An Introduction To The Microbial World: Chapter One

An Introduction to The Microbial World
CHAPTER ONE
Microbiology:
Definition, Scope & Branches
Microbiology
▪ Study of microscopic organisms (microorganisms) and their activities
Form Taxonomy (classification, nomenclature, &

identification)
Structure Distribution in nature
Reproduction Relationship
Physiology Beneficial & detrimental effects on man &
environment
Metabolism Physical & chemical effects on man &
environment
Microbiology
▪ Microorganisms are organisms that are too small to be seen by the
unaided or naked eye and requires a magnification tool called the
microscope
▪ Zacharias Janssen – inventor of the first compound microscope
▪ How small is small? (<0.1 mm)
▪ Units of measurement
▪ 1 micrometer = 0.000001 or 10-6 m
▪ 1 nanometer = 10-9 m
▪ 1 Angstrom = 10-20 m
Microbiology
Microbial Population
▪ 87 % nonpathogens
▪ 10 % opportunistic
▪ 3 % pathogens
Microbiology
▪ Branches can be classified as pure and applied microbiology
Pure Microbiology
Bacteriology ✔ Microbial cytology Predictive microbiology
Mycology ✔ Microbial physiology Astro microbiology
Protozoology ✔ Microbial ecology Biological agent

Phycology/algology Microbial genetics Nano microbiology
Virology ✔ Generation microbiology Prion biology
Parasitology ✔ Systems microbiology Immunology ✔
Cellular microbiology Evolutionary microbiology
Nematology ✔ Molecular microbiology

Microbiology
▪ Branches can be classified as pure and applied microbiology
Applied Microbiology
Medical microbiology ✔ Veterinary microbiology
Pharmaceutical microbiology Environmental microbiology
Industrial microbiology Water microbiology
Microbial biotechnology Aero microbiology
Food microbiology Biotechnology
Agricultural microbiology
Medical Microbiology
▪ The study of pathogenic microbes and the role of microbes in human illness
▪ A branch of medical science concerned with the prevention, diagnosis, and
treatment of infectious diseases
▪ Includes study of microbial pathogenesis and epidemiology and is related
to the study of disease pathology and immunology
▪ Microorganisms that cause infectious diseases are bacteria, fungi,
viruses, protozoa, parasitic animals (helminths), and prions
▪ Also referred to as clinical microbiology or diagnostic microbiology
Main roles of a diagnostics or clinical microbiologists
▪ Isolate microorganism that cause disease

▪ Identify in humans
▪ Analyze
Knowledge of microbial structure and physiology is
extremely important to clinical microbiologists in three areas:
▪culture of organisms from patient specimens
▪classification and identification of organisms after they have been

isolated
▪prediction and interpretation of antimicrobial susceptibility patterns

Basis of most bacterial identification
✔Determination of their
staining characteristics
based on the differences Determines its
in cell wall structure susceptibility to various antibiotics
✔observing the metabolic

biochemical differences
✔Microscopic characteristics
▪ Bacteria
▪ Prokaryotes
▪ Unicellular organisms
▪ No nuclear membrane
▪ No organelles (e.g. mitochondria,

endoplasmic reticulum, Golgi apparatus)
▪ Example - Mycobacterium tuberculosis,

etiologic agent for pulmonary tuberculosis
(PTB)
▪ Medical Bacteriology
▪ Protozoa
▪ Eukaryotes
▪ Unicellular organisms
▪ Kingdom Protista
▪ Examples:
▪ Entamoeba histolytica - amoebiasis
▪ Giardia lamblia – Giardiasis or
traveler’s diarrhea
▪ Plasmodium falciparum – malaria
▪ Medical Parasitology
▪ Helminths
▪ Eukaryotes
▪ Multicellular organisms
▪ Kingdom Animalia
▪ Example - Ascaris lumbricoides, which
causes ascariasis
▪ Medical Parasitology
▪ Fungi
▪ Eukaryotes
▪ Kingdom Fungi
▪ Unicellular (yeast) or multicellular

organisms (mold)
▪ Example – Candida albicans (part of

human normal flora or biota)
▪ Medical Mycology
▪ Viruses
▪ Neither prokaryotes nor eukaryotes
▪ Classified based on their nucleic acid

content
▪ DNA virus or RNA virus

▪ Examples:
▪ Human immunodeficiency virus (HIV)
▪ Hepatitis B virus (HBV)
▪ Medical Virology
Microbial Systematics
Microbial Systematics
▪Systematics is the scientific study of the kinds and diversity of

microorganisms and their relationships
▪Taxonomy (Greek taxes: arrangement; Greek nomos: law) is the orderly
classification and grouping of organisms into taxa (categories); a tool of
systematics
▪Modern Terminology:
Systematics = Taxonomy = Classification
MICROBIAL TAXONOMY
Bergey’s Manual of Systematic Bacteriology
▪Bacteriologists most important reference in bacterial taxonomy

