LECTURES IN

MICROBIOLOGY

The Science of
Microbiology
CHAPTER 1

Prof. Clark Joy L. Barias

 Learning Objectives
At the end of this Chapter, the student should be able to:
 Define Microbiology and give the importance of the
study of Microbiology
 Name important persons with significant contribution
to the field of Microbiology
 Differentiate the various staining methods used to
visualize microorganism; and
 Classify the different types of culture media based on
their physical state, chemical composition, and
functional type.
 Scope of Microbiology

Microbiology
 Derived from the Greek words mikros (“small”), bios
(“life”), and logia or logos (“study of”).
 study of organisms too small to be seen by the
naked eye.

Microbes or Microorganisms
 commonly referred to as “germs” or “bugs”
 include bacteria, viruses, fungi, algae, protozoa and
helminths.
 Prions (“infectious proteins”) are recent addition.
 Categories of Microorganisms or
Microbes

• Cellular
 Prokaryotes (bacterias, cyanobacteria, and
archeans)
 Eukaryotes (fungi, protozoa, and algae)
• Acellular
 Virus
 Branches of Study

 Bacteriology study of bacteria

 Mycology study of fungi and yeast

 Virology study of viruses

 Parasitology study of parasitic protozoans and

helminths

 Immunology study of the humoral and cellular

immune response to disease
agents and allergens

 Phycology study of algae

 Specializations in Microbiology

 Epidemiology and Public Health Microbiology

distribution and spread of diseases and their control and prevention

 Food Microbiology
use of microbes in the production of food products and drinks

 Agricultural and Veterinary Microbiology

use of microbes to increase crop and livestock yield and control of
plant pests and animal diseases

 Environmental Microbiology
study of the beneficial and harmful effects of microbes on the
environment
 Importance of Microbiology

 First bacteria
 Photosynthesis and decomposition
 Human use of microorganisms
 Infectious diseases
 The Progenote

Evolutionary Timeline: Bacteria appeared 3.5 billion years ago

 Photosynthetic Microbes

Microbes are involved in photosynthesis and accounts for

>50% of earth’s oxygen.
Also involved in decomposition and nutrient recycling.
Beneficial Uses of Microbes

Extraction of copper from ore

Beneficial Uses of Microbes

Synthesis of drugs, hormones and enzymes

 Beneficial Uses of Microbes

Bioremediation is the use of microbes to degrade organic

matter in sewage and detoxify pollutants such as oil spills.
 Modern Uses of Microbes

 Biotechnology, the use of microbes as miniature

biochemical factories to produce food and chemicals is
centuries old.
 Genetic engineering makes use of molecular biology
and recombinant DNA techniques as new tools for
biotechnology.
 Gene therapy replaces missing or defective genes in
human cells through genetic engineering.
 Genetically modified bacteria are used to protect crops
from pests and freezing.
 Infectious Diseases
United States Public Health Service
(USPHS) - agency where notifiable
diseases are reported

Centers for Disease Control (CDC)-

collects disease data around the U.S.
and publishes the MMWR (Morbidity
and Mortality Weekly Report)

World Health Organization (WHO)-

medical arm of the U.N., monitors
diseases worldwide.

Worldwide infectious disease statistics

Microbial Taxonomy

Traditional Whittaker 5 Kingdom System

Microbial Taxonomy

Woese-Fox 3 Domain System

 Nomenclature

 Linnaeus introduced the binomial system of scientific

nomenclature
 Each organism has two names: the genus and species
epithet
 Italicized or underline
 Genus name is capitalized and species in lower case.
 Scientific Names
Staphylococcus aureus
describes clustered arrangement of cells and golden
yellow color of colonies

Escherichia coli
Honors the discoverer, Theodor Escherich and
describes its habitat, the colon.

After the first use, scientific names may be abbreviated

with the first letter of the genus and full species
epithet. (Ex: E. coli)
 General Characteristics

 Prokaryotes no nucleus and organelles

 Eukaryotes membrane bound nucleus

and organelles

 Acellular agents genomes contain either

DNA or RNA; newer agent
is proteinaceous
 Cell Types

Comparative cellular structures of microbes

 The Microbes
viruses protozoa

bacteria

bacteriophage

algae
cyanobacteria
spirochaetes

fungi
 Size of Microbes

Microbes vary in size ranging

from 10 nm (nanometers) to
100 mu (micrometers) to the
macroscopic.

