CHAPTER 1 BIO461 Mac2019

CHAPTER 1
THE MICROBIAL WORLD AND

YOU : Introduction
1.1 Scope and subdivisions of Microbiology

1.2 Microbes in our lives
1.3 History of microbiology
1.4 Modern developments in microbiology
SCOPE AND SUBDIVISION OF MICROBIOLOGY
 Microbiology is the study of organisms beyond the scope of

human vision, particularly bacteria, viruses, algae, fungi (yeast
& molds), protozoa and microscopic algae.
 Since its founding in the 19th century, the science has largely
focused on the isolation, identification, and elimination of
pathogens from humans, animals, plants, food, and drinking
water.
 Microbiologists have also examined nonpathogenic forms,
seeking to understand their structure, function, and
classification in order to control or exploit their activities.
BIO461:DNA/UiTM CNS@2019
TYPES OF BACTERIA
MICROORGANISM •Singular : bacterium
•Simple
•Single-celled (unicellular)organism
•Genetic material enclosed in a nuclear membrane
•Bacteria cells are called PROKARYOTES
•Appear in several shapes : Bacillus/Coccus/Spiral/Star
shaped/Square shaped
• Formation : Pairs/Chains/Clusters
• Cell wall composed of peptidoglycan
• Reproduce by Binary fission
• For nutrition, bacteria use organic/inorganic
substances and some can manufactured their own
food.
• Bacteria can move @ “swim” by using appendages
called flagella.
TYPES OF ARCHAEA
MICROORGANISM
•Like Bacteria, consist of PROKARYOTIC cells
•But the cell walls lack peptidoglycan.
•Always found in extreme environments
•Divided into 3 groups:
• Methanogens – produce methane as a waste product
from respiration.
• Extreme halophiles (halo=salt ; philic = loving)- live in
extremely salty environments.
• Extreme thermophiles (therm = heat) – live in hot
sulfurous water
•Archaea are not known to cause disease in humans.
TYPES OF FUNGI
MICROORGANISM •Singular : fungus
•Fungi are EUKARYOTES
•Cells have a distinct nucleus containing the cell’s
genetic materials (DNA), surrounded by nuclear
membrane.
• Kingdom Fungi maybe Unicellular/Multicellular
• Cannot carryout photosynthesis
• Cell wall composed primarily of chitin.
• Ex.: mushroom, molds, yeasts etc.
• Reproduce by sexually/asexually
• For nutrition, they absorbs solution of organic
material from their environments.
• Slime molds have characteristics of both fungi and
amoebas.
TYPES OF PROTOZOA
MICROORGANISM
•Singular : protozoan
•Unicellular EUKARYOTIC microbes
•Move by pseudopods/flagella/cilia
•Appear in variety of shapes
•Live either as free entities or as parasites that absorbs
or ingest organic compounds from their environments.
• Ex. of protozoa, Euglena are photosynthetic.
• They use light source of energy and CO2 as their chief
source of carbon to produce sugars.
• Reproduce by sexually/asexually
TYPES OF ALGAE
MICROORGANISM
•Singular : alga
•Photosynthetic EUKARYOTES
•Single-celled (unicellular)organism
•Reproduce by sexual/asexual
•Cell wall composed of carbohydrate called cellulose
•Abundant in freshwater, saltwater, in soil and in
association with plants.
•As photosynthesizers, algae need light, water and CO2
but do not require organic compounds.
•Algae produce O2 and carbohydrates for others.
•Play important role in balance of nature.
TYPES OF VIRUSES
MICROORGANISM
•Very different from other microbes
•Small, only can be seen by EM
•Acellular (nor cellular)
•Simple
•Core made of by only ONE type of nucleic acid (DNA @
RNA)
•Core surrounded by protein coat @ enveloped
• Reproduce by ONLY by using cellular machinery of
other organisms.
• Considered as Parasites
• Viruses are NOT considered to be living because they
are inert outside living hosts.
MICROBES IN OUR LIVES
What is Microbes @ microorganisms :
minute living things that individually are
usually too small to be seen with the unaided
eye.
People tend to associate However, most of the
these small organisms only microorganisms make
with MAJOR DISEASES crucial
such as AIDS, uncomfortable CONTRIBUTIONS by
infections or such common helping to maintain the
inconvenience as spoiled balance of living
food. organisms and chemical in
our environment.
MINORITY are pathogenic (disease producing).
CONTRIBUTIONS to maintain the balance of living organisms and chemical
in our environment :
1 Marine & freshwater

