative agent of anthrax
- He discovered that bacillus
-he discovered mycobacterium
•tuberculosis- causative agent for
tuberculosis
Golden Age of microbiology
1. Edward Jenner
- He discovered vaccine for smallpox
-"father of immunology"
2. Joseph Lister
-English surgeon
-applied theory for the development of aseptic
surgery
-proved that microorganisms causes surgical
infection
3. Paul Erlich
- german chemist
- discovered "compound 606" an arsenic
compound that proved effective in treating
syphilis.
-"father of chemotherapy"
- arsphenamine-technical name
- salvarsan- trade name
4. Alexander Flemming
-Scottish bacteriology
-discovered the antibiotic penicillin from the
mold penicillium notatum.
Microscopy
Microscope optical instrument that can magnify
organisms a hundredfold or even a thousand
fold.
Parts of microscope
1. ocular lens or eyepiece- topmost part of the
microscope which is the lens the viewer looks
through to see specimen
2. revolving nose piece- located above the
stage, holds the objective lenses
3. diopter adjustment-used to focus on one
eyepiece in order to correct any difference in
vision between the two eyes
4. body tube or head- connect the eyepiece to
objective lenses
5. arm-connects the body tube to base of the
microscope
6. coarse adjustment- brings the specimen into
general focus
7. fine adjustment- fine tunes the focus and
increases the details of the specimen
8. objective lenses- held in place above the
stage by the revolving nosepiece and are the
lenses that are closest to specimen.
9. stage- platform on which the specimen is
placed
10. stage clip- hold the slide in place
11. stage control- these knobs move the stage
either left or right or forward or backward
12. aperture- hole in the middle of stage that
allows light from the illuminator to reach the
slide containing the specimen
13. on/off switch- switch located at the base of
the microscope that turns the illuminator on
and off
14. illuminator- light source of the microscope
15. iris diaphragm- used to adjust the amount
of light coming through the condenser
16. condenser- contains a lens system that
focuses light onto specimen
17. base- supports the microscope and it is
where the illuminator is found.
Types of Microscope
 Simple microscope - containing only
one lens for magnifying objects
-images appear about 3 to 20x
larger than the objects actual size
- First microscope
-Anton von Leeuwenhoek used simple
microscope to observed many tiny objects
Example: magnifying glass- specially shaped
piece of glass that is to a handle and used to
make object look bigger than it is.
1. Compound light microscope
- 1590 & 1595
- Hans Jansen- optician developed the first
compound microscope
-contains more than one magnifying lens
-can magnify objects a thousand times
their original size
-visible light its main source of illumination
- has 2 sets of lenses for magnifying
objects;
- ocular lenses- objective lens 10x
- objective lenses- most important part
which most produce a clear image
2. Bright field microscope 9. Scanning probe microscope
-specimen appears dark against -Dr. Gerd Binnig & Dr. Heinrich Rohrer (1980)
surrounding bright viewer field of this
microscope -a physical probe is used to scan back and
forth of a sample
- used to visualize bacteria and fungi
-used to study the molecular and atomic
3. Dark field microscope shape of organisms
- utilizes reflected light instead of Prokaryotic and Eukaryotic cells
transmitted light
2 Categories of Living Cell
- ideal viewing of spirochetes
1. Prokaryotes
4. Phase-contrast microscope
- genetic material
- George nomarski (1952)
- with 705 ribosomes
- has a contrast enhancing optical
technique in order to produce high contrast -no organelles
images of specimen that are transparent -organelles- for energy, harvest , making
new proteins
- cells in culture, sub cellular particles
5. Differential Interference contrast -cell wall- simple
microscope utilizes two beams of light and has -sexual reproduction- no meiosis only
a higher resolution transfer of DNA
- useful in examining specimen -meiosis- process where all nuclei divide to
6. Fluorescence microscope -make use of produce 2 copies
ultraviolet light and fluorescent dyes -20 to 60 mins.- duration of cycle cells
(fluorochromes)
-cell division
a. used to visualize small specimen (all)
•binary fission- parent cell splits. e.g;
b. detect the viability of all population bacteria & archae
c. used to visualize genetic material (DNA & 2. Eukaryotes
RNA)
-generic material- linear enclosed with
7. Confocal microscope -use an optical imaging membrane, associate with histones
technique that increases optical resolution
- with 805 ribosomes
8. Electron microscope - type of a microscope
that uses electron as a source of illuminator -nucleus-with true nucleus

- used to visualized viruses and sub cellular -multicellular

cell -cell division- mitosis
- 2 types: •transmission electron microscope- -mitosis- part of the cycle
produces 2 dimensional
-sexual reproduction- meiosis
•scanning electron microscope
 -meiosis- process where cell nuclei divide
to produce
Medically Important microorganisms
Have potential to produce significant clinical
disease in humans
 Normal flora -.microbes that which are
normally present but not causing
diseases
 True pathogens- microbes causing a
disease
1. Virus
-HIV, Hepatitis B, Influenza, Ebola virus,
adeno virus, bacteriophages
-how does viruses work?
