Various Disciplines of Study Within Microbiology

 Bacteriology
 Mycology
 Parasitology
 Immunology
 Epidemiology
 Biotechnology
 Virology
 Environmental Microbiology
 Bioremediation
Microbiology Lecture
• the anatomy, physiology, and genetics of microorganisms
bacteria, algae, fungi, and protozoans
• the roles of microorganisms in the environment
• their applications in industry and in medicine
• viruses, viroids and prion particles

Laboratory course
• practical experience in the study of microorganisms
• techniques for the identification of microorganisms based on -
physical characteristics
e.g. colony and cellular morphology
- physiological characteristics
e.g. growth patterns, antibiotic resistances
Laboratory:
Apply the use aseptic techniques for basic microbial
applications.
These applications include:
procedures for control of microbial growth,
screening for microbial contamination of food and water
samples and the use of microorganisms for
production in industry.
I. Origin and Evolution of Life Microbial Anatomy
II. History of Microbiology
III. Microbial Diversity/Survey of Microbial Growth Requirements
Microbial World A. Microbial Nutrition
A. Cellular B. Physical Factors Affecting Growth
1. Prokaryotes C. Microbial Reproduction
archaebacteria
eubacteria Microbial Metabolism
2. Eukaryotes A. Aerobic Metabolism
fungi, algae, protozoans B. Anaerobic Metabolism
B. Acellular C. Photosynthesis
1. Viruses
2. Viroids Microbial Infections and their Treatment
3. Prions A. Chemotherapeutic Agents
B. Physical Agents
Parasitic Protozoans
 Alveolata Parasitic Helminths
(Ciliates and Apicomplexans) Nematodes
 Amoebozoa Pentastomidans
 Discricristates Acanthocephalans
(Parabasalans and Kinetoplastida)
Parasitic Arthropods
Parasitic Platyheminthes Mosquitoes, Lice & Fleas
 Symbiotic Turbellaria Acarines and others
 Monogeneans  Diagnosis of Helminth Infections
 Cestodes
 Trematoda 
Candida albicans Neisseria gonnorhea

Common cold virus: Rhinovirus

Microbes in our Lives
 A few are pathogenic
 Decompose organic wastes
 Fix nitrogen  nitrate
 Producers in the ecosystem
o photosynthetic bacteria
 Produce industrial chemicals
o ethanol and acetone
 Produce fermented foods
o vinegar, cheese, and bread
 Produce enzymes and hormones
o cellulase and insulin
Knowledge of Microorganisms
Escherichia coli
 Enables human to prevent food  honors the discoverer, Theodor Escherich
spoilage  Describes the bacterium’s habitat
large intestine or colon
 Prevent disease occurrence
Staphylococcus aureus
 Apply aseptic technique to  clustered = staphylo, spherical = cocci
 gold-colored (aureus) colonies
prevent contamination in
medicine and microbiology
laboratories
Types of Microorganisms
 Archaea
 Bacteria
 Fungi
Plasmodium falciparum
 Protoza
 Algae
 Parasites

Acellular Agents
 Viruses
 Viroids
 Prions

Entamoeba histolytica
Bacteria
 Prokaryotes
 Cell wall: Peptidoglycan
 Reproduction: Binary fission
 Energy sources:
Use organic chemicals,
inorganic compounds or
photosynthesis
Typical Parts & Structures of Rod-shaped Bacterium
Domain Archaea
 Prokaryotes
 Lack Peptidoglycan
 Live in extreme environments

methanogens
extreme halophiles
extreme thermophiles
Domain Archaea
Methanogens
 produce methane gas as a metabolic
byproduct in areas of low O2 content
(hypoxic)
 obtain most of their metabolic energy from
the biosynthesis of methane
 found in large intestine of humans and
animals, forestomachs of ruminants,
wetlands, sewage treatment plants,
geothermal vents
 Example strain
Methanobacterium bryantii
Thermophiles
with optimum growth temperatures between
41 and 122 °C while hyperthermophilic
organisms are those with optimum growth
temperatures above 80°C (Blöchl et al., 1995).
Not all thermophiles belong to Archaea
previous record-holder: P. fumarii, could
live at temperature as high as 113 °C
new microbe record-holder: “Strain 121”
thrives at 121 °C and can even survive for
two hours at 130 °C.
Domain Archaea
Extreme Halophiles
o thrive in high salt concentrations
o name comes from the Greek word for "salt-loving“

o While most halophiles are classified into the Archaea domain, there
are also bacterial halophiles and some eukaryotes, such as the alga
Dunaliella salina or fungus Wallemia ichthyophaga.
o Some well-known species give off a red color from carotenoid
compounds, notably bacteriorhodopsin.

