Module 1 Unit 1-3 Merged

MODULE 1 IN
CLINICAL BACTERIOLOGY
MLS 223
Department of Medical Laboratory Science

SCHOOL OF NATURAL SCIENCES
Prepared by:
Kathyren C. Estimada, RMT, MSMT
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MODULE 1
INTRODUCTION TO MICROBIOLOGY
At the end of the module, you should be able to:
1. outline the development of microbiology as a science with emphasis on the

contributions made by several persons/scientists
2. name the various groups of microorganisms, and, along with viruses, describe
their basic characteristics and practical uses
3. define taxonomy and outline the various levels in the taxonomic classification
scheme to show how microbes are organized
4. describe the binomial system of nomenclature and show how microbial

names are written
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MODULE 1
Unit 1:
Microbiology Terminologies and Historical Background
Unit Learning Outcomes:

1. Define the science of microbiology and other common terms used in
microbiology.
2. Relate the historical background of microbiology.
Engage
Microbiology (Gk: micro: “small”; bio: “life”; logia “study of”) has often been
defined as the study of life forms that individually are too small to be seen clearly
by the unaided eye—or that is without magnification. Such organisms organisms
are collectively referred to as microorganisms or microbes. The group includes
bacteria, fungi (yeasts and molds), protozoa, algae, and helminths. It also
includes viruses, viroids, and prions which are described as noncellular entities.
Rationalize why viruses, viroids, and prions are more correctly referred to as
acellular entities or agents rather that microorganisms.
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Explore
The Diversity of the Microbial World.

Source: Talaro, K. P., & Chess, B. (2018). Foundations in Microbiology (10th ed.). McGraw Hill.
Most often, the word microorganism, microbes, or germs gives a negative

connotation such as disease and food spoilage. However, only a small fraction
of microorganisms cause disease. The majority of microorganisms actually make
crucial contributions by helping to maintain the balance of living organisms and
chemicals in our environment. They also have many commercial applications
such as in the synthesis of such chemical products as vitamins, organic acids,
enzymes, alcohols, and many drugs.
Microbiology is one of the largest and most complex of the biological sciences
because it deals with many diverse biological disciplines. One may specialize in
the study of specific types of microorganisms or the so-called “disciplines of
microbiology”.

Microbiology Disciplines by Organism or Agent Studied.

Source: Pommerville, J. C. (2018). Fundamentals of microbiology (11th ed.). Burlington: Jones & Bartlett Learning.
Explain

Bacteriology is a discipline of
Microbiology that deals with the study of
the structure, functions, and activities of
bacteria (sing. bacterium). The bacteria
are considered as the smallest
microorganisms. They are unicellular that
exhibit considerable degree of variations
A. B.
as to size and shape. Bacteria are
enclosed in cell walls that are largely A. Staphylococcus aureus
B. Pseudomonas aeruginosa
composed of a carbohydrate and Source: Willey, J. M., Sherwood, L. M., Woolverton, C. J., &
protein complex called peptidoglycan. Schneegurt, M. (2008). Study guide to accompany Prescott,
Harley, and Klein's Microbiology, 7th ed. New York: McGraw-Hill
They generally reproduce by dividing into Higher Education.
two equal cells; this process is called
binary fission. Currently, the bacteria are
divided into two major groups, the:
a. Eubacteria or “true bacteria”, to which disease-

causing bacteria belong to.
b. Cyanobacteria formerly called the “blue-green
algae”, distributed worldwide in marine and fresh
water. Bacteria that belong to this group can
manufacture their own food by photosynthesis; Cyanobacteria.
Source: Madigan, M. T.,
hence are photosynthetic. However, the Martinko, J. M., Bender, K. S.,
photosynthetic pigments, chlorophyll, are not Buckley, D. H., & Stahl, D. A.
(2015). Brock biology of
contained in chloroplast, instead in specialized microorganisms. Boston:
lamellae called thylakoids. Pearson.
The current science of bacteriology includes the study of Archaebacteria

