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Dr. Adnan S. Jaran
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Microbiology, The Science
• The biology comes from bios referring to living
organisms and logy means the study of, thus biology is
the study of living organisms.
• Micro means very small, viewed by microscope
• Microbiology is the study of very small living organisms
called microorganisms or microbes, these include
bacteria, algea, protozoa, fungi and viruses.
• Because many scientist do not consider viruses as living
organisms, the terms infectious agents or infectious
particles are often used in reference to viruses
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Dr. Adnan S. Jaran
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• A disease causing microorganisms called pathogens
(3% of all known microbes)
• The others are non pathogenic (97%), the beneficial
microbes are 87%
• Microbes live on and in our bodies e.g. skin, in the mouth
and intestine are known as indigenous microflora (or
indigenous microbiota). Some of them cause disease
accidentally and known as opportunistic pathogens
(10%)
• Diseases caused by microbes are called infectious
disease
• Ubiquitous microbes means that they are virtually found
every where in or on the body and in different
environment of the globe
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• Many bacteria and fungi are Saprophytes, which aid in
fertilization by returning inorganic nutrients to the soil.
• Saprophytes break down dead and dying organic
materials (plants and animals) into nitrates, phosphates,
carbon dioxide, water and other chemicals necessary for
plant growth
• Saprophytes also destroy papers, feces and other
biodegradable matters, although they cannot break down
most plastics or glass
• Nitrogen-fixing bacteria, that live in the root nodules of
certain plants called legumes are able to return nitrogen
from the air to the soil in the form of ammonia for use by
other plants
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Introduction to Microbiology
The spread of certain diseases from one person to
another long ago suggested the existence of invisible,
transmissible agent of infection.
Microscopic organisms (microbes) were not seen,
however, until Antony Van Leeuwenhock (1632-1723)
made microscopes with sufficient magnification, then
after, the science of microbiology began.
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Leeuwenhock observed motile microorganisms taken
from a decayed tooth under the microscope. He
observed major morphological classes of bacteria i.e.
spheres, rods and spirals as well as large microbes i.e.
protozoa, algae and yeast. In 1767 and after the
convention of compound microscope, Linnaeus
distinguished 6 species of microbes assigned to one
class, and 600 types were figured in 1838.
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Spontaneous Generation
Until recent centuries it was widely believed that living
organisms can arise spontaneously in decomposing
organic matter. For visible organisms, this notion was
dispelled in the 17th century. When Redi demonstrated
that the appearance of maggots in decomposing meat
depended on the deposition of eggs by flies. However,
the idea of spontaneous generation persisted for the new
w o r l d o f m i c r o b e s .
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The answer for spontaneous generation has been shown
by Spallanzani (1729-1799) who introduced the use of
sterile culture media: he showed that an infusion of meat
would remain clear indefinitely if boiled and properly
sealed. Moreover, in 1837 Schwann showed that hot air
passed through tubes and enter the boiled flask will not
decompose the meat infusion. Pasteur in 19th century
demonstrated that meat infusion remain clear if it kept far
from air-dust and live germs. Since then, the
spontaneous generation notion no more accepted.
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Problem of Spores
* Pasteur succeeded because he used sugar and yeast
extract as infusion. Others used hay infusion and they
never reached clear infusion after boiling.
British physicist John Tyndall, brought a bale of hay to
his laboratory and after then he could no longer achieve
sterility, in the same room by boiling. Tyndall concluded
that the hay had contaminated his laboratory with
incredible kind of living organisms: one that could survive
boiling.
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In the same year, 1877, Ferdinand Cohn demonstrated
that resistant forms as small, refractile endospores as
showed that they where stages in the life cycle of the
hay bacillus (Bacillus Subtilis). Then after, autoclaving
(Sterilization by heat (120oC) & moisture under pressure)
showed to be killing spores.
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• In 20th century, biological studies of microbes showed
that there are different kinds of microbes, which found in
different ecological niches and have different actions,
Microbiology then developed into there groups: microbes
responsible for; fermentation, for diseases in man,
animals and plants, and for the cycle of organic matter in
the nature. These developments gave rise to applied
fields of industrial, medical microbiology.
and agricultural
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The Role Of Microbes In Fermentation
• The study of fermentation came early and start by use of
fermentation in preserving food through accumulation of
lactic acid (soured milk, cheese and silage).
• In 1830s, Schwann & others showed that microbes are
responsible for alcoholic fermentation by using grape
juice. In 1857, Pasteur showed that different kinds of
microbes are associated with different kinds of
fermentation (yeast in alcoholic fermentation and small
rods (lactobacilli) in lactic acid fermentation).
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• Fermentation refers to the microbial decomposition of
vegetable matters which contains mostly carbohydrates,
while putrefaction refers to the formation of more
unpleasant products by the decomposition of high
protein materials, such as meat and eggs.
• Pasteur on his studies on microbial fermentation,
developed the study of microbial metabolism or microbial
physiology. In particular, Pasteur showed that life is
possible without air, that some organisms (obligatory
anaerobic) are even inhibited by air.
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Selective Cultivation
By study fermentation, investigators showed that type of
substrate (media) affect growth of different microbes. In
alcoholic fermentation using grape juice (high sugar
concentration and low protein contents) lead to a condition
now known as low pH, that favors the out-growth of acid-
resistant yeasts and thus yields an alcoholic fermentation. In
contrast, in milk neutralizing of acid by high protein contents
favors the out-growth of faster-growing but more sensitive,
which cause a lactic acid-fermentation. Contamination of the
starting inoculum will affect the fermentation process and then
the end-products.