o found in areas with a concentration of salt 5 times greater than the

salt concentration of the ocean, such as the Great Salt Lake in Utah,
Owens Lake in California, the Dead Sea, and in evaporation ponds.
Fungi
 Eukaryotes
 Cell walls made of chitin
 Use organic compounds
for energy sources
 Molds and mushrooms
are multicellular,
consisting of masses of
mycelia which are
composed of filaments
called hyphae
 Yeasts are unicellular
Protozoans
 Eukaryotes
 Absorb or ingest
organic compounds
 May be motile
through cilia,
pseudopodia, or
flagella
Disease-causing Protozoans
Algae
 Eukaryotes
 Cell walls made: cellulose
 Plant-like multicellular or unicellular
 Produce Oxygen and organic Volvox colonies
compounds that sustain life
 Energy: Photosynthesis
 Multi-celled algae: seaweed
 Single-celled algae: seaweed
 Single-celled algae: phytoplankton.
› cyanobacteria and microalgae

Alexandrium tamarense (toxic alga)

Viruses
 Acellular
 DNA or RNA core
 surrounded by protein
coat
 Coat may be enclosed in a
lipid envelope
 Viruses are replicated only
when they are in a living
host
Some common

V
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r
u
s
e
s
V
i
r
u
s
e
s
Parasites
 Eukaryotes
 Multicellular animals
 Parasitic flatworms
or roundworms are
called helminths
 Microscopic stages in
life cycle
Classifications of Organisms
 Archaea
 Bacteria 3 Domains
 Eukarya
› Protists
› Fungi
› Plants
› Animals
Historical Review of the Science of
Microbiology

• Robert Hook (1665) – Englishman,

used a primitive compound (two
magnifying lenses)

• microscope, reported that life’s

smallest units were little boxes –
cells

• His work started the process of the

development of the Cell Theory of
life
Antoni Van Leeuwenhoek
(1673)
 amateur scientist
 probably the first person to
observe living cells with a
simple microscope
 ground his own lenses and
described what we know
today as bacteria – rod
shaped , spiral shaped , etc.
“animalcules”
Antoni Van Leeuwenhoek (1673)
 opposed the prevailing theory of
Spontaneous Generation
 He used covered jars to show that
maggots came from flies –strong
evidence against spontaneous
generation
 Now we teach the theory of
Biogenesis – Life comes from Life
 But the issue of Spontaneous
Generation was actively believed for
many more years
 • Italian physician, naturalist,
biologist and poet
• the "founder of experimental
biology“
• "father of modern parasitology“
• first to challenge the theory of
Spontaneous Generation by
demonstrating that maggots come
from eggs of flies
Francesco Redi – 1668
Francesco Redi’s Experiment
 Early writings:
1. Babylonian epic
Gilgamesh:

Records of the
presence of
pestilence and
.  disease

Early writings:
2. Ancient Egypt: descriptions of disease
Existing belief: Bubonic Plague or the

Disease and pestilence

were punishment
rendering as a result of
“bad deeds” or “evil
thoughts”.

Biblical belief
Old testament:

A disease was regarded as a

chastisement from God. 
430 B.C. – Thucydides (Greek historian), recorded about the great plague in
Athens.
His observation: Those who contracted the disease and recovered were the
ones who could tend to the sick and dying without worrying about catching
it again.

The first challenge of the plague to an individual apparently conferred

resistance to any further attack regardless of exposure level.
SMALLPOX
• Smallpox was probably the
greatest single incentive
towards the precipitation of
modern western science and
to the onset of the field of
immunology.
• Historically, smallpox has
been a worldwide terror Smallpox pustules
killing millions of people.
Variolation

• 1400 – in the Middle East, the practice of “variolation”

was common

• Variolation - applying powdered smallpox "crusts"

and inserting them with a pin or “poking” device into
the skin.
• also called “inoculation”
Variolation
• The smallpox was given to children and young adults when
their ability to defend against disease was at its greatest. (when
the individual was at his/her healthiest).

• The risk of death from variolation was around 2%, a risk but a
considerable improvement on the death rate for uncontrolled
infection.
Introduction of smallpox inoculation (variolation) in England

1700 - Dr. Martin Lister received a letter from a trader in China which
reported a method that would prevent a future smallpox disease but he
didn’t pay attention to it.

1714 – a Greek-Italian physician working in Istanbul for the British ambassador

wrote a letter to the Royal Society about an account, or history, on the procuring
the smallpox by incision or inoculation.
1721 - Lady Mary Wortley
Montagu, wife of the British
ambassador in Istanbul, helped to
popularize inoculation.