•invasion
•replication
•destruction
- a strand of genetic material that is coded to
replicate
-encloses the genetic material of the virus
-contain capsid- protein coat of a virus
-composed of capsomers
•capsomers- small protein units that
protect the genetic material of a virus
-possess only single nucleic acid (DNA or RNA)
-DNA -deoxyribonucleic acid
-carries hereditary material that controls
all activities of the cell
-RNA- molecular compound necessary in
cellular protein synthesis
viruses classified based the following:
 type of nucleic acid possess
 shape and the capsid
a. Icosahedral- polio, rabies mumps
b. Helical- mumps, influenza HIV-AIDS
c. Complex virus (bacteriophages)- cholera
 number of capsiomeres
 size of the capsid
 presence or absence of an envelop
 type of host they infect (humans, plants
or animals)
 type of disease they produce
 target cell or tropism (t-helper for HIV)
Characteristic (virus):
a. obligate intercellular parasites
b. similarly shaped like star
-transfer of genetic material from one
bacterium to another (transduction)
-transduction- process of genetic
recombination in bacteria which genes from a
host cell are incorporated into the genome of
bacterial virus.(bacteriophages)
2. Bacteria
-prokaryotic cells
-possess both DNA & RNA
- No true nucleus
-no organelles
-cell division: binary fission
-outer covering: cell wall composed of
peptidoglycan
-peptidoglycan- component of the bacterial
cell that protects the cells from bursting to
maintain cell shape
-acts as the cell wall's backbone, offering
strength to the cell wall
Categories of bacteria:
 gram-negative cell wall
-contain a thin layer of peptidoglycan
-e.g; eschirichia col

 gram-positive cell wall
-contains a thick layer of peptidoglycan
-e.g; staphylococcus aureus
 acid-fast cell wall
- also known as AFB are microorganisms
resistant to declorization by an acids.
3. Protozoa
-representative for parasites
-eukaryotic cells
-unicellular organisms
•morphologic forms:
-cysts- infective stage
-trophozoites- pathogenic stage
4. Algae
-eukaryotic cell, aquatic, plant like organisms
-no true roots, stems & leaves
-outer surface made of cellulose
-plant like: chlorophyll & capable of
photosynthesis
-use of CO2 as energy source
•mostly beneficial:
-food, iodine & mineral
-fertilizers, emulsifiers for pudding
-stabilizers
•vary size form:
-single celled phytoplankton
- large seaweeds found in ocean floor.
5. Diatomy
-characterized by being unicellular with a
silical based cellual
- unicellular
-responsible for "red tide"
-produce neurotoxin
-causes paralytic shellfish poisoning
Bacterial Morphology
Major components
 outer envelope
 cell membrane
 internal structures
Classification based on shape
1. Cocci -spherical or round shaped organisms
-e.g; staphyloccus
-single, diplo (pairs), strepto (chains),
staphylo (cluster), tetrad (group of 4), tetrad
(group of 8)
2. Baccilus -rod shaped organisms
•coccobacilli- very short,resembling
elongated cocci e.g; escheri
3. Spiral shaped or curved
•vibrio cholerae- comma shaped
•treponema pallidum- spiral in shaped
while the causative agent of diphtheria
•corynebacterium diphtheria
-club shaped
Envelope structures of bacteria
1. Glycocalyx -outermost covering of some
bacteria
-a gelatinous substance that is located
external to the cell wall, composed of
polysaccharide or polypeptide, or both.
