Fundamental of

Lecture # 1
By Amir Afzal Khan
Early history of microbiology
• Robert Hooke
• Historians are unsure who made the
first observations of microorganisms,
but the microscope was available during
the mid‐1600s, and an English scientist
named Robert Hooke made key
observations.
• Robert Hooke FRS was an English
polymath active as a scientist and
architect, who, using a microscope,
was the first to visualize a micro-
organism.
Leeuwenhoek
• In the 1670s and the decades
thereafter, a Dutch merchant
named Anton van
Leeuwenhoek made careful
observations of microscopic
organisms, which he
called animalcules.
• Discovery of microorganisms in
1670s by van Leeuwenhoek
• Until his death in 1723, van
Leeuwenhoek revealed the
microscopic world to scientists of
the day and is regarded as one of
the first to provide accurate
descriptions of protozoa, fungi, and
bacteria.
theory of spontaneous generation

• After van Leeuwenhoek died,

the study of microbiology did
not develop rapidly because
microscopes were rare and
the interest in
microorganisms was not high.
• In those years, scientists
debated the theory
of spontaneous generation,
which stated that
microorganisms arise from
lifeless matter such as beef
broth.
This theory was disputed by Francesco Redi
Disproving spontaneous generation

• This theory was

disputed (un
clear)
by Francesco Redi,
who showed that
fly maggots do not
arise from
decaying meat (as
others believed) if
the meat is
covered to
prevent the entry
of flies.
Theory of biogenesis

• An English cleric
named John Needham
advanced spontaneous
generation, but Lazzaro
Spallanzani disputed
the theory by showing
that boiled broth would
not give rise to
microscopic forms of
life.
Louis Pasteur and the germ theory
 Germ theory of disease
• Pasteur postulated the germ theory of
disease, which states that microorganisms
are the causes of infectious disease.
• A series of swan‐necked flasks filled with
broth.
• He left the flasks of broth open to the air,
but the flasks had a curve in the neck so
that microorganisms would fall into the
neck, not the broth
• The flasks did not become contaminated
(as he predicted they would not), and
Pasteur's experiments put to rest the
notion of spontaneous generation. His
work also encouraged the belief that
microorganisms were in the air and could
cause disease.
•Louis Pasteur worked in the middle and late
1800s.
•He performed numerous experiments to
discover why wine and dairy products became
sour, and he found that bacteria were to blame.

•Pasteur called attention to the importance of

microorganisms in everyday life and stirred
scientists to think that if bacteria could make
the wine “sick,” then perhaps they could cause
human illness
Koch's postulates 
• The procedures used by Koch
came to be known as Koch's
postulates
• They provided a set of principles
whereby other microorganisms
could be related to other
diseases.
The development of microbiology
•  In the late 1800s and for the first decade of the 1900s, scientists
seized the opportunity to further develop the germ theory of disease
as enunciated by Pasteur and proved by Koch.
• There emerged a Golden Age of Microbiology during which many
agents of different infectious diseases were identified.
• Many of the etiologic agents of microbial disease were discovered
during that period, leading to the ability to halt epidemics by
interrupting the spread of microorganisms
• Despite the advances in microbiology, it was rarely possible to render
life‐saving therapy to an infected patient.
• Then, after World War II, the antibiotics were introduced to medicine.
The incidence of pneumonia, tuberculosis, meningitis, syphilis, and
many other diseases declined with the use of antibiotics.
• Work with viruses could not be effectively performed until
instruments were developed to help scientists see these disease
agents. 
Modern microbiology. 
• In the 1940s, the electron microscope was developed and perfected.
• In that decade, cultivation methods for viruses were also introduced,
and the knowledge of viruses developed rapidly.
• With the development of vaccines in the 1950s and 1960s, such viral
diseases as polio, measles, mumps, and rubella came under control
• Modern microbiology reaches into many fields of human endeavor,
including the development of pharmaceutical products, the use of
quality‐control methods in food and dairy product production, the
control of disease‐causing microorganisms in consumable waters, and
the industrial applications of microorganisms.
• Microorganisms are used to produce vitamins, amino acids,
enzymes, and growth supplements.
• They manufacture many foods, including fermented dairy
products (sour cream, yogurt, and buttermilk), as well as other
fermented foods such as pickles, sauerkraut, breads, and
alcoholic beverages.
• One of the major areas of applied microbiology
is biotechnology. In this discipline, microorganisms are used as
living factories to produce pharmaceuticals that otherwise could
not be manufactured.
• These substances include the human hormone insulin, the
antiviral substance interferon, numerous blood‐clotting factors
and clot dissolving enzymes, and a number of vaccines.
 MICROBIOLOGY
• It is the study of microscopic organisms
• Microbes are organisms that we need a microscope to see.
• They are very small forms of life, often times single celled organisms
so tiny that you need a microscope to see them.
• The lower limit of our eye's resolution is about 0.1 to 0.2 mm or 100 -
200 um (microns).
• Most microbes range in size from about 0.2 um to the 200 um upper
limit, although some fruiting bodies of fungi can become much
larger.
• Microbes belonging to different communities collectively are called
as microbiome
Microbes include several different species like bacteria, fungi, algae and protozoa that exist in the soil, most
abundantly found in the topsoil where food sources are plentiful.
THE FIELDS OF MICROBIOLOGY
• Bacteriology is the identification and characterization of bacterial
species.
• Mycology is the study of fungi, both in terms of their natural habitats
and genetics, and in terms of their ability to cause disease in humans,
other animals, and plants.
• Parasitology is the study of parasites of animals and humans. These are
all eukaryotic (not bacterial or archaeal) and include protists and
worms.
• Virology is the study of viruses and simple nonviral entities, such as
viroids (RNA molecules that behave like infectious agents) and prions
(proteins that behave like infectious agents)
• Medical microbiology is the study of pathogenic microorganisms that
cause infectious disease in humans and animals and ways to prevent
and treat infections.