She had her son (6 yrs old) and

daughter (3 yrs old) inoculated
by the surgeon of the embassy
for fear of the deadly smallpox
epidemic.

The physician called for some witnesses, so

his reputation would remain intact.
 “The Royal Experiment of Immunology”

1721 - The King accepted the request of a group

of physicians to perform experiments
with smallpox inoculation in condemned
criminals on condition that the prisoners
received pardon.

Despite the success of the Royal Experiment, it was vehemently

opposed by the Church and was highly discouraged, particularly if
one was a Christian. It was claimed to be unsafe, and above all,
against God and Nature.
The use of cowpox virus against smallpox

The first step to a safer procedure was to substitute material derived

from the lesion of a cowpox (vaccinia) for the inoculation. 

Cowpox is a benign disease caused by a virus closely related to the smallpox

(variola) virus.

1774- Benjamin Jesty, a farmer who inoculated his wife with

the vaccinia virus.

First record of anyone using vaccinia virus to "protect" against

smallpox.
 Edward Jenner (in 1796)
- tested whether the belief that cowpox sufferers
were actually immune to smallpox was true

His experiment:
1 boy – inoculated with pus from a cowpox sore;

result: the boy caught cowpox

After 3 months – the boy was inoculated with

pus from a smallpox sore
result: the boy did not catch the smallpox.
Edward Jenner (1749-1823)
Edward Jenner was credited with first vaccine
 During the epidemics of
smallpox in late 1700’s -
he observed that
milkmaids didn’t get the
disease, cattle had a
similar disease – cowpox

 milkmaids had cow pox lesions, but

not small pox, he purposefully took
scrapings from cowpox blister and
scraped a 8 year old volunteer. With
the material – child got mild illness
but not small pox
Jenner called this new method ‘VACCINATION'
- from a cow (“vacca”; vaccinia virus that caused cowpox) as a way of
distinguishing it from the process of 'inoculation'.

1879 by Gaston Melingue

Edward Jenner Performing the First Vaccination
Against Smallpox in 1796.
 The Recommendations for Production and Control of
Smallpox Vaccines were last revised in 1965.

Since then, an intensified global eradication program implemented from 1967 to 1980, and
led by WHO, has resulted in the global eradication of smallpox.
 Louis Pasteur (1822-1895)

The development of the Germ theory of disease

by Louis Pasteur furthered the advancement of
the fledging science of microbiology

The Germ theory of Disease

proposed that most diseases are caused
by microorganisms, transmitted from an
infected individual to a non-infected one.
1881 - Louis Pasteur theorized that immunization protects people
against disease by exposing them to a version of a microbe that is
harmless but is just enough like the disease-causing organism, or
pathogen, that the immune system learns to fight it.
Louis Pasteur became the first experimental immunologist.  He He
developed attenuated vaccines against anthrax, cholera, and and
rabies.

The following modern vaccines against diseases are

based on this principle:
Measles
Polio
Chicken pox
Louis Pasteur (1861)
 French scientist who dealt the death blow to the spontaneous
generation theory.

 He devised the ingenious curved necked flasks that prevented

contaminated air from reaching boiled beef broth – the broth
remained uncontaminated even though exposed to the air

 He was very lucky – NO endospores present, or his

experiment would have failed (resistant to boiling)
Louis Pasteur and his Pasteurization
 developed Pasteurization – he
heated wine to kill
contaminating
microbes
– cured sick wine (today
we heat treatment to
kill pathogens in milk

 proved that fermentation was

caused by a yeast
Louis Pasteur
 developed vaccines for rabies and anthrax

 Vaccines led to immunity to diseases that routinely killed many

people, used to help people long before they understood how they
even worked (science of Immunology)

 began the revolution in science that led to the Golden Age of

Microbiology (from 1857-1914)
Robert Koch
• developed Koch’s postulates – important technique for
determining the actual microbial cause agent of a disease

• discovered the tuberculosis bug

(Tubercle bacillus, Mycobacterium tuberculosis)

• discovered the cause of anthrax (Bacillus anthracis) – from blood

of dead cattle
cultured bacteria in pure culture  injected bacteria in
live cattle  cattle died  cultured bacteria in pure culture

- This led to the establishment of a procedure for

determining microbial cause of disease
(Koch’s Postulates)
 KOCH’S
POSTULATES
Iwanowski (1892)
• Discovered that plant disease can be caused by small organisms that
were so small they passed through filters
• Tobacco mosaic virus (TMV) was later identified as the cause -
beginning of virology
• Today we have discovered new and weird things like
viroids, prions
Paul Ehrlich
 German doctor who wanted to find a “magic bullet” an agent
that would kill the disease agent without hurting the patient