microorganisms- basis 2 Soil microbes - help
of food chain in oceans, breakdown waste and
lakes and rivers. incorporate N gas from the
air into organic compound.
3
5
The food industry Certain microbes
uses microbes in play important roles
producing vinegar, in photosynthesis.
pickles, soy sauce,
cheese, yogurt,
bread and alcoholic 4
beverages. Human and animals depends on
microbes for digestion and synthesis of
some vitamins, organic acids, enzymes,
alcohols and many drugs.
NOMENCLATURE @ NAMING
• Established in 1735 by Carolus Linnaeus
• Scientific names are latinized
• Assign each organism two names
Genus (Plural : Genera) Specific epithet @ species
(first name and always capitalized) (not capitalized)
Examples :
Staphylococcus aureus @ S. aureus
Staphylococcus aureus @ S. aureus
• Both names are underlined or italicized
HISTORY OF MICROBIOLOGY
• Milestones in
Microbiology, highlighting
those that occurred
during the Golden Age of
Microbiology
The First Observations : Robert Hooke
• The history of biology occurred in 1665
with the help of a relatively crude
microscope.
• Robert Hooke observing a slice of cork,
and reported to the world that life’s
smallest structural units were “little
boxes” or “cells” as he called them.
• Using improved version of compound
microscope, Hooke was able to see
individual cells.
• Hooke’s discovery marked the beginning
of the cell theory – the theory that all
living things are composed of cells.
The First Observations : Anton van Leeuwenhoek
Anton van Leeuwenhoek was probably

the first actually to observe life
microorganisms through the
magnifying lenses of more than 400
microscopes he constructed.
1673-1723 : he wrote a series of letters to the Royal

Society of London describing the “animalcules” he
saw through his simple, single-lens microscope in
rainwater, his own feces and in material scraped from
his teeth.
Ignaz Semmelweis Francesco Redi
(1818-1865) (1626-1697)
1 1
2 2
3 3
Spallanzani (1729-1799) Joseph Lister(1827-1912)
1 1
2 2
Louise Pasteur
(1822-1895) Florence Nightingale
(1820-1910)
The Debate Over Spontaneous Generation (@ abiogenesis)
and biogenesis
• In the seventeenth century, some

scientists set out to determine
whether living organisms could
indeed arise through
spontaneous generation
(abiogenesis), or if they arose
only from other living organisms
(biogenesis).
“Living organisms arise from
preexisting life”, is called
biogenesis.
Evidence Pro and Con
1668: The Italian physician Francesco Redi filled six jars with
decaying meat.
Conditions Results
Jars covered with fine net No maggots
Open jars Maggots appeared
From where did the maggots come?

What was the purpose of the sealed jars?
Spontaneous generation or biogenesis?
1745: An Englishman, John Needham put boiled nutrient broth
into covered flasks.
Conditions Results
Nutrient broth heated, Microbial
before pouring it into sealed growth
flask
From where did the microbes come?
1765: An Italian Scientist, Lazzaro Spallanzani boiled nutrient
solutions in flasks.
Conditions Results
Nutrient broth placed in flask, heated, No microbial growth

then sealed
1861: A French Scientist, Louis Pasteur demonstrated that
microorganisms are present in the air.
Conditions Results
Nutrient broth placed in flask, Microbial growth
heated, not sealed
Nutrient broth placed in flask, No microbial growth
heated, then sealed
The Theory of Biogenesis
• Issue was still unresolved in 1858.
• Rudolf Virchow challenged the

case for spontaneous generation
with the concept of biogenesis, the
claim that living cells can arise only
from preexisting living cells.
• Arguments about spontaneous