2. Cell wall -also called murei sacculus
-multi layere in gram (+) & single layered in
gram (-) bacteria
2 components of gram-positive cell walls
1. Techoic acid
-can elicit antibody response
-staphylococcus aureus- techoic acid
function for the attachment of the organism to
the host cell
2. Polysaccharide
-include neutral sugars such as mannose,
arabinose, rhamnose, and glucosamine
3 components of gram-negative cell walls
1. outer membrane- bi layered structure where
the inner leaflet composed of a
lipopolysaccharide
2. lipoprotein -function to anchor the outer
membrane to the peptidoglycan layer and
stabilities the outer membrane
3. periplasmic space-fluid filled space between
the outer membrane and inner plasma
membrane
Projecting structures
1. Flagella -thread like structures made up
entirely of molecules of protein sub unit
flagellin.
 monotrichous- single polar flagellum
 lophotrichous- taft of flagella at one
end of bacterium
 amphitrichous- flagella of both ends of
bacterium
 peritrichous- flagella all around the
bacterium
 antrichous- bacteria without flagella
2. Pili or fimbrae -rigid surfaces appendages
found in many gram negative bacteria
-fine and short in comparison with flagella
-also function for motility
-function for adherence to cell surface
(common pili) or attachment to another
bacterium during a form of bacterial gene
exchange called conjugation (sex pili)
3. Axial filaments -also called endoflagella
-found in sporochetes
- composed of bundles of fibrils structure
of which are similar to flagella
Cytoplasmic Membrane
-located beneath cell wall
-selectively permeable membrane that allows
for transport of selected solutes
Internal structures
1. Nucleoid -genetic materials is packaged in a
structure
2. Mesosomes -functions for cell division; also
involved in secretion of substance produced by
bacteria
3. Ribosomes -function for protein synthesis
4. Granules or Inclusion bodies -found in
certain bacteria and serve for storage of food
and energy
5. Endospores -structures produced by many
bacteria when they are placed in a hostile
environment
 dipicolinic acid - confers resistance
to heat, drying, chemical agents and
radiation; making it very difficult to
destroy
 sporulation - process of spore
production
 germination - endospore revert to
their vegetative state through a
process
Bacterial Growth Requirements
Growth- involves an olderly and organized
increase in the sum of all components of
organism
Microbial growth- concerned with increase on
the number of cells, not increase in size of
organism
Bacterial colony- composed of thousands of
cells
Nutritional Requirements
1. Carbon -makes up structural backbone and
skeleton of all organic molecules
microorganism may be classified as:
 autotrophs (lithotrops)- utilize
inorganic compounds snd inorganic
salts as their sole carbon source
 organotrophs (heterotrophs)- make
use of organic substance like sugars
or glucose as their carbon source
2. Nitrogen, sulfur, phosphorus -nitrogen and
sulfur required for the synthesis of proteins;
nitrogen and phosphorus essential for synthesis
of nucleic acids and ATP.
-14% dry weight bacterial cell is nitrogen and
4% sulfur and phosphorus
3. Inorganic Ions
 magnesium- stabilize ribosome, cell
membrane & nucleic acid
 potassium- required for the normal
functioning & integrity of ribosomes
 calcium- important component of
gram (+) bacterial cell wall
 Iron- component of cytochrome
 trace elements- components of
enzyme
4. Growth factors -essential to promote the
growth and development of the bacterial cell
includes vitamin B & amino acids
Physical Requirements
1. Moisture/ water -serve as the medium from
which bacteria acquire the nutrients
2. Oxygen - used by aerobic bacteria for cellular
respiration and serve as the final electron
 obligate anaerobes- microbes that
cannot survive in the presence of
oxygen
 facultative- can grow under both
anaerobic and aerobic condition
 microaerophiles- grow at low
oxygen tension but their rate of
growth is diminished
 capnophiles- require the addition
of carbon dioxide to enhance their
growths
3. Temperature
classified into 3 groups:
 thermophiles- grow best
temperature higher than 40' C
 mesophiles- optimal temperature
of 20' C-40' C
 psychrophiles- optimum of 10' C to
20' C
4. pH - another requirement of bacteria is the
extent of acidity or alkanity of their
environment
5. Osmotic Conditions -most organisms grow
best under ideal conditions of osmotic pressure,
which is determined by the salt concentration
-normal microbial cytoplasmic salt
concentration is approximately 1%
Bacterial growth curve-illustrates the phases in
growth of population of bacteria when they
grown in a culture of fixed volume