▪Main resource for determining the identity of prokaryotic organisms,
emphasizing bacterial species using every characterizing aspect
▪Sometimes referred to as Bacteriologist’s “bible”
▪First published in 1923 by David Hendricks Bergey
✔ classify bacteria based on their structural and functional
attributes by arranging them into specific familial orders
✔ to make this information accessible in the form of a key
MICROBIAL TAXONOMY
Three separate but interrelated areas of taxonomy:
1. Classification
2. Nomenclature
3. Identification
MICROBIAL TAXONOMY
CLASSIFICATION TAXA
organization of microorganisms that share similar:

✔ morphologic traits
✔ physiologic traits
✔ genetic traits
Classification
▪ Taxa (plural of taxon) are the categories or subsets in taxonomy
General Taxa Bacterial Classification Taxa

Domain Domain
Kingdom Kingdom
Phylum Division
Class Class
Order Order
Family Family
Tribe
Genus Genus
Species Species
Subspecies, serovarieties, biovarieties,
phage typing
The classification system is consists of the following
taxa designations:
▪Domain
✔reflects the characteristics of the cells that make up the
organism
▪Kingdom
▪Division
▪Class
✔ In prokaryotic nomenclature, the name of the class ends in the
suffix – ia
▪Order
✔ In prokaryotic nomenclature, the name of the order ends in the suffix –
ales
The classification system is consists of the following
taxa designations:
▪Family
✔ In prokaryotic nomenclature, the name of the family ends in the
suffix – aceae
✔ First letter of family name is capitalized
▪Tribe
▪Genus
▪Species
Species abbreviation:
sp. – singular
spp. – plural
The classification system is consists of the following taxa
designations:
▪subspecies (subsp.)– based on phenotypic differences
▪biovarieties (biovar) / biotype – based on biochemical results differences
▪serovarieties (serovar) – based on serologic differences
▪phage typing – based on susceptibility to specific bacterial phages
NOMENCLATURE
▪ bacteria are given names according to an official set of an

internationally recognized rules, the International code for the
Nomenclature of Bacteria
▪ naming of microorganisms according to established rules and
guidelines
▪ provides the accepted labels by which organisms are universally
recognized
NOMENCLATURE
▪binomial (two-name) system of nomenclature

✔ every organism is assigned a genus and species name of Latin
or Greek derivation
▪ Genus – always capitalized
▪ Species epithet – never capitalized
Ex. Escherichia coli
▪ Both components are always used simultaneously
▪They are printed in italics, or underlined in script.
Ex. Escherichia coli , Escherichia coli
NOMENCLATURE
▪Name may be abbreviated

✔ by using the proper case form of the first letter of the genus
designation
✔ followed by a period (.) and the full species name, which is never
abbreviated
Ex. E. coli
▪an informal designation (e.g. staphylococci, streptococci) may be
used to label a particular group of organisms, but such designations
are not capitalized or italicized
NOMENCLATURE
▪genus name followed by the word species may be used to refer to

the genus as a whole
Ex. Escherichia sp.
▪to eliminate confusion, the first two letters or the first syllable are
used when two or more genera names begins with the same first
letter
Ex. Staph, Strep
✔ for Staphylococcus and Streptococcus
Esch and Ent
✔for Escherichia coli and Entamoeba coli
Nomenclature
Family Names Scientific Names of Bacteria
Clostridiaceae Clostridium tetani

Corynebacteriaceae Corynebacterium diphtheriae
Enterobacteriaceae Escherichia coli

Mycobacteriaceae Mycobacterium tuberculosis
Neisseriaceae Neisseria gonorrhoeae

Streptococcaceae Streptococcus pyogenes
Nomenclature
▪Rules for denoting bacterial names
Scientific Names Abbreviations