Viruses in nm = 10-9 m (meter)

Bacteria in um = 10-6 m

Helminths in mm = 10-3 m
 Bacteria

Prokaryotes

Peptidoglycan cell walls

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Binary fission

Ex: Escherichia coli

 Archaea

Prokaryotes
Lack peptidoglycan
Live in extreme environments
(extremophiles)
Include:
 Methanogens
 Extreme halophiles
 Extreme thermophiles
 Fungi

Eukaryotes

Chitin cell walls

QuickTime™ and a
TIFF (Uncompressed) decompressor
Molds and mushrooms are needed to see this picture.

are multicellular

Yeasts are unicellular

 Protozoa

Eukaryotes

Mostly saprobes and

commensals
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
May be motile by means
of pseudopod, cilia or
flagella
 Algae

Eukaryotes
Cellulose cell walls
QuickTime™ and a
Photosynthetic TIFF (Uncompressed) decompressor
are needed to see this picture.
Produce molecular oxygen
and organic compounds
Part of food chain
 Helminths

Eukaryotes
Multicellular animals
Parasitic flatworms and QuickTime™ and a
TIFF (U ncompressed) decompressor
roundworms called are needed to see this pi cture.
helminths
Microscopic stages in life
cycles
 Viruses

Acellular
Obligate intracellular parasites
Genome consist of DNA or
QuickTime™ and a
RNA called Core TIFF (Uncompressed) decompressor
are needed to see this picture.
Core surrounded by protein
coat called Capsid
Virion may be enclosed in lipid
envelope
 Prions

Proteinaceous infectious
agents

Causes Bovine Spongiform

Encephalopathy (BSE) QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.

Also causes Creutzfeldt-

Jacob Disease (CJD)

An Emerging Infectious

Disease (EID)
 Microbiology As A Science

 Science a systematized body of knowledge

explaining the occurrence of natural phenomena
 Qualities of a scientist:
curiosity
open-mindedness
skepticism
creativity
objectivity
 Scientific Approach

 Deductive reasoning
starts with a general idea that are tested to
prove or disprove it.

 Inductive reasoning
starts with drawing patterns from specific
observations resulting in generalization.
 Scientific Method

 Hypothesis
 Laboratory experimentation or field Studies
 Data collection and analysis
 Conclusion, either reject or accept hypothesis
 Theory or Law
Microbiological Experiment
 Brief History of Microbiology

 The Microscope
 Spores and Sterilization
 Spontaneous Generation
 Aseptic Technique
 Germ Theory
The First Microscope

In mid-1600s, Robert Hooke

discovered the cell.
Microbes were first observed by
Antonie van Leeuwenhoek using
a simple microscope (ca. 1673)
Reported his “animalcules” to the
Royal Society of London
 MICROSCOPES
• MAGNIFIES OBJECTS (MAKES
OBJECTS LOOK BIGGER)
• HELP SCIENTISTS STUDY
OBJECTS & LIVING THINGS TOO
SMALL TO SEE WITH THE NAKED
EYE
 Ocular lens
(Eyepiece)
Body Tube

Nosepiece
Arm
Objectives

Stage
Stage Clips
Coarse Adjustment
Diaphragm
Fine Adjustment
Light

Base
Always carry a microscope with one hand
holding the arm and one hand under the base.
 3 Types of Microscopes
• simple microscope has only 1 lens.
compound microscope has 2 sets of
lenses. It can magnify things 100 -
200 times larger than they really are.
• electron microscope can magnify
objects up to 300,000 times. They
do not use lenses, but use electrons
to enlarge the image.
 PARTS OF A MICROSCOPE
1. ocular (lens) eyepiece
• the lens of the microscope that you
look through
2. course adjustment
• the large knob on the microscope
that you turn to bring the object
into focus
3. fine adjustment
• the small knob on the microscope
that brings the image into focus
 PARTS OF A MICROSCOPE

4. arm
• the part of the microscope
supporting the body tube
5. body tube
• the part that holds the eyepiece and
the objective lenses.
6. nosepiece
• the part at the bottom of the body
tube that holds the objective lenses
and allows them to be turned
7. high power objective lens
• the lens that magnifies the object
the greatest amount. (usually 40x)
8. Low power (scanner) objective lens
• the lens that magnifies the object
the least amount (usually used to find
the object; magnifies only 3x or 4x)

9. middle power objective lens

• the lens that usually magnifies the
object more than the scanner lens,
but less than the high power lens
(usually 10x to 20x)
10. stage
• the flat part below the
objectives lens where the slide
is placed
11. clip
• the part that holds the slide in
place so it doesn’t move
12. diaphragm
• the part that controls the
amount of light entering the
field of view
13. light source
• the lamp (or mirror) under the
stage that sends light through
the object being viewed.
14. base
• the bottom part that supports
the rest of the microscope
 Ocular lens
(Eyepiece)
Body Tube

Nosepiece
Arm
Objectives

Stage
Stage Clips
Coarse Adjustment
Diaphragm
Fine Adjustment
Light

Base
Always carry a microscope with one hand
holding the arm and one hand under the base.
 Field of View
• Field of view is the area (circle)
that you see when looking through
the eyepiece
Comparing Powers of Magnification

We can see better details with higher the

powers of magnification, but we cannot see
as much of the image.

Which of these images

would be viewed at a
higher power of
magnification?
What’s my power?
To calculate the power of magnification, multiply the power of the
ocular lens by the power of the objective.