1. Lag phase - period of adjustment for the
bacteria in the new environment
2. Log phase-characterized by rapid cell
division, resulting in an increase in the number
of bacteria
3. Stationary phase -period of equilibrium
-rates of growth slows down, nutrients start &
toxic wastes begin to accumulate
4. Death or decline phase -period of rapid cell
death where the number of dead cells is greater
than the number of living cells
Normal flora of human body
Microbial Ecology- study of the relationship
between microorganisms and their
environment
- relationship of microbes with human including
normal flora
Normal or Indigenous flora- consist of the
group of organisms that inhabit the body of a
normal healthy individual
 non pathogenic
 pathogenic
 opportunist pathogens
2 types of Normal Flora:
1. Resident flora also known as normal flora are
microorganisms that are regularly found in a
given area of the body at a given age
2. Transient flora are those that inhabit the
skin and mucous membrane temporarily for
hours, days, or weeks and are derived from the
environment
Normal flora are beneficial in Human body:
Advantage:
- inhibit the growth of pathogenic organisms
- protects the body organ's and systems in
direct contact with the external environment
- synthesize important vitamins essential to
humans
Disadvantage:
- production of disease if the individual
becomes immune compromised or if they
change their usual anatomic locations
- production of disease since most of the are
pathogens or opportunist
Other beneficial effects of Normal flora
- prevent pathogenic organisms from attaching
to and penetrating and the skin and other tissue
by producing MUCIN
- Aid in the digestion of food by producing
energy (cellulose, galactosid,glucosidase)
- intestinal flora help in the metabolism of
steroids
normal flora of fetus derived from:
- mother's genitial tract during delivery
- skin and respiratory tract into the handled the
newborn
Sterile body fluids in the body:
1. Cerebrospinal fluids (CSF)
2. Synovial fluid
3. Blood
Sterile tissue in the body:
1. Urinary bladder
2. Uterus, fallopian tubes
3. Middle ear
4. Paranasal sinuses
Normal flora on different sites in the body:
1. Skin is the part of the human body that is in
constant with the environment
factors that eliminate non-resident flora from
the skin:
- Lysozyme in the skin
- Acidic pH of the skin
- Free fatty acids in sebaceous secretions
- Sloughing off of the skin
normal flora consist of bacteria and fungi
 three regions:
 Axilla, perineum, and toe webs
- with higher moisture level, high body
temperature, higher level of lipids
- inhibit by gram negative bacilli
 Hand, face, and trunk
- dry sites diverse flora because of their
exposure to the environment
- staphylococcus epidermis, staphylococcus
hominis
 Upper arms and legs
- dry sites diverse flora because of their
exposure to the environment
- staphylococcus epidermis, staphylococcus
hominis
2. Mouth and Respiratory tract tongue and
buccal mucosa- inhabited by streptococcus
viridams
dental carries and gingival grevices, tonsillar
crypts- e.g; S. mutans, S. salivarius, S. sanguis
3. Conjunctiva- normal flora are scanty due to
flow of tears that contain lysozymes
4. Digestive tract
 Esophagus - contains transient
mouth flora
 Stomach- with minimal bacteria
due to hostile environment
- acidity in the stomach increase after
meals due to the release of gastric acid (pH 2)
-Helicobacter pylori- bacteria that are
able to survive in acidic environment
- causes of duodenal ulcers
 Colon-1% to 4% of flora of the colon
are facultative aerobes
 facultative anaerobe- is an
organism which can survive in the
presence of oxygen
roles in intestinal flora:
 synthesize of vitamin B complex
and vitamin K
 conversion of bile into bile acids
 competition with transient flora for
nutrients
 prevention of colonization of the
intestine by transient flora
 production of potentially
pathogenic end-products of
metabolism that are toxic transient
flora
5. Genitourinary Tract
 Urinary tract is sterile above the
distal 1 cm of the urethra
- mycobacterium smegmatis found normal in
both males and females as normal secretions
- gardnerella vaginalis, bacteriodes and alpha
streptococci- present in penile urethra
- female urethra- sterile or contains
staphylococcus epidermidis
- vaginal flora varies depending on the
following:
 Age
 Hormonal levels
 Vaginal pH
- female infants- vaginal flora lactobacillus
- 1 month age- puberty vaginal pH higher (pH
7.0)
- onset of puberty there is resumption of
glycogen secretions- vaginal pH acidic
- young girls prone to gonococcal infection
- Menopause- pH increase due to less
production of glycogen the same during pre-
puberty
- fungi such as Torulapsis and Candida (0% -
30%)