• Aquatic, soil, and agricultural microbiology study the microorganisms

associated with aquatic (including wastewater treatment systems),
soil, and agricultural environments, respectively.

• Industrial microbiology applies the large-scale use of microorganisms

to make things like antibiotics or alcohol.
• Immunology is the study of the body’s response to infection by
microorganisms. Included within this field is the area of vaccine
research, which aims to develop more and better ways of immunizing
people from microorganisms that cause life-threatening infections.

• Microbial biochemistry aims to understand the enzymes and

chemical reactions inside microbial cells.

• Microbial biotechnology is genetically engineering microorganisms to

produce a foreign gene or pathway so that it may either make a
product for human use (for example, human insulin) or perform a
function that we need (for example, degradation of environmental
contaminants).
• Microbial ecology is the study of microbial diversity in nature, as well as
microbial populations and microbial communities and their effects on their
environments.
• This includes nutrient cycling and biogeochemistry (biological, chemical, and
physical processes that control the composition of the natural environment).

• Microbial genetics is the study of the genomes of microorganisms, including

how the genetic code varies between microbes and how genes are passed
on.

• Microbial systematics is the study of how microorganisms diversified

through time. It includes the naming and organizing of microbial groups with
respect to one another.
• Epidemiology is the study of health in populations to understand the
causes and patterns of health and illness.

• Etiology the study of the causes of diseases that cause a disease.

