Fundamentals of Microbiology

Course code: 4403

Delivered by: Dr. Mutiullah Khattak

 Course Outline
(3+1)

Unit 1. Overview
Microorganisms and their respective place in the living world.
Differentiation between prokaryotic and eukaryotic cells. Historical
development of Microbiology and its scope.
Unit 2. Classification of microorganisms
General Concepts: Classification, Nomenclature, Species, Diagnostic
Identification, Subtyping, New and Unusual species.
Unit 3. Life cycle
Morphology and life cycle of bacteria and viruses, Transformation,
transduction, conjugation
Unit 4. Microbial growth requirements
Growth, nutrition (physical and nutritional requirement and
nutritional types; sources of energy, C, N, H, O, S, P, H 2O, trace
elements, growth factors)
Media required and its composition, sterilization of media, growth
factors, optimum conditions, growth curve
Unit 5. Control of microorganisms by physical and chemical methods
Heat, radiation, sterilization, disinfection, moist heat and dry heat,
Low Temperatures, Filtration, Phenolics, Alcohols, Halogens, Heavy
metals, Quaternary Ammonium Compounds, Aldehydes, Sterilizing
Gases, Evaluating Effectiveness of chemical Agents.

Unit 6. General methods of studying microorganisms

Cultivation, isolation, purification and characterization of
Microorganisms.

Unit 7. Chemotherapeutic agents and antibiotics

Chemotherapeutic agents, Antibiotics and Resistance problems,
Mode of action of antibiotics and development of resistance.

Unit 8. Safety in Microbiology

Laboratory associated infections, Routes and sources of laboratory-
associated infections, classification of hazardous microorganisms.

Unit 9. Introduction to Modern Techniques in Microbiology

Diagnostic techniques, Fermentation techniques, automation in
microbiology.
Recommended Books

• Kathleen P. T., Arthur T. Foundations in Microbiology: Basic Principles McGraw-Hill Companies

(2001)
• Gerard J. J. Tortora, Funke, Berdell R.Christine L. Microbiology: An Introduction, Study Guide.
Benjamin-Cummings Publishing Company Case (2000).
• G. J. Tortora, B.R. Funke, C. L. Care, Microbiology: an introduction 8th Edition, , published by,
Pearson Education, USA (2004).
• I. E. Alcamo, Fundamentals of Microbiology, published by Jones & Bartlett Publishers, USA
(2001).
• J. G. Black Microbiology: principles & explorations, 6th Edition, published by J. Wiley & Sons,
USA, (2005).
• Tortora . Microbiology, an introduction (2006)
• Levinson.W Medical Microbiology and Immunology.(2000)
• Cheesbrough.M District Laboratory Practice in Tropical Countries 6th Edition (2000)

Laboratory Manual:

1. J. G. Cappuccino & N. Sherman Microbiology: a laboratory manual, published by Pearson

Education, USA (2004).
2. R. A. Pollack, L. Findlay, W. Mondschein, R. R. Modesto Laboratory Exercises in Microbiology,
2nd Edition, published by J. Wiley & Sons, USA.
• List of Practicals

• Brief demonstration for proper handling of apparatus /chemicals etc, lab

safety and maintenance.
• Brief demonstration of Principle and use of microscopy. An introduction to
compound microscopy, dark field microscopy, Phase contrast microscopy
and electron microscopy.
• Preparation, sterilization and distribution of culture media.
• Gram-staining, Acid fast staining, capsule staining, spore staining.
• Culturing of Aerobic microorganisms on different media, isolation of pure
colony and identification of the organisms using differential media.
• Culturing of Anaerobic microorganisms, isolation of pure colony and
identification of the organisms using differential media.
• Antibiotic sensitivity testing.
 What is Microbiology
The branch of biology dealing with the structure, function,
uses and modes of existence of microscopic organisms.

Branch of biology involving the study of microorganisms.

The scientific study of microorganisms.