Rudolf Virchow
generation continued until 1861,
when the issue was resolved by
the French scientist, Louise
Pasteur.
Louise Pasteur first experiment : He demonstrated that microorganisms are
present in the air and can contaminate sterile solutions, but the air itself does
not create microbes.
Pasteur’s experiment disproving the theory of spontaneous

1. Pasteur first poured beef broth into a long-necked flask.
2. Next he heated the neck of the flask and bent it into an S-shaped curve; then
he boiled the broth for several minutes.
3. Microorganisms did not appear in the cooled solution, even after long periods.
Results : Microbes in the air were the agents responsible for contaminating nonliving
matter such as the broths in Needham’s flasks.
Pasteur’s conclusion :
1 1. The bended neck allowed air
to enter the bottle and the
liquid but trapped any
particulates including
microorganisms.
2 2. No microbial growth as long

as the liquid broth did not
come in contact with the
microbes.
3. Hence air alone was not

3 sufficient to generate life.
The Golden Age of Microbiology
• 1857-1914
• Beginning with Pasteur’s work, discoveries included the
relationship between microbes and disease, role of immunity
in preventing and curing diseases, and antimicrobial drugs.
• Microbiologists studied the chemical activities of
microorganisms, improved the techniques for performing
microscopy and culturing microorganisms, developed
vaccines and surgical techniques.
Events occurs during the Golden Age
of Microbiology: Fermentation and Pasteurization
Fermentation is the conversion of
1 2 sugar to alcohol to make beer and
wine.
Pasteur showed that microbes

are responsible for
fermentation.
Bacteria that use alcohol and produce acetic acid spoil wine by turning
3 it to vinegar (acetic acid).
4 Microbial growth is also responsible for spoilage of food.
Fermentation and Pasteurization
Pasteur demonstrated that
these spoilage bacteria could
be killed by heat that was not
hot enough to evaporate the
alcohol in wine.
Pasteurization is the application of

a high heat for a short time.
The Germ Theory of Disease
1835:AGOSTINO 1840: IGNAZ 1860S: JOSEPH 1865: PASTEUR 1876: ROBERT

BASSI SEMMELWEIS LISTER KOCH
believed that
showed that a advocated hand used a chemical another silkworm proved that a
silkworm disease washing to prevent (phenol) disinfectant disease was bacterium causes
was caused by a transmission of to prevent surgical caused by a anthrax and
fungus. puerperal fever from wound infections after protozoan. provided the
one obstetrical looking at Pasteur’s experimental
patient to another. work showing steps, Koch’s
microbes are in the postulates, to
air, can spoil food, prove that a
and cause animal specific microbe
diseases causes a specific
disease..
• Koch thus established Koch’s
postulates, a sequence of
experimental steps for
directly relating a specific
microbe to a specific disease.
• During the past 100 years,
these same criteria have
Koch’s Postulates
been invaluable in
investigations proving that
specific microorganisms
cause many diseases.
Koch’s Postulates
Evidence required to establish
etiologic relationship between
STEP 1 microorganism and diseases:
Steps: The same