Clostridium tetani C. tetani Clost. tetani
Escherichia coli (bacterium) E. coli Esch. coli
Entamoeba coli (protozoa) E. coli Ent. coli
Staphylococcus aureus S. aureus Staph. aureus
Streptococcus pyogenes S. pyogenes Strept.
pyogenes
Mycobacterium tuberculosis M. tuberculosis Myc.
tuberculosis
Classification By Cellular Type
Three distinct group of organisms based on cell organization and

function
▪ Archaebacteria
▪ Prokaryote
▪ Eukaryote
VARIOUS CATEGORIES OF MICROORGANISMS:

▪Those that are truly cellular:
▪ Prokaryotic
✔ Bacteria
✔ Archaeans
▪ Eukaryotic
✔ Algae
✔ Protozoa
✔ Fungi
VARIOUS CATEGORIES OF MICROORGANISMS:

▪Those that are acellular or often referred to as
infectious agent:
✔Viruses
✔Viroids
✔Prions
Classification by cellular type
Diversity of life is organized into three domains:
▪Domain Bacteria (Eubacteria)
▪Domain Archaea (Archaebacteria)
▪Domain Eukarya (Eukaryotes)

✔ Domain Bacteria (Eubacteria)
▪ prokaryotes
▪unicellular
▪organisms are broadly divided into three phenotypic categories
b. Those that are gram negative and have cell wall
c. Those that are gram positive and have cell wall
d. Those that lack a cell wall
▪ Pathogenic bacteria are prokaryotic cells that infect eukaryotic hosts
✔Domain Archaea (Archaebacteria)
▪ prokaryotes
▪ unicellular
▪ cell walls lack peptidoglycan that is why they are separated from
bacteria
▪ can be stain gram-positive or gram-negative
▪ cell walls composed of polymers
▪ structure of their cell envelope and enzymes allows them to survive
under stressful or extreme conditions
ex. Halophiles – salt-loving cells

Thermophiles – heat-loving cells
Anaerobic methanogens – give off swamp gas
▪ Domain Eukarya (Eukaryotes)
▪ Unicellular or multicellular
▪ Interior organization of eukaryotic cells is more complex than
prokaryotic cells
▪ Larger and contains organelles
✔ Algae
✔ Protozoans
✔ Fungi
✔ Plants
✔ Animals
IDENTIFICATION
▪ the process by which a microorganism’s key features are delineated

▪ Numeric taxonomy – used in which phenotypic characteristics are
assigned a numeric value
▪ Derived number indicates the genus and species of the bacterium
Classification By Genotype and Phenotype
▪Organisms are arrange based on the similarities and differences in:
Genotype
genetic make-up of an organisms or combinations of forms of
one or a few genes under scrutiny in an organism’s genome
Phenotype
readily observable physical and functional features of an
organism expressed by its genotype
Identification Criteria and Characteristics for
Microbial Classification
GENOTYPIC CRITERIA
- Methods are increasingly being used to identify bacteria
Examples Principles
an organism with G + C content of 50%
DNA base composition will not be closely related to an organism
ratio whose G = C content is 25%
Nucleic acid (DNA and the degree of similarity in the sequences

RNA) base sequence is a measure of the degree of organism
analysis relatedness
PHENOTYPIC CRITERIA
- Most of these methods do not require sophisticated equipment and
can easily be done anywhere
Examples Principles
Macroscopic Colonial characteristics such as:

morphology size, texture and pigmentation of bacterial colonies
Microscopic Size, shapes, intracellular inclusions, cellular

appendages and arrangement of cells when
morphology observed with the aid of the microscope
PHENOTYPIC CRITERIA
Examples Principles
Staining Ability of the organism to take up a particular color

characteristics with the application of specific dyes and reagents.
Ability of organism to grow at various temperatures,

Environmental in the presence of oxygen and other gases, at
requirements various pH levels, in the presence of other ions and
salts such as NaCl
PHENOTYPIC CRITERIA
Examples Principles
Nutritional Ability of organism to utilize various carbon and nitrogen

sources as nutritional substrates when grown under
requirements specific environmental conditions
Resistance Exhibition of a characteristic inherent resistance to

specific antibiotics, heavy metals, or toxins by certain
profile microorganisms
PHENOTYPIC CRITERIA
Examples Principles
Establishment of profiles of microorganisms by various
Antigenic serologic and immunologic methods that are useful for
properties determining the relatedness among various microbial
groups
Subcellular Establishment of the molecular constituents of the cell