What are the powers of

magnification for each of
the objectives we have on
our microscopes?
Fill in the table on
your worksheet.
 Calculating Magnification
1. Find the power of the lens. It is found on
the side of the lens. Magnification power of
a lens is always identified by the label of x
(10x, 1000x)
2. Multiply the power of the eyepiece by the
power of the objective lens.
3. Examples:
eyepiece obj. lens
10x times 100x
10x times 50x
10x times 40x
 Appearance of the Specimen
• Objects appear upside-down &
backward

• Movement appears to be in opposite

direction than actual movement 1
2

move slide
slide appears to move
2 1
 Evolution of Microbiology
• Middle and late 1800s, Louis Pasteur performed
countless experiments that led to his germ theory
of diseases.
 Postulated that microorganisms were in the
environment and could cause infectious diseases.
 He developed the process of pasteurization, which
kills microorganisms in different types of liquids, and
which became the basis for aseptic techniques.
 He also introduced the terms “aerobes” and
“anaerobes” and developed the fermentation process.
 Historical Contributions to the
field of Microbiology
• 1800s to the first decade of the 1900s came to be known
as “The Golden Age of Microbiology”
• Edward Jenner – discovered the vaccine for smallpox
• Joseph Lister – applied the theory to medical procedures
paving the for the development of aseptic surgery.
• Paul Ehrlich – discovered Salvarsan for the treatment of
syphilis.
 Heralded as the “magic bullet” of chemotherapy.
• Alexander Flemming – discovered the antibiotic penicillin
from the mold Penicillum notatum.
 Spores and Sterilization

 John Tyndall showed that some microbes in

dust and air were resistant to heat.
 Ferdinand Cohn discovered and described
endospores
 a resistant asexual spore that develops inside
some bacteria cells.
 Term “sterile” was introduced to mean the
complete removal of all life forms including
endospores
 Abiogenesis vs. Biogenesis

 “Spontaneous Generation” was an early belief

that living things can arise from vital forces
present in nonliving and decaying matter -
Abiogenesis
(Ex: maggots from meat or mushrooms from
rotting wood)
 The alternative hypothesis that living organisms
can arise only from preexisting life forms is called
“Biogenesis”
The Pros and Cons

Francisco Redi (ca. 1668)

 The Pros and Cons
 1745 -John Needham boiled nutrient broth into
covered flasks

Conditions Results
Nutrient broth heated All showed growth
then placed in sealed
flasks

From where did the microbes come?

Spontaneous generation or biogenesis?
The Pros and Cons

Louis Jablot
 The Pros and Cons

Franz Schultze and Theodor Schwann

The Pros and Cons

Louis Pasteur put an

end to Abiogenesis
debate with his

Goose Neck Flask

Experiment

He is the father of
Microbiology
 Louis Pasteur

 Showed microbes caused

fermentation
 Studied spoilage and
introduced “Pasteurization”
to prevent it
 Used cotton plugs in his
cultures to prevent air borne
contamination, devised
Aseptic Technique.
 Antiseptics and Hand Washing

 1860s - Joseph Lister used, carbolic acid, a

chemical antiseptic to prevent surgical wound
infections
 Ignaz Semmelweis, a Hungarian physician
introduced hand washing as a means of
preventing transfer of puerpueral sepsis in
obstetrical patients
 Germ Theory of Disease
 1876 - Robert Koch
provided proof that a
bacterium causes anthrax
using experimental steps
now called the Koch’s
Postulates

 He was the first to use agar

as solid culture medium in
bacteriology.
 Koch’s Postulates

 The microbe must always be present in every

case of the disease
 It must be isolated in pure culture on artificial
media
 When inoculated into healthy animal host it
should produce the same disease
 It must be isolated from the diseased animal
again
 Infection and Disease
 Infection the entry of a microbe into the host.

 Disease infection followed by the appearance of

signs and symptoms.

 Pathogen an infectious or disease agent.

 Saprobe a microbe that lives on dead or

decaying organic matter.

 Opportunistic pathogen
is a microbe that cause disease in immunocompromised hosts
or when the normal microbiota is altered.
 Emerging Infectious Diseases

 Occurrence of new diseases and increasing incidence of

old ones (EID)
 Factors:
(a) evolutionary changes in existing organisms
(b) spread of known diseases into new
geographic areas by modern transportation
(c ) ecological changes resulting in introduction of
unusual agents
(d) emergence of antimicrobial resistance
 Emerging Infectious Diseases
 West Nile Encephalitis, first diagnosed in Uganda in 1937;
appeared in New York City in 1999.
 Invasive Group A Streptococcus, also known as the “flesh eating
bacteria”
 Escherichia coli 0157:H7, causes “bloody diarrhea” and
hemorrhagic uremic syndrome (HUS)
 Bovine Spongiform Encephalopathy (BSE) or “mad cow” disease
caused by prions
 Acquired Immunodeficiency Syndrome (AIDS) caused by HIV and
Africa is hardest hit
 Anthrax caused by Bacillus anthracis was sensationalized in 2001
when spores were disseminated via the mail