1.Microorganism must be
micro-organism
must be present
observed in every case of the
in every deceased
disease.
host.
2.It must be isolated and grown
in pure culture.
STEP 2
3.The pure culture when
Steps: The micro-
organism must be
inoculated in animals, must
isolated and
reproduce the disease.
cultured in the
laboratory and 4.Microorganism must be
accurately
described and recovered from the diseased
recorded.
animal.
Vaccination
• 1796: Edward Jenner
inoculated a person with
cowpox virus. The person was
then protected from smallpox.
• Vaccination is derived from
1796: Edward Jenner vacca for cow.
• The protection from disease
provided by vaccination (or by
recovery from the disease
itself) is called immunity.
The Birth of Modern Chemotherapy :
“Magic bullet”
• Treatment of disease by using chemical substances is
chemotherapy.
• Chemotherapeutic agents used to treat infectious disease can be
synthetic drugs.
• Antibiotics are chemicals produced by bacteria and fungi that
inhibit or kill other microbes.
• Quinine from tree bark was long used to treat malaria.
• 1910: Paul Ehrlich developed a synthetic arsenic drug, salvarsan,
to treat syphilis.
• 1930s: Sulfonamides were synthesized.
The Birth of Modern Chemotherapy
• 1928: Alexander Fleming
discovered the first
antibiotic.
• He observed that Penicillium

notatum fungus made an
antibiotic, penicillin, that
killed S. aureus.
• 1940s: Penicillin was tested

clinically and mass produced.
MODERN DEVELOPMENTS IN MICROBIOLOGY
New branches Recent advances in genomics, the study of The development of a set of
of microbiology an organism’s genes, have provided new new method called
were developed. tools for classifying microorganisms. recombinant DNA
techniques has
revolutionized research and
practical applications in all
areas of microbiology.
New branches of microbiology:
• Immunology is the study of
immunity. Vaccines and
interferons are being
investigated to prevent and cure
viral diseases.
• The use of immunology to
identify some bacteria according
to serotypes (variants within a
species) was proposed by
Rebecca Lancefield in 1933.
• Virology is the study of viruses.
• Recombinant DNA is DNA made from two different sources. In the
1960s, Paul Berg inserted animal DNA into bacterial DNA and the
bacteria produced an animal protein.
• Recombinant DNA technology, or genetic engineering, involves
microbial genetics and molecular biology.
• Ex. Tobacco Mosaic Virus (TMV)
Recombinant DNA Technology
• Microorganism can be genetically modified to
manufacture large amounts of human hormones
and other urgently needed medical substances.
• Ex. : Pail Berg at 1960s showed that fragments of
human or animal DNA that code for important
proteins can be attached to bacterial DNA. 
Resulting hybrid was the 1st example of
recombinant DNA.
• When recombinant DNA was inserted into
bacteria or other microbes, it can be used to
make large quantities of desired proteins.
Recombinant DNA Technology
The technique developed is label as recombinant DNA Techniques.
TWO RELATED FIELDS
1 2
Microbial genetic Molecular biology
specifically studies how genetic

Studies the mechanisms by
information is carried in molecules
which microorganisms inherit
of DNA and how DNA directs the
traits.
synthesis of proteins.
• Using microbes
– George Beadle and Edward
Tatum showed that genes encode
a cell’s enzymes (1942).
– Oswald Avery, Colin MacLeod,
and Maclyn McCarty showed that
DNA was the hereditary material
(1944).
– Francois Jacob and Jacques
Monod discovered the role of
mRNA in protein synthesis (1961).
Selected Novel Prizes in
Physiology & Medicine
1901* von Behring Diphtheria antitoxin

1902 Ross Malaria transmission
1905 Koch TB bacterium
1908 Metchnikoff Phagocytes
1945 Fleming, Chain, Florey Penicillin
1952 Waksman Streptomycin
1969 Delbrück, Hershey, Luria Viral replication
1987 Tonegawa Antibody genetics
1997 Prusiner Prions
* The first Nobel Prize in Physiology or Medicine.
Microbes And Human Welfare
Only MINORITY of all microorganisms are
pathogenic.
Microbe can cause food spoilage, such as soft
spots on fruits and vegetables, decomposition
of meats and rancidity of fats and oils are also a
MINORITY.
The vast MAJORITY of microbes benefit
humans, other animals and plants in many
ways.
1 Recycling Vital Elements
• Discoveries made by 2 scientist,
Martinus Beijerinck & Sergei
Winogradsky (1880s) : have formed
the the basis for today understanding
of the biogeochemical cycle that
support life on earth.
• Microbial Ecology : the study of the