that are typical of a particular taxon, or organism group,
properties by various analytic methods.
Among the most significant event in the early
history of microbiology were the development of:
✔microscopes
✔bacterial staining procedures
✔techniques that enabled microorganisms to be cultured
in the laboratory
✔steps that could be taken to prove that specific
microorganisms were responsible for specific infectious diseases
Historical Review of
Microbiology
Ancient Times
▪Existence of microorganisms were hypothesized for many
centuries before their actual discovery
▪Aristotle (384-322 BC)
• Ancient philosopher and naturalist
• Believed that living organisms could develop from non-living
materials
• Theory of Spontaneous Generation or Abiogenesis states that:
“life can arise spontaneously from non living material”
• He concluded that aphids, fleas, flies and even mice could
spontaneously form from other organic substrates
Ancient Times
▪Jainism
▪ Postulated the existence of unseen microbiological life which is
based on Mahavira’s teachings as early as 6th century
▪ Jain scriptures describe nigodas
• Sub-microscopic creatures living in large clusters and having a
very short life
• Said to be present in each and every part of the universe, even in
tissues of plants and flesh of animals
Ancient Times
▪Marcus Terentius Varro

▪ He warned against locating a home in the vicinity of swamps
▪ There are certain minute creatures which cannot be seen by the
eyes, which float in the air and enter the body through the mouth
and nose and there by cause serious diseases
Medieval Times
▪At the golden age of Islamic civilization, some scientists had

knowledge about microorganisms
• Ibn Sina in his book The Canon of Medicine
• Ibn Zuhr - discovered scabies mites
• Al-Razi - gave the earliest known description of smallpox in his
book The Virtuous Life (al-Hawi)
▪ Girolamo Fracastoro proposed that epidemic diseases were

caused by transferable seed-like entities that could transmit
infection by direct or indirect contact, or vehicle transmission
Early Modern Times
Robert Hooke (1635-1703)
▪Englishman
▪Used a primitive compound microscope (two
magnifying lenses)
▪Reported that life’s smallest units were little
“boxes” – cells
▪His work started the development of the Cell
Theory of Life, which states that:
▪ “all living things are composed of cells”
▪Made his first recorded microscopic
observation, of the fruiting bodies of molds
Early Modern Times
Anton van Leeuwenhoek (1632-1723)

▪“Father of Microbiology”
▪ Dutchman
▪ Probably the first person to observe and
accurately describe living
microorganisms
▪ Amateur scientist (not trained)
▪ Created single-lens microscopes
▪ Described microorganisms which we
know today as protozoa - called them
“beasties” or “animalcules”
Early Modern Times
Francesco Redi (1626-1697)
▪Italian
▪Opposed Theory of Spontaneous
Generation
▪Redi’s experiment:
✔ Jars (sealed and unsealed) with
decaying meat left for 3 days
✔ After 3 days, unsealed or open jars
contained maggots while sealed jars did
not contain maggots
Early Modern Times
Early Modern Times
John Needham (1713 – 1781)
▪English biologist
▪Believed in spontaneous generation and
argued that “microorganisms develop
spontaneously from fluids”
▪Needham’s experiment:
✔ Briefly boiling a broth mixture and then
cooling the mixture in an open container to
room temperature
✔ Later, the flasks would be sealed, and

microbes would grow a few days later.
Early Modern Times
John Needham (1713 – 1781)
▪Experiments seemed to show that there
was a life-generating force that produced
spontaneous generation
▪Today, it is now known that the boiling time
was insufficient to kill any endospores of
microbes
▪The cooling of flasks left open to the air
could have caused contamination
▪Did not use proper sterile technique
Early Modern Times
Lazzaro Spallanzani (1729-1799)

▪Italian scientist
▪Challenged and repeated John Needham’s

experiments
▪Using a slightly different protocol (with a longer

boiling time), Spallanzani did not have any
microbes grow in his sealed flasks, contradicting
Needham's findings
▪His experiment showed that imicrobes can be

destroyed by an hour of boiling
Early Modern Times
Early Modern Times
▪ Lazzaro Spallanzani (1729-1799)

