MICROBIOLOGY AND PARASITOLOGY –

PRELIMS

Why study Microbiology?

MICROBIOLOGY - Microbes play significant roles in our
lives; essential for life in the planet
- Mikros -> Small - Photosynthetic algae and bacteria (such
- Bios -> Life as cyanobacteria) produce much of the
- Logos -> Study of oxygen in our atmosphere
 Advance Biology Course dealing with the - Microbes decomposes waste products
study of microbes - Serves food for tiny animals; important
link for food chains
- Helps in digestion
 Living Microbe (Cellular) - Used as cell models for research
- Prokaryotes - Microbes used in industries
Bacteria - Genetic Engineering
Archaea - Biotechnology
- live almost everywhere life is possible
- Eukaryotes - more numerous than any other kind of
Algae organisms
Protozoa - global ecosystem depends on their
Fungi activities
- influence human society in many ways
 Non- Living Microbe ( Acellular) - medical and most populous group of
- Viroids organisms and are found everywhere on
- Prions the planet
- Viruses - play a major role in recycling essential
elements
- Microbes are Ubiquitous - source of nutrients and some carry out
photosynthesis
- Microbes that cause disease are - benefit society by their production of
sometimes referred to as “germs” food, beverages, antibiotics and vitamins
- causative agents of some important
- Scientific term for disease-causing diseases
microbes is pathogens (3%)
 3.5 billion years ago, fossils of primitive
- Non pathogens – non disease causing microbes where discovered
(97%)  First microbes Archaea &
Cyanobacteria
Indigenous Microbiota /

(Human Microbiome) (Indigenous Microflora)

- Microbes that lives in our body

- Some are opportunistic pathogens (e.g.
E.Coli)

 Opportunistic Pathogens
- Microbes that can cause disease, but
usually do not. Earliest Known Infectious Diseases
- They wait for opportunity to cause
- Infectious Diseases of humans and
disease
animals have existed for as long as
humans and animals have inhabited the
earth
Categories of Diseases Caused by
- Earliest known account of pestilence
Pathogens
occurred in Egypt in about 3180 BC
 Infectious Disease
- A pathogen colonizes a person’s body
- Causes a disease

 Microbial Intoxication Early Microbiology

- A person Ingest the toxin (that cause  Varro suggests disease caused by
disease) “invisible” organisms.
  1546 Fracastoro using the example of the - Francesco Redi (1688) placed meat in 6 wide
“French Disease”, describes how diseases mouthed jars. Three were covered with a type of
are spread. wide weave cloth – three jars were left open.
 1590 - first compound microscopes,
- All jars underwent a “spiritual matter
crude.
conversion”. They turned gray and began to
 1665 Hooke draws “cell”
issue spiritual vapors, but only the meat in the
uncovered jars were able to be transformed into
flies
Anton van Leeuwenhoek (1632-1723)
- “Father of Microbiology”
- Made the single-lens microscope or
simple microscopes 2. John Needham (1713-1781)
- Observed “animalcules”  his experiment : mutton broth in flasks →
- Discovered protozoa in 1674 and boiled →sealed with cork :
bacteria in 1676  broth became cloudy & contained
microorganisms
 First Catholic clergyman to become a
member of the Royal Society of London.
SPONTANEOUS GENERATION OF LIFE  1754, boiled chicken broth and put it into
a flask and sealed it. Saw growth
Von Helmont  Needham and “Vital Atoms”

 Early 1600’s performed an experiment. - Needham and Georges Comte de

Obtained the seed of life in the form of a Buffon proposed “vital atoms” life.
corn kernel “germ of life.” cause they could be seen in pond
 Obtained some garments from local water and infusions.
laborers “energy of life.” Incubated the
corn and energy containing garments in - “Vital atoms” escape dying
an attic. The corn properly energized organic material and move into the
turned into mice! Proving beyond doubt soil or water to be taken up the
that life arises from non-living material. plants.
 Organized religion was very happy about
this because of the logical spirituality of  Needham and others vitalists reply…
medicine - Argue the experiment only proves
that spontaneous generation
requires air.
The Conflict over Spontaneous Generation - Need the “vital force.”
- Even Spallanzani agrees in some
Spontaneous generation: living organisms can cases- regeneration and other
develop from nonliving or decomposing matter cases of microbes