 Organisms and biological entities studied
by microbiologists can be,
• Cellular
• Acellular
 Bacteria
• They are prokaryotes that are usually single-celled organisms.
• Most have cell walls that contain the structural molecule peptidoglycan.
• They are abundant in soil, water, and air and are also major inhabitants
of our skin, mouth, and intestines.
• Some bacteria live in environments that have extreme temperatures,
pH, or salinity.
• Although some bacteria cause disease, many play more beneficial roles
such as cycling elements in the biosphere, breaking down dead plant
and animal material, and producing vitamins.
• Cyanobacteria produce significant amounts of oxygen through the
process of photosynthesis.
 Archaea
• They are prokaryotes that are distinguished from
Bacteria by many features, most notably their unique
ribosomal RNA sequences.
• They also lack peptidoglycan in their cell walls and have
unique membrane lipids.
• Some have unusual metabolic characteristics, such as
the methanogens, which generate methane gas.
• Many archaea are found in extreme environments.
• Pathogenic archaea have not yet been identified.
 Protists
• They are generally larger than prokaryotes and
include unicellular algae, protozoa, slime molds,
and water molds.
• Algae are photosynthetic protists that together
with the cyanobacteria produce about 75% of
the planet’s oxygen.
• They are also the foundation of aquatic food
chains.
 Protozoa
• They are unicellular, animal-like protists that are usually motile.
• Many free-living protozoa function as the principal hunters and
grazers of the microbial world.
• They obtain nutrients by ingesting organic matter and other
microbes.
• They can be found in many different environments and some
are normal inhabitants of the intestinal tracts of animals, where
they aid in digestion of complex materials such as cellulose.

• A few cause disease in humans and other animals.

 Slime molds
• They are protists that are like protozoa in one stage
of their life cycle, but are like fungi in another.
• In the protozoan phase, they hunt for and engulf food
particles, consuming decaying vegetation and other
microbes.
• Water molds, as their name implies, are found in the
surface water of freshwater sources and moist soil.
• They feed on decaying vegetation such as logs and
mulch.
• Some water molds have produced devastating plant
infections, including the Great Potato Famine of 1846–
1847.
 Fungi
• Fungi are a diverse group of microorganisms that range from
unicellular forms (yeasts) to molds and mushrooms.
• Molds and mushrooms are multicellular fungi that form thin,
threadlike structures called hyphae.
• They absorb nutrients from their environment, including the
organic molecules that they use as a source of carbon and energy.
• Because of their metabolic capabilities, many fungi play beneficial
roles, including making bread rise, producing antibiotics, and
decomposing dead organisms.
• Other fungi cause plant diseases and diseases in humans
and other animals
 Viruses
• Viruses are acellular entities that must invade a host cell in
order to replicate.
• They are the smallest of all microbes (the smallest is 10,000
times smaller than a typical bacterium), but
their small size belies their power—they cause many
animal and plant diseases.
• They have caused epidemics that have shaped human
history.
• The diseases they cause include smallpox, rabies, influenza,
AIDS, the common cold, and some cancers
Historical events leading to the development of Microbiology
 The Scope of Microbiology

• Microbiology is one of the largest and most complex of the

biological sciences because it integrates subject matter
from many diverse disciplines.

• Microbiologists study every aspect of microbes—their

genetics, their physiology, characteristics that may be
harmful or beneficial, the ways they interact with the
environment, the ways they interact with other organisms,
and their uses in
industry and agriculture.
• Each major discipline in microbiology contains
numerous subdivisions or specialties that deal with
a specific subject area or field.
• In fact, many areas of this science have become so
specialized that it is not uncommon for a
microbiologist to spend an entire career
concentrating on a single group or type of microbe,
biochemical process, or disease.
 A Sampling of Fields and Occupations in Microbiology

A. Immunology
This branch studies the complex web of protective substances and
reactions caused by invading microbes and other harmful entities. It
includes such diverse areas as blood testing, vaccination and allergy.