▪ Microbes did not re-appear as long as the
material was sealed
▪ Proposed that air carried microorganisms to
the culture medium and that they could be
killed through boiling
▪ His experiments paved the way for research
by Louis Pasteur, who defeated the theory of
spontaneous generation almost a century
later
Early Modern Times
▪ Oliver Wendell Holmes (1809-1894)
▪ American physician
▪ Observed the apparent spread of

puerperal fever (Group B Streptococcus)
by healthcare providers
▪ Published findings with guidelines to

reduce transmission
▪ However, results largely ignored

Early Modern Times
Ignaz Semmelweis (1818-1865)
▪Hungarian physician
▪Described as the “savior of mothers”
▪Discovered that the incidence of puerperal

fever could be drastically cut by the use of
hand disinfection in obstetrical clinics
▪Proposed the practice of washing hands

with chlorinated lime solutions in 1847 while
working in Vienna General Hospital's First
Obstetrical Clinic
▪ Proposal was largely ignored

Golden Age of Microbiology
▪ From 1857 to 1914, saw the rise of the

first microbiologists
▪ Equipped with better microscopes and a
growing understanding of the scientific
method
▪ Identify the organisms responsible for
specific diseases in quick succession
▪ Rapid advances were brought about by
works of Louis Pasteur and Robert Koch
▪ Microbiology became a science
Edward Jenner (1749-1823)
▪English physician and scientist
▪“Father of Immunology”
▪Pioneer of smallpox vaccine, the world’s first

vaccine
▪Terms "vaccine" and "vaccination" are derived

from Variolae vaccinae (smallpox of the cow),
the term devised by Jenner to denote cowpox
▪Vaccination comes from Latin word vacca,

meaning cow
Edward Jenner (1749-1823)

▪Before Jenner’s discovery of the vaccine,
smallpox wiped out 90% of the American
Indians in the US and killed thousands in
Europe (smallpox epidemic during the late
1700)
▪Jenner laid the foundation for Louis Pasteur’s

work with other vaccinations
Rudolf Virchow (1821-1902)
▪German physician
▪Father of Modern Pathology
▪Refuted Theory of Spontaneous Generation
through Theory of Biogenesis states that:
“life arise from pre-existing life or life
comes from life”
▪His most widely known scientific contribution
is his Cell Theory of Life
Golden age of Microbiology
Rudolf Virchow (1821-1902)

•The three principles to the cell theory are
described below:
✔ All living organisms are composed of
one or more cells
✔ The cell is the basic unit of structure
and organization in organisms
✔ Cells arise from pre-existing cells
•Exceptions to this theory are the viruses and
prions
Louis Pasteur (1822 – 1895)

✔French chemist and biologist
✔numerous contributions to the newly
emerging field of microbiology
✔foundation of the Science of
Microbiology
✔a cornerstone of modern medicine
▪Dealt the fatal blow to the Theory of
Spontaneous Generation
▪ Devised a curve-neck or swan-neck

flask that prevented contaminated air
from reaching boiled beef broth
▪ Broth remained uncontaminated even
though exposed to air
▪ Very lucky – no endospores present, or
it would have failed
✔Pasteur discovered what occurs during alcoholic
fermentation
✔He also demonstrated that different types of
microorganisms produce different fermentation
products
✔For example:
o yeasts convert the glucose in grapes
to ethyl alcohol (ethanol) by
fermentation
o certain contaminating bacteria, such
as Acetobacter, convert glucose to
acetic acid (vinegar) by fermentation,
thus ruining the tastes of wine.
▪Pasteurization
A process that kills microbes (mainly
bacteria) in food and drink
Applies heat to remove microorganisms

responsible for spoilage
Pasteur’s process involved heating

liquids such as milk and wine between
60°C and 100°C
Killed mostly bacteria and molds

▪Germ Theory of Disease states that:
microorganisms can cause diseases
Proposed by Girolamo Fracastoro in

1546, however not widely accepted
More formal experiments on the

relationship between germ and disease
were conducted by Pasteur between
1860 and 1864
▪Germ Theory of Disease
Beverage contamination led Pasteur to the

idea that microorganisms infecting animals
and humans cause disease
Pasteur proposed preventing the entry of

microorganisms into the human body
Discovered the pathology of puerperal

fever and pyogenic vibrio in blood

▪Developed vaccines for rabies,
anthrax, chicken cholera and swine
erysipelas
▪Introduced the term aerobic and
anaerobic in describing the growth of
yeast at the expense of sugar in the
presence or absence of O2
Joseph Lister (1827-1912)
▪English surgeon
▪Pioneer of antiseptic surgery
▪Applied the germ theory to medical/surgical

procedures
▪Applying Louis Pasteur's studies

in microbiology, Lister championed the use of
carbolic acid or phenol as an antiseptic,
such that it became the first widely used
antiseptic in surgery
▪Phenol is the basic agent of Lysol