• Microbial metabolism is the means by which a microbe obtains the

energy and nutrients (e.g. carbon) it needs to live and reproduce.
From where microbes comes up?
Microbes make the oldest form of life on earth.
Нese have been around for more than 3.5 billion
years. From the past six million years, these
microbes are evolving together with humans.
Introduction to Some of the Important
Microbes
MICROORGANISUM
 1: Bacteria 
• Bacteria are typically unicellular,
microscopic, prokaryotic organisms
• The word prokaryote comes from the Greek
(pro) "before" and (karyon) "nut or kernel".
• They lacks a membrane-
bound nucleus (karyon), mitochondria, or
any other membrane-bound organelle that
reproduce by binary fission.
 Classification of Bacteria
• Archaea and Eubacteria are both prokaryotes,
meaning they do not have a nucleus and lack
membrane-bound organelles.
• All prokaryotes, are keep in kingdom Monera which
are further divided into eubacteria and
Archaebacteria
• They are tiny, single-cell organisms which cannot be
seen by the naked human eye called microbes.
• When we look at them through a microscope, we
find that archaea and bacteria resemble each other
in shape and size.
• They exist as rods, cones, plates, and coils.
• Both archaea and bacteria have flagella, thread-like
structures that allow organisms to move by
propelling them through their environment
 Eubacteria
• Eubacteria are microscopic single-celled
organisms.
• They are sometimes referred to as the
“true bacteria,” differentiating them from 
Archaebacteria, due to their metabolism
and preference for exotic environment.
• This makes them evolutionarily distinct
from other living organisms, and has led
to a number of innovative adaptations.
• e.g: E. coli (a common bacterium in the human
gut) and the cyanobacteria (blue-green algae).
Cyanobacteria
 Archaebacteria
• It is type of prokaryote, that is, a unicellular organism
 without a cell nucleus.
• They make up the kingdom Archae, one of the main
kingdoms of life. These organisms are difficult to classify
because they have similarities to both normal bacteria and
the larger eukaryotes.
• In structure, they are like unicellular prokaryotes, but the
genetic transcription and translation underlying their
creation is similar to that of the more complex eukaryotes.
• Live in a variety of environments, archaebacteria are
known as extremophiles.
• Certain species are able to live in temperatures above
boiling point at 100° Celsius or 212° Fahrenheit.
• They can also thrive in very saline, acidic, or alkaline
aquatic environments.
Why Archaebacteria differ then Bacteria?
Food for Microorganisms
• Microorganisms are classified as autotrophs or heterotrophs based on whether or
not they require pre-formed organic matter.
• Autotrophs derive energy from either light absorption (photoautotrophs) or
oxidation of inorganic molecules (chemoautotrophs). In most of the light reactions
the bacteria are fixing carbon dioxide into organic carbon, just as green plants do.
• Some photosynthetic bacteria (photoheterotrophs) require pre-formed organic
matter as reducing agents, but generate ATP from the absorption of light energy.
• Finally, some bacteria and fungi (heterotrophs) used pre-formed organic matter as
both a source of energy to generate ATP and as a source of carbon for the cell, just
as animals do.  
 
Antisepsis, Disinfectants, Sterelization
• Antisepsis ( Greek anti, against, and sepsis putrefaction)
• Putrefaction involves the action of bacteria on the tissues of
the body.
• The process of decay or rotting in a body or other organic matter.
• Antispsis is the destruction or inhibition of microorganisms on
living tissue; it is the prevention of infection or sepsis
• Antiseptics are chemicals agents applied to tissue to prevent
infection by killing or inhibiting pathogen growth: they also
reduce the total microbial population
• An antiseptic is a chemical that is applied to living tissue to kill or
inhibit microorganisms.
• Iodophors, chlorhexidine, and the alcohols (ethanol and isopropanol) are
commonly used antiseptics
• A disinfectant is a chemical that is applied to inanimate objects to kill
microorganisms.
• Bleach (sodium hypochlorite), phenolic compounds, formaldehyde,
hydrogen peroxide liquid, ortho-phthalaldehyde, and quaternary
ammonium compounds are examples of currently used disinfectants.
• Neither antiseptics nor disinfectants have complete sporicidal activity.
• A sterilant is a chemical that is applied to inanimate objects (a thing that is not
alive, such as a rock, a chair, a book) to kill all microorganisms as well as spores.
• Ethylene oxide, glutaraldehyde, hydrogen peroxide gas, and peracetic acid are
examples of sterilants.
• Sterilization ( Latin sterilis, unable to produce offspring)
• Is the process by which all living cells, spore and acellular entities( e.g viruses, viroids,
and prions) are either destroyed or removed from an object or habiatat.
• A sterile object is totally free of viable microorganisms, spores and other infectious
agents
• When sterilization is achieved by a chemical agent, the chemical is called a steriliant.
• Sanitization is closely related to disinfection.
• In sanitization, the microbial population is reduced to levels that are
considered safe by public health standards.
• For example sanitizers are used to clean eating utensils in restaurants.
• According to the CDC, sanitizing refers to lowering the number of
germs on a surface to a safe level, "as judged by public health standards
or requirements." This process works either through cleaning (which
physically removes germs from surfaces) or disinfecting (which kills
germs).
• Sanitizing is generally a little more gentle than disinfecting.
• What is the principal and conditions of autoclaving?
• The autoclave works on the principle of moist heat sterilization where
steam under pressure is used to sterilize the material present inside the
chamber.
• When this steam comes in contact on the surface, it kills the microbes by
giving off latent heat. The condensed liquid ensures the moist killing of the
microbes.
• The autoclave must reach and maintain a temperature of 121° C for at least
30 minutes by using saturated steam under at least 15 psi of pressure.
• Increased cycle time may be necessary depending upon the make-up and
volume of the load.