 Developed Salvarsan, “salvation from syphilis” agent

 This was an arsenical – arsenic compound

• was effective against syphilis
• Antimicrobial agent - medicine that treats a
microbial disease
Syphilis spirochete: Treponema pallidum

Paul Ehrlich
Joseph Lister – 1860’s
 English surgeon who applied ideas of the germ theory to surgery

 remembered the work of Semmelweis in Hungary in the 1840’s, if a Dr.

would wash their hands childbed fever was prevented.

 knew that phenol would kill bacteria; so he treated wounds with phenol =
no more infection
(phenol is the basic agent of today’s – Lysol)
› First antiseptic use in surgery or chemical agent used on tissue before surgery
› Tissue treated with an antimicrobial agent – antiseptics, betadine disinfectants
are chemicals used on nonliving matter
 proved that microbes cause surgical infections
today’s scourge – Methicillin-Resistant Staphylococcus aureus (MRSA)
Lister
used chemical disinfectant to prevent surgical wound infection
Antisepsis in surgery
 Ignaz Philipp Semmelweis
Hungarian physician of
ethnic-German ancestry,
now known as an early
pioneer of antiseptic
procedures.

Described as the "savior

of mothers", Semmelweis
discovered that the
incidence of puerperal
fever could be drastically
cut by the use of hand
disinfection in obstetrical
While being the Director of the maternity clinic in 1840 at the Vienna clinics.
General Hospital in Austria, he declared that washing could drastically
reduce the number of women dying after childbirth.
Alexander Fleming
• Scottish physician and bacteriologist - 1928
• Observed mold growing on a bacteria culture, there was a ring of clearing
around the mold where the bacteria didn’t grow, the mold was later found to
be a Penicillium species and the naturally secreted chemical was called
penicillin, an antibiotic.

1. Antibiotics are natural agents.

2. Synthetic drugs are chemicals produced in labs (sulfas).
3. Problems with them - toxicity, resistance, allergic reactions
4. Fleming’s work - shelved until early WWII, sulfas were failing, needed
penicillin to cure battle field wounds
5. Now we’ve got thousands of antibiotics and synthetics and a significant
problem  antimicrobial resistance…
Fleming and Penicillium
Salk – 1963 - Polio vaccine
1950 - Polio was a scary epidemic
 developed a vaccine by treating
the virus with formalin (IPV) 
Inactivated Polio Virus

 His work on polio

revolutionized the science of
Virology and we are seeing the
results today in advances with
Hepatitis and HIV viral
infections
Sabin – Oral Polio Virus

OPV is an attenuated vaccine,

produced by the passage of the
virus through nonhuman cells at
a subphysiological temperature,
which produces spontaneous
mutations in the viral genome.

Oral polio vaccines were

developed by several groups, one
of which was led by Albert
Sabin.
Classification of Bacteria
• A clinical rapid ID is often important
when trying to find causative agent
of a disease

• Bergey’s manual: a reference when

doing unknown bacteria

• Developed on 1940’s for grouping

bacteria according to standard
diagnostic lab techniques available at
the time (such as Grams stain)
 Classification of Bacteria
Gram + cocci Gram - bacilli
Classification of Bacteria
Classification of Bacteria
• Bergey’s Manual - divides bacteria into 4 groups
or divisions on the basis of their Cell Wall
1. Gram + (stained violet)
2. Gram - (destained, and are counterstained
pink or reddish color)
3. Bacteria that lack a cell wall (mycoplasma)
4. organisms that have a cell wall, but lacking
“peptidoglycan”
(archaeobacteria – Now called “Archaea”
 Classification of Bacteria
More modern methods now used:
1. DNA studies, genomics, gene probes
2. using Bacterial viruses “bacteriophages”
3. Serology – antibody – antigen reactions
Examples:
• Salmonella typhi
• Salmonella typhimurium
• Azotobacter vinelandii 12837
• E. coli 0157H7 nasty strain of E. coli
Structure and Classification of Animal Viruses

• Classification of animal viruses

• Taxonomic criteria based on Genomic structure
• DNA or RNA
• Single-stranded or double-stranded
• Virus particle structure
• Isometric
• Pleomorphic
• Helical
• Presence or absence of envelope
Structure and Classification of Animal Viruses
Groupings based on route of transmission
Disease-causing viruses often grouped by route of transmission
• Enteric viruses (Polio)
• transmitted via fecal-oral route
• gastroenteritis
• Respiratory viruses (coronavirus)
• Inhaled respiratory droplets
• localized in respiratory tract
• Zoonotic viruses (WestNile, rabies)
• animal vector
• Sexually transmitted viruses (herpes, HIV)
Interactions of Animal Viruses
with Their Host: Acute infections