Joseph Lister (1827-1912)

▪Soaking of surgical instruments to phenol
▪Had proven that microorganisms cause

surgical infections (e.g. today’s scourge –
methicillin-resistant Staphylococcus aureus or
MRSA)
Robert Koch (1843-1910)

▪a German physician
▪Established Koch’s postulates
✔ proof of the germ theory of disease
▪Developed the methods of:
✔ Fixing
✔ Staining
✔ Photographing bacteria

▪discovered that Bacillus anthracis produces
spores, capable of resisting adverse conditions
▪discovered:
✔ Mycobacterium tuberculosis that causes
tuberculosis
▪ work on tuberculin (a protein derived
from Mycobacterium tuberculosis)
ultimately led to the development of a
skin test valuable in diagnosing
tuberculosis.
✔ Vibrio cholerae that causes cholera
▪ Developed methods of cultivating
bacteria on solid media
To grow bacteria, initially used solid
nutrients such as potato slices, and
through these, he observed individual
colonies of identical, pure cells
Later found out that potato slices were
not suitable media for all organisms, and
began to use nutrient solutions with
gelatin
▪Developed methods of cultivating bacteria
on solid media
Later realized that gelatin was not the
optimal medium for bacterial growth, as it
did not remain solid at 37°C
As suggested by Walther and Fanny
Hesse, he began to utilize agar to grow
and isolate pure cultures because
this polysaccharide remains solid at 37°
C, is not degraded by most bacteria, and
results in a transparent medium
▪ Robert Koch (1843-1910)
▪ Koch’s Postulates
▪ Discovery of Bacillus anthracis, the
etiologic agent of anthrax, led to the
formation of a generic set of
postulates which can be used in
determining the cause of infectious
diseases
▪ These postulates not only outlined a
method for linking cause and effect
of an infectious disease but also
established the significance of
laboratory culture of infectious
agents
KOCH’S POSTULATES:
1. The causative agent must be present in every case of the disease and
must not be present in healthy animals or humans.
2. The pathogen must be isolated from the diseased host animal or
human and must be grown in pure culture.
3. The same disease must be produced when microbes from that pure
culture are inoculated into healthy susceptible animals.
4. The same pathogen must be recovered from this artificially infected
host animal, and grown again in pure culture.
Associate
Isolate
Inoculate
Re-isolate
Exemptions to the Koch’s Postulates
1.Many healthy people carry pathogens but do not exhibit symptoms
of the disease - carriers
Examples
Gonorrhea – Neisseria gonorrhoeae
Typhoid fever – Salmonella enterica subsp. enterica serotype Typhi
Diphtheria – Corynebacterium diphtheriae

Epidemics of certain hospital-acquired infections (nosocomial
infections)
Pneumonia – e.g. TB pneumonia
Human immunodeficiency virus (HIV)
2.Some microbes are very difficult or impossible to grow in vitro in
artificial media
Examples
Viruses
Rickettsia spp.
Chlamydia spp.
Mycobacterium leprae – etiologic agent of leprosy
Treponema pallidum subsp. pallidum – etiologic agent of
syphilis
2.Some microbes are very difficult or impossible to grow in vitro in
artificial media
▪ Pure cultures of these pathogens are difficult to obtain
▪ However, many of these fastidious pathogens (those having
complex nutritional requirements) can be grown in culture of living
human and animal cells of various types
▪ Mycobacterium leprae – culture in Armadillos
▪ Treponema pallidum – culture in rabbit testes
▪ HIV proliferates in human lymphocyte cultures and chimpanzees
3.To induce disease from culture, the experimental animal must be
susceptible to the pathogen
▪ Animals such as rats are very resistant to microbial infections
▪ Pathogens are species specific (for example, pathogen that cause
cholera in humans does not cause cholera in hogs and vice versa)
▪ Human volunteers are difficult to find and ethical considerations
limit their use
▪ Researchers may only be able to observe changes caused by the
pathogen in human cells that can be grown in the laboratory
4.Certain diseases develop only when an opportunistic pathogen
invades a weakened host
▪ These secondary invaders or opportunists cause disease in a
person who is ill or recovering from another disease
▪ Examples include certain pneumonias and ear infections, which
may follow influenza
Ferdinand Cohn (1828-1898)
▪German biologist
▪Contributes to the founding of the science of

bacteriology
▪First to classify bacteria into four groups

based on shape (spherical, short rods,
threads, and spirals)
▪First to show that Bacillus can change from a

vegetative state to an endospore state when
subjected to an environment deleterious to
the vegetative state
John Tyndall (1820-1893)
▪English physicist
▪Found a way to eradicate the bacterial spores

that came to be known as Tyndallization or
fractional sterilization
▪Tyndallization historically was the earliest

known effective way to destroy bacterial
spores
▪Affirmed the germ theory against a number of

critics
▪Finally laid abiogenesis to rest

Julius Richard Petri (1852-1921)
▪German microbiologist
▪Generally credited with inventing the