1. Francesco Redi (1626-1697): 3. Lazzaro Spallanzani (1729-1799):

 disproved spontaneous generation for  his experiment: boiled seeds in flasks &
large animals water →sealed → boiled:
 showed that maggots on decaying meat  no growth of microorganisms in sealed &
came from fly eggs open flasks had animalcules
 1668, first controlled, experiment to  Italian priest who suggested that the
disprove spontaneous generation. Rotten microbes entered the broth from the air
meat experiment refutes abiogenesis . after boiling.
 In 1765, he describes another experiment
to test if microbes appear spontaneously

4. Louis Pasteur (1822-1895)

• Mid to late-1800s
• French chemist and a “founder” of the
modern science of microbiology
• Settled the Spallanzani Needham
debate with the “swan-necked flask”
experiment & put to rest the
Theory of Biogenesis Spontaneous generation theory
 Investigated different fermentation
products Developed the pasteurization
process
 Discovered life forms that could exist
without oxygen (anaerobes)
 Made significant contributions in the
germ theory of disease
 Discovered the infectious agents that
were causing the silkworm disease
 Championed changes in hospital
practices to minimize spread of disease
by pathogens
 Developed several vaccines, including
rabies and anthrax vaccines
 PASTEURIZATION

Final Blow to Theory of Spontaneous

Generation

5. John Tyndall (1820-1893):

- demonstrated that dust carries
microorganisms
- showed that if dust was absent,
nutrient broths remained sterile,
even if directly exposed to air
- Demonstrated directly that the
growth of microbes in
contaminated flasks was due to
microbial cells from airborne dust
particles, not from spontaneous
generation

Theory of biogenesis Vs Spontaneous

generation

- The theory of biogenesis states that living

things can only arise from living things and
cannot be spontaneously generated.

- The Spontaneous generation hypothesis

 discovered that microorganisms produce
proposed by scientists to explain the origin
different fermentation products
of the “animalcules” observed by Antoni
van Leeuwenhoek in his magnifying lenses
had received wide acceptance all over
Europe from Antoni’s time until the time of
Louis Pasteur.

The Golden Age of Microbiology (1857-

1914

 Many disease producing organisms were

discovered
 Swan Necked Flask  Microbial metabolism studies undertaken
 Microbiological techniques refined
 A better understanding of the role of
immunity and ways to control and
prevent infection by microbes

The Role of Microorganisms in Disease

 • was not immediately obvious  Develop the Koch’s postulates: used
• establishing connection depended on today to establish the link between a
development of techniques for studying particular microorganism and a particular
microbes disease
• once established, led to study of host
Koch Postulates
defenses – immunology
1.Similar pathogen must be present in every
Recognition of the Relationship between
case of the disease.
Microorganisms and Disease
2. The pathogen should be isolated from the
 Agostini Bassi (1773-1856): showed
diseased animal host and grown in pure culture.
that a disease of silkworms was caused
by a fungus 3. A healthy laboratory animal inoculated with
 M. J. Berkeley (ca. 1845): the pathogen taken from the pure culture must
demonstrated that the great Potato Blight acquire the disease.
of Ireland was caused by a water mold
 Heinrich de Bary (1853): showed that 4. The pathogen must be isolated from the
smut and rust fungi caused cereal crop inoculated animal and should be the same from
diseases the microbe in the original animal.
 Louis Pasteur (1860s - 80s) : showed
that the pébrine disease of silkworms was
caused by a protozoan

Joseph Lister ( 1867):

 provided indirect evidence that

microorganisms were the causal agents
of disease

 developed a system of surgery designed
to prevent microorganisms from entering
wounds as well as methods for treating
instruments and surgical dressings
 his patients had fewer postoperative
infections

Ignaz Semmelweis: The Father of Sanitary

Practices

 1800’s, Autopsy to child birth; puerperal

(childbed) fever.
 Encouraged sanitary practices by
physicians.  1882 – Walther and Fannie Hesse
 Ridiculed, had a nervous breakdown, proposes using agar as a solidifier.
asylum and died of an infection  1887 -Petri proposes growing cultures in
a modified dish
Robert Koch (1843-1910)

 German physician who made numerous  The Development of Techniques for

contributions to microbiology Studying Microbial Pathogens
 Made significant contributions to the
germ theory of disease - Koch’s work led to discovery or
 Discovered that Bacillus anthracis development of:
produce spores, capable of resisting - agar
adverse conditions - petri dish
 Developed methods of fixing, staining - nutrient broth and nutrient agar
and photographing bacteria - methods for isolating
 Developed methods to cultivate bacteria microorganism
 Discovered Mycobacterium tuberculosis
and Vibrio cholerae
 Developed Tuberculin testing  1884 -Metchnikoff describes
 1881 - Koch tries to attain pure cultures phagocytosis and proposes the “cellular
using gelatin. theory of immunity”.
 Established the relationship between
Bacillus anthracis and anthrax
 1890 - Ehrlich proposes the “humoral
theory of immunity” antibodies.