relationship between microorganisms
and their environment.
Sewage Treatment : using microbes
2 to Recycle Water
• Sewage treatment plants remove the undesirable
materials and harmful microorganisms.
• Treatments combine various practical processeswith
the action of beneficial microbes.
• Large solid wastes such as paper, wood, glass and
plastic are removed from sewage ; left behind are liquid
and organic materials that bacteria convert into such
by-products as CO2, nitrates, phosphates, sulfates,
ammonia, H2S and methane.
Bioremediation : using microbes to
3 clean up pollutants
• Bacteria degrade organic matter in
sewage.
• Bacteria degrade or detoxify

pollutants such as oil and mercury.
• Ex. Bacillus, Pseudomonas
UN 2.1
4 Insects Pest Control by Microorganisms
• Microbes that are pathogenic to insects are
alternatives to chemical pesticides in preventing
insect damage to agricultural crops and disease
transmission.
• Bacillus thuringiensis infections are fatal in many
insects but harmless to other animals, including
humans, and to plants.
– By producing dusting powder that is applied on crops that insects
eat.
– Bacteria produce protein crystal that are toxic to the digestive
system of the insects
– Toxin gene inserted into the plant to make the insect resistant.
Modern Biotechnology and Recombinant
4 DNA Technology
• Biotechnology, the use of microbes to produce foods
and chemicals, is centuries old.
• Genetic engineering is a one of the new technique in
biotechnology. Through genetic engineering, bacteria
and fungi can produce a variety of proteins including
vaccines and enzymes.
• Last several years, revolution of recombinant DNA
technology have expand the potential of bacteria, virus,
yeast cell and other fungi as miniature biochemical
factories.
Modern Biotechnology and Recombinant
DNA Technology(continued)
• Another exciting and important outcomes of
recombinant DNA technique is gene therapy.
• Missing or defective genes in human cells can be
replaced in gene therapy.
• In agriculture, genetically modified bacteria and
recombinant DNA technique are used to protect
crops from insects and from freezing.
Microbes And Human Disease
• Microbes normally present in and on the human body are
called normal microbiota @ flora.
• Normal microbiota not only do us no harm but also in
some cases can actually benefits.
• Normal microbiota prevent growth of pathogens.
• Normal microbiota produce growth factors such as folic
acid and vitamin K.
• Resistance is the ability of the body to ward off disease.
• Resistance factors include skin, stomach acid, and
antimicrobial chemicals.
Several types of bacteria found as part of normal microbiota on human tongue
Biofilms
• In nature, microorganisms may exist as single cells that float or swim
independently in a liquid, or they may attach to each other and/or
some usually solid surface.
• Biofilm : a complex aggregation of microbes.
• Biofilm can be beneficial : to protect your mucous membrane from
harmful microbes etc.
• Biofilm can also be harmful : they can clot water pipes and cause
infections such as endocarditis (inflammation of the heart)
• Bacteria in biofilm are ofthen resistant to antibiotics because the
biofilm offers a protective barrier.
Infectious Diseases
• An infectious disease : is a disease in which
pathogens invade a susceptible hosts
(human/animals).
• Example : Malaria, Cholera etc.
Emerging Infectious Diseases (EID)
• When a pathogen overcomes the host’s
resistance, disease results.
• Emerging infectious diseases (EID) are not
disappearing but rather seem to be re-emerging
and increasing.
• EID - New diseases and diseases increasing in
incidence.
Factors contribute to the development of EIDS are :
• An increase number of incident in recent years highlight the extent of the