Petri dish (1888)
▪Worked as an assistant to Robert Koch

Hans Christian Gram (1853-1938)
▪Danish bacteriologist
▪Noted for his development of the Gram

stain, making bacteria more visible under
the microscope
▪Gram stain plays a major role in classifying

bacteria – gram positive and gram
negative
▪ Dmitri Ivanovsky (1864-1920)
▪ Russian botanist
▪ Discovered viruses and one of the
founders of virology
▪ First evidence of viruses came from
experiments with bacterial filters that
had pores small enough to retain
bacteria
▪ In 1892, he used one of these filters
to show that sap from a
diseased tobacco plant remained
infectious to healthy tobacco plants
despite having been filtered
▪ Martinus Beijerinck (1851-1931)
▪ Dutch microbiologist and biologist
▪ One of the founders of virology
▪ In 1898, he independently replicated

Ivanovsky's experiments and became
convinced that the filtered solution
contained a new form of infectious
agent, which he named virus
▪ Beijerinck subsequently
acknowledged Ivanovsky's priority of
discovery
Paul Erlich (1854-1915)
▪ German physician
▪ Worked in the fields of hematology,
immunology, and antimicrobial
chemotherapy
▪ His laboratory discovered
arsphenamine (Salvarsan), the first
effective medicinal treatment
for syphilis, thereby initiating and also
naming the concept of chemotherapy
▪ Popularized the concept of a magic
bullet
▪ Paul Erlich (1854-1915)
▪ Also made a decisive contribution to

the development of an antiserum to
combat diphtheria
▪ In 1908, he received the Nobel

Prize in Physiology or Medicine for his
contributions to immunology
Era of Sophistication
Alexander Fleming (1881-1955)
▪ Scottish biologist and pharmacologist

▪ Associated with two major discoveries
–lysozyme (1923) and Penicillin G
(1928)
▪ Testing the nasal secretions from a
patient with a heavy cold, he found
that nasal mucus had an inhibitory
effect on bacterial growth
▪ This was the first recorded discovery
of lysozyme, an enzyme present in
many secretions including tears,
saliva, skin, hair and nails as well as
mucus
▪ On September 3, 1928, he returned to

his laboratory having spent August on
holiday with his family
▪ Before leaving, he had stacked all his

cultures of staphylococci on a bench
in a corner of his laboratory
▪ On returning, he noticed that one

culture was contaminated with a
fungus, and that the colonies of
staphylococci immediately
surrounding the fungus had been
destroyed
▪ Fleming grew the mold in a pure

culture and found that it produced a
substance that killed a number of
disease-causing bacteria. He
identified the mold as being from
the Penicillium genus, and, after some
months of calling it "mould juice",
named the substance it released
penicillin on March 7, 1929
▪ In 1940, Howard Florey and Ernst

Chain demonstrated its antibacterial
action in vivo
▪ In 1945, Fleming, Florey and Chain

shared the Nobel Prize in Physiology
and Medicine for the discovery of
penicillin
Molecular Biology
▪ In 1928, Frederick Griffith discovered
that traits of the "smooth" form
of Pneumococcus could be transferred
to the "rough" form of the same bacteria
by mixing killed "smooth" bacteria with
the live "rough" form
▪ In 1934, the electron microscope was

invented
▪ In 1943, Avery, Macleod, and

McCarthy identified DNA as the
transforming principle (transformation)
Molecular Biology
▪ In 1946, Lederberg and Tatum
observed bacterial conjugation in
Escherichia coli
▪ In 1951, Lederberg and Zinder

confirmed bacterial transduction
▪ In 1952, Alfred Hershey and Martha

Chase showed that DNA is
the genetic material of the T2 phage
▪ In 1953, Watson and Crick developed

the 3D model of DNA
Molecular Biology
▪ In 1958, Meselson and Stahl show

the semiconservative nature of DNA
replication
▪ In 1961, Jacob and Monod

developed the lac operon model - the
first determination of a mechanism by
which an environmental cue turns
on/off a gene
▪ In 1977, Fred Sanger developed a