• Short in duration
• Develop long-lasting immunity
• Productive infections
• Disease symptoms result from tissue damage and infection of new
cells
 Interactions of Animal Viruses
with Their Host
• Acute infections
• Essential steps include
• Attachment
• Entry
• Targeting site of reproduction
• Uncoating of virion
• Replication of nucleic acid and protein
• Maturation
• Release from cells
• Shedding outside host
• Transmission to next host
 Interactions of Animal Viruses
with Their Host
• Persistent infections
• Viruses continually present in
host
• Release from infected cell via
budding
• Three categories distinguished by
detection of virus during period of
persistence
• Latent infections
• Chronic infections
• Slow infections
 Interactions of Animal Viruses
with Their Host: Persistent Infections
 Latent infections
› Infection is followed by symptomless period, then reactivation
› Infectious particles not detected until reactivation
› Symptoms of reactivation and initial disease may differ
› Example
 Herpes simplex viruses 1 and 2 (HSV1 and HSV2)
 Shingles (zoster, chicken pox)
 Interactions of Animal Viruses
with Their Host: Persistent Infections
• Chronic infections
• Infectious virus can be detected at all times
• Disease may be present or absent during extended times or may develop
late
• Best known example
• Hepatitis B
• a.k.a serum hepatitis
 Interactions of Animal Viruses
with Their Host: Persistent Infections
• Slow infections
• Infectious agent gradually increases in amount over
long period of time
• Two groups of infectious agents cause slow infections
• Retroviruses which include HIV
• Prions
• Similar to the lysogenic cycle of λ-phage
 Viruses and Human Tumors

 Double-stranded DNA viruses responsible for most virus-induced tumors in humans

› Cancers caused by DNA viruses result from integration of viral genome onto host DNA
 Transformed genes are expressed
 Uncontrolled growth results
Viruses and Human Tumors: Effects of Animals Viruses
 Viral Genetic Alterations
 Viruses can alter properties through
 Mutation
 Genetic reassortment
› Genetic reassortment of viruses results from
two viruses infecting the same cell
 Each virus incorporates segments of viral DNA
 One segment comes from one virion
 Rest of segments come from other virion
 Reassortment responsible for antigenic shift and
antigenic drift in Influenza virus
 Methods of Studying Viruses

 Cultivation of host
› Viruses multiply only inside
host cell
› Host cells are cultivated in the
laboratory in cell culture or
tissue culture
 Plant Viruses
 Number of plant diseases are
caused by viruses
 Infection may be recognized via
outward signs including
› Pigment loss
› Marks on leafs and fruit
› Tumors
› Stunted growth
 Plants generally do not recover
from viral infections
Other Infectious Agents
• Prions
• Proteinaceous infectious agent
• Linked to a number of fatal human diseases
• transmissible spongiform encephalopathies
• Brain tissue develops sponge-like holes
• Symptoms may not appear for years after infection
Prions
 Abnormal pathogenic agents that are transmissible and are able to
induce abnormal folding of specific normal cellular proteins called prion
proteins
 Normal prion proteins are most abundantly in the brain
 The functions of these normal prion proteins are still not completely
understood. The abnormal folding of the prion proteins leads to brain
damage and the characteristic signs and symptoms of the disease. Prion
diseases are usually rapidly progressive and always fatal.
Other Infectious Agents
 Prions
› Mutation caused protein to have
different folding properties
› Mutated protein resistant to proteases
› Inactivated by chemicals that denature
proteins
Other Infectious Agents

NORMAL SPONGIFORM
Other Infectious Agents
• Viroids - infect plants
• Define group of pathogens much smaller
and distinctly different from viruses
• Consist solely of small single-stranded
RNA molecule
• Have no protein coat
 Other Infectious Agents

• Viroids
• Other viroid properties include
• Replicate autonomously in susceptible cells
• Viroid RNA is circular and resistant to nuclease digestion
• Diseases include
• Potato spindle tuber
• Chrysanthemum stunt
• Cadang-cadang
 Distinguishing Characteristics
of Viruses, Viroids, and Prions
Viruses Viroids Prions
Obligate intracellular Obligate intracellular Abnormal form of a
agents agents cellular protein

Consist of either DNA or Consist only of RNA; no Consist only of protein;

RNA surrounded by a protein coat no DNA or RNA
protein coat