problem.
Emerging Infectious Diseases (Examples…)
• West Nile encephalitis (inflamation of the brain)
– West Nile virus
– First diagnosed in the West Nile region of Uganda in 1937
– Appeared in New York City in 1999
– The virus is carried by birds, is transmitted between birds, and
to horses and humans by mosquitoes.
• Bovine spongiform encephalopathy (BSE or mad cow
disease)
– Caused by an infectious protein called Prion
– Also causes Creutzfeldt-Jakob disease (CJD)
– New variant CJD in humans is related to cattle feed containing
protein
• Escherichia coli O157:H7
– Toxin-producing strain of E. coli
– First seen in 1982
– Leading cause of diarrhea worldwide
• Invasive group A Streptococcus
– Rapidly growing bacteria that cause extensive
tissue damage (so-called flesh-eating bacteria)
– Increased incidence since 1995
• Ebola hemorrhagic fever
– Ebola virus
– Causes fever, hemorrhaging, and
blood clotting
– First identified near Ebola River,
Congo
– Outbreaks every few years
• Humans can be infected with avian and other zoonotic influenza viruses
H5N1
Avian influenza virus subtypes A H7N9
H9N2
H1N1
Swine influenza virus subtypes A
H3N2
Influenza viruses type A - Influenza A viruses infect humans and many different
animals
Influenza viruses type B - Influenza B viruses only circulate among humans and
cause seasonal epidemics
Influenza viruses type C - Influenza C viruses can infect both humans and pigs but
infections are generally mild and are rarely reported.
• Influenza type A viruses are classified into subtypes according to the combinations of
different virus surface proteins haemagglutinin (H) and neuraminidase (N).
• There are 18 different haemagglutinin subtypes and 11 different neuraminidase
subtypes. BIO461:DNA/UiTM CNS@2019
• Severe acute respiratory syndrome (SARS)
– SARS-associated Coronavirus
– Occurred in 2002-2003
– Person-to-person transmission
• Cryptosporidiosis
– Cryptosporidium protozoa
– First reported in 1976
– Causes 30% of diarrheal illness in developing countries
– In the United States, transmitted via water
Fatal Epidemic Diseases
• Acquired immunodeficiency syndrome (AIDS)
– Human immunodeficiency virus (HIV)
– First identified in 1981
– Worldwide epidemic infecting 44 million people; 14,000 new infections every
day
– Sexually transmitted disease affecting males and females
– In the United States, HIV/AIDS cases: 30% are female and 75% are African
American
QUESTIONS…
Question Explain about spontaneous generations in
No.
details. How spontaneous generation
disproved? Give on example.
Question Explain the importance of Koch’s

No. Postulates in the germ theory of disease.
The End

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CHAPTER 1

THE MICROBIAL WORLD AND

1.1 Scope and subdivisions of Microbiology

 Microbiology is the study of organisms beyond the scope of

1 Marine & freshwater

Anton van Leeuwenhoek was probably

1673-1723 : he wrote a series of letters to the Royal

• In the seventeenth century, some

Jars covered with fine net No maggots

Open jars Maggots appeared

From where did the maggots come?

Nutrient broth placed in flask, heated, No microbial growth

Spontaneous generation or biogenesis?

• Rudolf Virchow challenged the

• Arguments about spontaneous

Pasteur’s experiment disproving the theory of spontaneous

2 2. No microbial growth as long

3. Hence air alone was not

Pasteur showed that microbes

4 Microbial growth is also responsible for spoilage of food.

Pasteurization is the application of

1835:AGOSTINO 1840: IGNAZ 1860S: JOSEPH 1865: PASTEUR 1876: ROBERT

STEP 1 microorganism and diseases:

Steps: The same

• He observed that Penicillium

• 1940s: Penicillin was tested

TWO RELATED FIELDS

specifically studies how genetic

1901* von Behring Diphtheria antitoxin

• Microbial Ecology : the study of the

• Bacteria degrade or detoxify

• Ex. Bacillus, Pseudomonas

• An increase number of incident in recent years highlight the extent of the

Question Explain the importance of Koch’s

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