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Microbiology and Medicine
• The germ theory of disease:
The contagious diseases are transmitted or spread by
seeds (microbes) either directly or indirectly (transmitted
from diseased to healthy person).
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Transmission of Infection
• Demonstrated in 18th century by John Hunter, who inoculated
himself with pus-material from a patient with gonorrhea
(experimental animal was not used until 20 years later) and
used for transmission of the tuberculosis causative agent
(direct & indirect).
• The indirect transmission of disease was recognized later in
1840s, physician move with unwashed hands between patients
in hospitals lead to puerperal sepsis and cause of maternal
death. In London, John Snow showed that cholera agent is
spread through contaminated water with fecal matters.
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Recognition of Microbes as agents of Infection
• In 1836, Agostin Bassi showed that fungi cause
of a disease of silk worms and 3 years later
Schönlein discovered the association of fungus
with human skin disease (favus).
• The etiological role of bacteria in anthrax was
established by Robert Koch in1867 confirmed by
Pasteur and his colleagues.
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• Koch then isolated anthrax-bacillus in pure culture and
showed that culture could transmit the disease to mice.
Also Koch identified tubercle bacilli and introduced his
postulates for distinguishing a pathogenic from
adventitious microbes:
• 1- The microbe is regularly found in the lesions of the
disease.
• 2- It can be isolated in a pure culture on artificial media.
• 3- Inoculation of this culture produces a similar disease
in experimental animals.
• 4- The microbes can be recovered from the lesions in
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• In 1879, Albert Neisser discovered that the disease
gonorrhea is caused by Neisseria gonorrhea. In 1892,
Dimitri Ivanovisky discovered a virus called Tobacco
Mozaic virus.
• In 1910, Howard Rickets discovered an organism called
Rickettsia caused a disease named Typhus.
• In 1798, Edward Jenner used cowpox virus as a vaccine
to protect people from smallpox. Edward Gaffky
discovered that salmonella typhi cause Typhoid fever.
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• Leofler discovered that diphtheria is caused by
Corynebacterium diphtheriae.
• Ketasato discovered that the disease tetanus is caused
by Clostridium tetani.
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Microbiology Branches
Basic Microbiology:
1. Deal with all microorganisms.
2. Classification of microorganisms.
3. Visualization of microorganisms (microscopes &
staining).
4. Metabolism and metabolic pathways.
5. Nutrition, growth and its requirements.
6. Techniques of sterilization & the disinfection.
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Medical Microbiology
1. Is the study of organisms that cause diseases to
humans (pathogenic organisms).
2. The relationship between microorganism and the
disease, e.g. S. typhi cause typhoid fever.
3. Characteristics of microorganism causing disease,
and how microorganism cause disease as invasion of
tissue or by producing toxic products.
4. Mechanism of disease establishment called
Pathogenesis.
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5. Virulence factor of the microorganism called
Pathogenicity, e.g. ability to invade host tissue,
production of toxins as by-products.
6. Epidemiology of the disease, deal with source of the
disease and method of spread.
7. Diagnosis of disease, based on:
8. Proper sampling.
9. Stain and culturing.
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10. Recovery of pathogenic organism.
11. Treatment of the disease by antimicrobial agents,
e.g. antibiotics.
12. Prevention of infection: by vaccination & quarantine.
13. Control of infection: by isolation of human or animal,
and by proper treatment.
Food Microbiology:
1. Microorganism (M.O.) used in food processing and
ripening are not pathogenic.
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2. M.O. can cause food infection & poisoned food,
e.g. Staphylococcus aureus.
3. M.O. can cause Spoilage of food.
4. Preservation of food: drying, salting, freezing, jamming,
canning &
use of preservatives (chemicals such as sodium
benzoate & sodium nitrite). The method of preservation
must be suitable for the food type and must retain food
quality and prevent its destruction by M.O.
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Industrial Microbiology:
1. Deal with M.O. used in the industry.
2. Characteristics of the bacterial strains.
3. Maintain the bacterial strains unchanged.
4. Concern with quality of the products & its quantity.
5. Deal with storage condition of the products.
6. Shelf-life of the products: for how long the material
will be stored under proper condition without being
destructed or spoiled.
7. Mostly industrial microbiology use fermentation
process to produce certain product.
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Pharmaceutical Microbiology:
1. It’s the use of M.O. in the production of
pharmaceutical products such as antibiotics,
alcohols, enzymes and vitamins.
2. Deal with check of contamination and spoilage of
pharmaceutical preparation by adding preservative.
3. Use different sterilization techniques and
preservation of pharmaceutical products.
4. Proper use of antibiotic and chemotherapeutic
agent (give proper type of antibiotic in proper time for
proper organism in proper dose for proper duration).
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Agricultural Microbiology:
1. Deal with the N (nitrogen), C (carbon) and S
(sulfur) cycle in nature.
2. Fertility of soil.
3. Disease of plants.
4. M.O. in ruminants used for digestion in the rumen.
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Sanitary Microbiology:
1. Deal with proper disposal of sewage and garbage.
2. Disposal of waste and wastewater.
3. Safety of water and food.
4. Control of flies and vectors, e.g. mosquitoes.
Microbial physiology and genetics:
1. Research in microbial physiology lead to better
understanding of the functions of microbes
2. DNA structure and genetic manipulation with
virus and bacteria
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• Environmental microbiology (microbial ecology):
• It becomes important branch because the concern about
pollution of soil, air, water, sewage, food and dairy
products
• Also cycling of elements by microbial, environmental and
geochemical processes
• In addition, the biodegradation of toxic chemicals by
various microorganisms is being used as method for
cleaning up hazardous materials found in soil and water