A specialist in the CDC special pathogens unit reads a microscopic test to

screen for infection that is based on an immune reaction
 B. Public Health Microbiology and Epidemiology
These branches monitor and control the spread of diseases in
communities. Some of the institutions charged with this task are the
U.S. Public Health Service (USPHS) and the Centers for Disease
Control and Prevention (CDC). The CDC collects information and
statistics on diseases from around the United States and publishes it
in a newsletter.

Public health microbiologists examine mice and take samples to

determine if they carry the hantavirus, one of the emerging
pathogens that concerns the CDC.
 C. Biotechnology

This branch is defined by any process that harnesses the actions of living
things to arrive at a desired product, ranging from beer to stem cells. It
includes industrial microbiology, which uses microbes to produce and
harvest large quantities of such substances as vaccines, vitamins, drugs and
enzymes.

A biotechnology technician
prepares a bioreactor for vaccine production.
 D. Genetic Engineering and Recombinant DNA Technology

These interrelated fields involve deliberate alterations of the genetic makeup of

organisms to create novel microbes, plants, and animals with unique behavior and
physiology. This is a rapidly expanding field that often complements biotechnology.

A geneticist at the US
Department of Agriculture examines a wheat
plant that has been genetically engineered to
resist a fungal pathogen.
 The Origins of Microorganisms
The fossil record dating from ancient rocks and sediments points to
bacteria-like cells that existed at least 3.5 billion years ago. They were the
only form of life for half of the earth’s history.

Evolutionary time line

 The Cellular Organization of Microorganisms

Basic structure of cells and viruses

The six basic types of microorganisms
 Microbial Dimensions: How Small Is Small?

• The dimensions of macroscopic organisms are usually

given in centimeters (cm) and meters (m).
• Most microorganisms fall within the range of
micrometers (μm) and, sometimes, nanometers (nm)
and millimeters (mm).
• The size range of most microbes extends from the
smallest viruses, measuring around 10 nm and actually
not much bigger than a large molecule.
• Protozoans measure 3 to 4 mm and visible with the
naked eye.
 Microbial Involvement in Energy
and Nutrient Flow
• Earth’s temperature is regulated by “greenhouse gases,” such
as carbon dioxide and methane, that create an insulation
layer in the atmosphere and help retain heat. A significant
proportion of these gases is produced by microbes living in
the environment.
• Up to 50% of all organisms exist within and beneath the
earth’s crust in soil, rocks, and even the frozen Antarctic. This
enormous underground community of microbes is a major
force in weathering, mineral extraction and soil formation.
• Bacteria and fungi live in complex associations with plants.
They assist the plants in obtaining nutrients and water and
may protect them against disease. Microbes form similar
interrelationships with animals, notably as residents of
numerous bodily sites.
• A summer pond is heavily laden with surface scum that
reveals golden-colored diatoms and blue green bacteria in
strands (600X magnification)
• Even a dry lake in Antarctica, one of the coldest places on earth (-35°C),
can harbor microbes under its icy sheet. Here we see a red
cyanobacterium, Nostoc (3,000X), that has probably been frozen in
suspended animation there for 3,000 years. This is one kind of habitat
on earth that may well be a model for conditions on Mars.
• A rotting tomato being decomposed by a furry forest
of mold including Rhizopus, bearing tiny sacs of
spores on a stalk (250X).
 Human Use of Microorganisms

• Algae specialists peer from their biodiesel bioreactor, a

platform of hanging bags containing cultures of single-celled
algae (see inset 750X). Their research will test the capacity of
algae to mass produce oil that could be used as an alternative
to fossil fuels. So far, this alternate way of growing renewable
fuels looks very promising and may truly provide a “green”
source of energy.
• Workers remove waste from the Hanford Nuclear Facility in
Washington state that has been dangerously contaminated
with spent radioactive substances. The cleanup of this site is
expected to take several years. A newly discovered bacterium,
Shewanella (inset 5,000X), is being tested as a bioremediation
measure. It is capable of reducing and detoxifying even
dangerous elements such as uranium.
 Microbial Roles in Infectious
Diseases
• Worldwide infectious disease statistics. This
figure depicts the 10 most common infectious causes
of death.