method for determining the nucleotide
sequence of DNA
Molecular Biology
▪ In 1982, Prusiner discovered a new

type of infectious agent – an
infectious protein called prion
▪ In 1983, Montaigner and Gallo

identified HIV as the cause of AIDS
▪ In 1988, Kary Mullis developed the

method of DNA amplification called
polymerase chain reaction
History-Altering Microbes
▪ Plasmodium spp.
▪ Protozoa
▪ Etiologic agent of malaria
▪ Mosquito-borne infectious disease
▪ Thought to have killed Alexander the

Great in 323 BC
▪ Kills 2,000,000 people annually

▪ Yersinia pestis
▪ Bacterium
▪ Etiologic agent of bubonic plague
▪ Vector is oriental rat flea
▪ Three outbreaks
▪ Plague of Justinian (6th to 8th) killing
25M to 50M people worldwide
▪ Black Death (1347-1351) killed a
third of the human population
▪ Third plague pandemic (1855-1959)
killing 12M people (China and India)
▪ Smallpox virus
▪ Variola major
▪ Double-stranded DNA virus
▪ Directly transmissible disease
▪ 40% mortality rate
▪ Eradicated by vaccination in 1979

An Introduction To The Microbial World: Chapter One

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An Introduction to The Microbial World

Form Taxonomy (classification, nomenclature, &

Mycology ✔ Microbial physiology Astro microbiology

Protozoology ✔ Microbial ecology Biological agent

Parasitology ✔ Systems microbiology Immunology ✔

Cellular microbiology Evolutionary microbiology

Nematology ✔ Molecular microbiology

Medical microbiology ✔ Veterinary microbiology

Pharmaceutical microbiology Environmental microbiology

Industrial microbiology Water microbiology

Microbial biotechnology Aero microbiology

Food microbiology Biotechnology

Main roles of a diagnostics or clinical microbiologists

▪ Isolate microorganism that cause disease

▪culture of organisms from patient specimens

▪classification and identification of organisms after they have been

▪prediction and interpretation of antimicrobial susceptibility patterns

✔observing the metabolic

▪ No organelles (e.g. mitochondria,

▪ Example - Mycobacterium tuberculosis,

▪ Unicellular (yeast) or multicellular

▪ Example – Candida albicans (part of

▪ Neither prokaryotes nor eukaryotes

▪ Classified based on their nucleic acid

▪ DNA virus or RNA virus

▪Systematics is the scientific study of the kinds and diversity of

▪Bacteriologists most important reference in bacterial taxonomy

Three separate but interrelated areas of taxonomy:

organization of microorganisms that share similar:

General Taxa Bacterial Classification Taxa

▪ bacteria are given names according to an official set of an

▪binomial (two-name) system of nomenclature

▪Name may be abbreviated

▪genus name followed by the word species may be used to refer to

Family Names Scientific Names of Bacteria

Clostridiaceae Clostridium tetani

Enterobacteriaceae Escherichia coli

Neisseriaceae Neisseria gonorrhoeae

Scientific Names Abbreviations

Three distinct group of organisms based on cell organization and

VARIOUS CATEGORIES OF MICROORGANISMS:

VARIOUS CATEGORIES OF MICROORGANISMS:

Diversity of life is organized into three domains:

▪Domain Bacteria (Eubacteria)

▪Domain Archaea (Archaebacteria)

▪Domain Eukarya (Eukaryotes)

ex. Halophiles – salt-loving cells

▪ the process by which a microorganism’s key features are delineated

Nucleic acid (DNA and the degree of similarity in the sequences

Macroscopic Colonial characteristics such as:

Microscopic Size, shapes, intracellular inclusions, cellular

Staining Ability of the organism to take up a particular color

Ability of organism to grow at various temperatures,

Nutritional Ability of organism to utilize various carbon and nitrogen

Resistance Exhibition of a characteristic inherent resistance to

Subcellular Establishment of the molecular constituents of the cell

▪Marcus Terentius Varro

▪At the golden age of Islamic civilization, some scientists had

▪ Girolamo Fracastoro proposed that epidemic diseases were

Anton van Leeuwenhoek (1632-1723)

✔ Later, the flasks would be sealed, and

Lazzaro Spallanzani (1729-1799)

▪Challenged and repeated John Needham’s