 1889 - Kitosato discovers tetanus

bacillus and toxin.
 1890 - Von Behring discovers
diphtheria toxin and develops antitoxin.
 1892 - Ivanovsky discovers tobacco
mosaic virus.
 1898 - Beijerinck discovers foot and
mouth virus. Careers in Microbiology
 1900 -Walter Reed proves yellow fever
virus carried by mosquitos. 1.) Agricultural Microbiology
 1902 - Landsteiner describes the 4 - is concerned with the relationship
blood group types. between microbes and crops, with an
 1905 -Schaudinn and Hoffman emphasis on improving yields and
discover the syphilis spirochete. combating plant diseases
 1910 - Ehrlich develops salvarsan, a 2.) Biotechnology
mercurial agent effective in treating - a tool used in industrial microbiology,
syphilis which is concerned with the uses of
 1928 - Fleming discovers the first microbes to produce or harvest large
antibiotic, penicillin. quantities of substances such as amino
 1928 - Griffith demonstrates bacterial acids, beer, drugs, enzymes and
transformation with Strep. pneumoniae. vitamins
 1941 - Beadle and Tatum propose “one
gene, one protein” theory.
3.) Environmental microbiology
- Application of microbiology in
ecology
4.) Medical and clinical microbiology
- aim to monitor and control the
spread of diseases in communities
5.) Genetic engineering
- involve techniques that alter the
genetic makeup of organisms to
produce hormones and
pharmaceuticals, create totally
new substances
6.) Microbial physiology
- use of microbial cell as cell models
7.) Paleomicrobiology
- Involves the study of ancient
microbes through molecular fossils
8.) Parasitology
- Study of Parasites

9.) Sanitary microbiology

- includes the processing and
disposal of garbage and sewage
waste, as well as the purification
and processing of water supplies to
ensure that no pathogen are
carried to the consumer by
drinking water
10.) Veterinary microbiology
11.) Clinical Microbiology /
Diagnostic Microbiology
- A branch of medical microbiology
concerned with the laboratory
diagnosis of infectious diseases of
humans
 Microbial Morphology and Classification

A. Cell Structure and Taxonomy

CELLS

- Fundamental unit of any living organism

Categorized into two:

– Eucaryotes
– Procaryotes CELLULAR STRUCTURE OF EUCARYOTIC
CELLS
CYTOLOGY
– study of the structure and function of cells
A. Eukaryotic Cell Structure
Importance
- identification of various microorganisms Cellular Membrane
- understand differences in metabolism
- encloses and holds the cell intact
The Cell Theory - regulates the passage of nutrients,
wastes products, and secretions into and
 All living things are composed of cells.
out of the cell
 Cells are the basic units of structure and
function in living things. Nucleus
 New cells are produced from existing
- differentiates prokaryotic and eukaryotic
cells.
cells
- controls the function of the entire cell
and acts as the command center of the
cell

3 components
 Nucleoplasm
- a type of protoplasm that is
composed of thick fluid and
constitutes chromatin fibres made
up of DNA and usually found in the
nucleus of the eukaryotic cells.
 Chromosome
- threadlike structures made of
protein and a single molecule of
DNA that serve to carry the
genomic information from cell to
cell.
 Nuclear Membrane
- a double layer that encloses the
cell's nucleus, where the
chromosomes reside.
- acting as barriers that prevent the
free passage of molecules between
the nucleus and the cytoplasm,
maintain the nucleus as a distinct
biochemical compartment.
- separates the contents of the
nucleus from the cytoplasm and
provides the structural framework
of the nucleus.

Nuclear Pores

- large complex of proteins

that allows small molecules and
ions to freely pass, or diffuse, into
or out of the nucleus.
 - allow necessary proteins to enter - lysozymes and digestive enzymes
the nucleus from the cytoplasm if break down foreign materials, cell
the proteins have special debris or the whole cell
sequences that indicate they
Peroxisomes
belong in the nucleus.
- protects other parts of the cell
from the harmful effect of
hydrogen peroxide

Nucleolus

- dark area in the nucleus where the

rRNA molecules are manufactured

Cytoplasm

- contains insoluble storage granules

and organelles Mitochondria
- site for most of the cell’s
metabolism - site for ATP formation by cellular
- called Cytosol if there is no respiration
present membrane bound
organelles.

Endoplasmic reticulum

- Passageway of materials inside a

cell
 Smooth ER
- without attached ribosomes and
plays a role in lipid synthesis
 Rough ER
- with attached ribosomes
Plastids
Ribosomes (80S):
- energy-producing organelle
- CHON synthesizers (Carbon,
containing various photosynthetic
Hydrogen, Oxygen and Nitrogen)
pigments
- consist mainly of rRNA and protein
and helps in the synthesis of Cytoskeleton
proteins
- strengthens, supports and stiffens
the cell giving its shape

Golgi apparatus

- completes the transformation of

newly synthesized protein into
mature, functional ones
- packages proteins into vesicles for
storage within the cell or transport
outside the cell
Cell wall

- external structure that provides

rigidity, shape and protection
- Composed of various
polysaccharides unlike the
prokaryotes

Lysosomes
 Ribosomes (70S)

- same function with eukaryotic ribosome

- All prokaryotes have 70S (where
S=Svedberg units) ribosomes while
eukaryotes contain larger 80S ribosomes in
their cytosol. The 70S ribosome is made up
of a 50S and 30S subunits. Ribosomes play
a key role in the catalysis of two important
and crucial biological processes.

Cell wall

- provides strong structural support

Flagella and cilia that prevents the cell from bursting
or collapsing
- organelles of locomotion which is
- consists of peptidoglycan
eventually necessary for survival
(murein)
 Flagella
- Exhibits positive and negative
phototaxis and chemotaxis but do
not run and tumble

B. Prokaryotic Cell Structure

Cell membrane
- same in structure and function to
the eukaryotic cell membrane

Mesosomes

- site for cellular respiration in

bacteria

Chromosomes

- single, long, supercoiled DNA

molecules
- serves as the control center of the
bacterial cell

Nucleoid

- DNA-occupied space within a

bacterial cell

Plasmid

- small, circular molecules of double

stranded DNA that are not part of
the chromosomes

Cytoplasm  The bacterial cell wall ranges from 20–80

- semiliquid containing a complex nm thick for Gram positive and between
mixture of all materials required for 1.5–10 nm thick for Gram negative
metabolism bacteria.
Glycocalyx

- thick layer of materials produced

by the cell membrane and
extruded outside the cell wall for
protection and adhesion

 Desiccation
- the removal of moisture from
something.

- Two proteins in the flagellar motor, called MotA

and MotB, form a proton channel through the
 Capsules may protect bacteria from cytoplasmic membrane and rotation of the
complement activation. As a flagellum is driven by a proton gradient.
result, encapsulated bacteria are not
immediately recognized as invaders by - This driving proton motive force occurs as
the phagocytes. Capsulated Strep. protons accumulating in the space between the
pneumoniae resist engulfment by cytoplasmic membrane and the cell wall as a
macrophages and PMNs and are virulent; result of the electron transport system travel
however, noncapsulated strains are easily through the channel back into the bacterium's
phagocytosed and are avirulent. cytoplasm.

Flagella - Most bacterial flagella can rotate both

counterclockwise and clockwise and this
- Primary function: motility or self rotation contributes to the bacterium's ability to
propulsion and eventually change direction as it swims. A protein switch in
chemotaxis through runs and the molecular motor of the basal body controls
tumbles the direction of rotation.
1. A bacterium with peritrichous flagella: - thinner than flagella, more rigid
and not associated with motility
- If a bacterium has a peritrichous arrangement
of flagella, counterclockwise rotation of the
flagella causes them to form a single bundle
that propels the bacterium in long, straight or
curved runs without a change in direction.

- Counterclockwise rotation causes the flagellum

to exhibit a left-handed helix. During a run, that
lasts about one second, the bacterium moves
10 - 20 times its length before it stops.
This occurs when some of the flagella rotate
clockwise, disengage from the bundle, and
trigger a tumbling motion.
Endospores
- Clockwise rotation causes the flagellum to
assume a right-handed helix. A tumble only - either terminal or subterminal
lasts about one-tenth of a second and no - related to the survival rather than
real forward progress is made. After a on the reproduction of bacteria
“tumble”, the direction of the next bacterial run
is random because every time the bacterium
stops swimming, Brownian motion and fluid
currents cause the bacterium to reorient in a
new direction.

2. A bacterium with polar flagella:

Most bacteria with polar flagella, like the

peritrichous above, can rotate their flagella
both clockwise and counterclockwise. If the
flagellum is rotating counterclockwise, it pushes
the bacterium forward. When it rotates
clockwise, it pulls the bacterium backward.
These bacteria change direction by changing
the rotation of their flagella.

Taxis - highly retractile and thick-walled

structures formed inside the
Around half of all known bacteria are motile.
bacterial cells.
Motility serves to keep bacteria in an optimum
- It is most common for Bacillus
environment via taxis. Taxis is a motile response
species as well as Clostridium
to an environmental stimulus. Bacteria can
species to create endospores.
respond to chemicals (chemotaxis), light
- Endospores are spores that are
(phototaxis), osmotic pressure
formed within the cells, mainly in
(osmotaxis), oxygen (aerotaxis), and
bacteria. These spores are formed
temperature (thermotaxis). Chemotaxis is a
within bacteria vegetative cells
response to a chemical gradient of attractant or
or mother cells known as
repellent molecules in the bacterium's
sporangia
environment.
- ensure the survival of bacteria in
adverse environmental conditions
such as nutrient deficiency (carbon
and nitrogen) and overpopulation.
- Bacillus cereus, Bacillus
anthracis, Bacillus
thuringiensis, Clostridium
botulinum, and Clostridium
tetani

Eukaryotes Prokaryote
s
Size 10 – 100 0.2 – 2.0
Fimbriae (Pili) micrometers micrometers
Nucleus Present Absent
- observed mostly on Gram-negative Glycocalyx Present in Present as
bacteria some animal organized
 cells capsule or
slime
Motility Undulating Rotating
flagella flagella
Flagella Present in Present in
some some
Cilia Present in Absent in all
some
Fimbriae Absent in all Present in
and pili some
Cell wall Present in Present in
most most
Cytosol Present in Present in For any given organism there is a minimum
all all growth temperature, optimum growth
Endospore Absent in all Present in temperature and maximum growth
some
temperatures. These are known as the
Ribosomes Larger (80S) Smaller
(70S) cardinal temperatures
Nucleus Present in Absent in all dependence of growth of microorganisms on
all
temperature is largely related to activation and
Nuclear Present in Absent in all
membrane all inactivation of enzyme systems in
Endoplasm Present in Absent in all microorganisms.
ic all
Three different effects of temperature
reticulum
Mitochondr Present in Absent in all contribute to the death of microbial cells:
ia most 1. Denaturation of proteins (enzymes) by heat
MICROBIAL GROWTH
2. Intoxication due to accelerated metabolic
reactions
 Microbial growth of cells = increase 3. Changes in essential lipids. Melting points of
in number, not cell size the fats found in the organisms and
Growth in Batch Culture temperature ranges of death are related.

 “Growth” is generally used to refer to the

acquisition of biomass leading to cell
division, or reproduction.
 A “batch culture” is a closed system in
broth medium in which no additional
nutrient is added after inoculation of the
broth

Requirements for Growth: Physical

Requirements

▪ Temperature

▪ pH  Psychrophiles
- Most belong to genera
▪ Osmotic pressure Psuedomonas, Flavobacterium,
Achromobacter and Alcaligenes.
- Proteins function best at low
temperatures( 0’C-20’C, optimum
15’C), Clamydomanos nivalis
- membranes contain high levels of
unsaturated fatty acids
- Their enzymes, transport systems
and protein synthesis function well
at low temperature
 Psychrotrophs/Facultative
- Psychrophiles-Psychtrophic
bacteria and fungi
- Proteins function best at low
temperatures( 0’C-35’C, optimum
20’C-30’C)

 Mesophiles
 - grow best at temperatures of 20-
45’C(15-20’C-45’C)
- Most microorganism fall to this
category, most human pathogenic
bacteria fall to this category.

 pH
- Most bacteria grow between pH 6.5 and
7.5
- Molds and yeasts grow between pH 5
and 6
- Acidophiles grow in acidic
environments
 Neutrophiles (Most bacteria) can grow
between pH 5.5-8 E.coli
 Acidophiles prefer pH between 0 and
5.5.Thiobacillus thiooxidans
 Alkalophiles prefer pH above 10.
Bacillus alcalophilus
- Fungi prefer pH 4-6

Hypertonic Hypotonic

If a cell is placed in a hypertonic solution,

water will leave the cell, and the cell will shrink.
In an isotonic environment, there is no net
water movement, so there is no change in the
size of the cell. When a cell is placed in a
hypotonic environment, water will enter the cell,
and the cell will swell.
PHYSICAL METHODS

CHEMICAL METHODS