which are the earliest or ancient type of bacteria. They are inhabitants of
environments that are something like the earth 3.86 billion years ago (hot,
salty, low in organic material, etc.), so they are described as
extremophiles. They are divided into three main groups. The methanogens
produce methane as a waste product from respiration. The extreme
halophiles (L. salt-loving) live in extremely salty environments. The extreme
thermophiles (L therm: heat) live in hot sulfurous water. Although they
share the cellular configuration of bacteria, with the outbreak of
molecular techniques, they are otherwise not related to each other, so
are now renamed Archaea.
Mycology is the study of fungi (sing. fungus). Fungi are a group of nonmotile and
non-photosynthetic organisms whose cell wall is chiefly made up of chitin. They
absorb ready-made nutrients from their environment, including the organic
molecules that they use as a source of carbon and energy. The group include
the microscopic yeasts and molds, and the macroscopic mushrooms. However,
as a discipline of Microbiology, Mycology only includes the study of microscopic
forms which are either:
A.
a. Unicellular - the yeasts reproduce asexually by
budding. During budding, the daughter cell
protrudes on the surface of the parent cells and
becomes free or detached.
b. Multicellular - molds, consists of fundamental unit

structure called called the hypha (pl. hyphae) B.
which grows as long, threadlike filaments that may
bear spores. Individually, hyphae are microscopic
in size. However, when large numbers accumulat,
brach and interlace with each other — they form
a fuzzy mass called a mycelium (pl. mycelia) that
is visible to the naked eye.
A. A typical budding yeast.
B. Penicillium mold under
10x objective.
Parasitology studies certain organisms — parasites, that live at the expense of

another organism (host). Parasites exist as unicellular organisms of microscopic
size such as some protozoa. Others, such as some helminths and arthropods are
multicellular and are mostly macroscopic. Hence, among the three, the diverse
science of Microbiology only includes the study of protozoa, Protozoology.
Protozoology is the science of protozoa which is a group of animal-like,

unicellular, non-photosynthetic microorganisms that lack cell wall. Whereas
others are nonmotile, most are motile and possess varied types of locomotory
organelle including:
a. Pseudopodia (Gk. false feet) are temporary cytoplasmic extensions
which confer movement to amoeba (pl. amoebae or amoebas),
protozoans under the subphylum Sarcoastigophora. An example is
Entamoeba histolytica, a parasitic, pathogenic amoeba.
b. Flagellum (pl. flagella) (L. whiplike) is a long, whiplike appendage seen

among protozoans under subphylum Mastigophora or are collectively
called flagellates such as the pathogenic Giardia lamblia.
c. Cilia (sing. cilium) (L. eyelash) are short, hairlike processes surrounding
the protozoa. A ciliate of medical significance is Balantidium coli which
are classified under the Phylum Ciliophora.
A fourth major group of protozoa, the sporozoa, particularly those

grouped under the Phylum Apicomplexa, are strict parasites that are
usually immobile; most of these reproduce sexually and asexually in
alternate generations.
A. B. C. D.
A. Entamoeba histolytica trophozoite (pseudopodia: arrow)
B. Giardia lamblia trophozoite
C. Balantidium coli trophozoite
D. Plasmodium falciparum gametocyte
Virology encompasses the study of viruses (sing. virus) and their effects on living
cells of all types. Viruses are a group of minute particles that parasitize living
things. They are described as ultramicroscopic, hence can only be observed
with an electron microscope. Being very small particles, they were also once
referred to as filterable agents since they are able to pass through bacteriologic
filter (with a pore diameter of 0.22 or 0.45 µm) that normally retain bacteria.
Viruses lack a cell structure. That is, a virus do not possess a cytoplasm, neither a
cell membrane, nor a nucleus, rather, they are composed of:

a. Nucleic acid. Of which, viruses posses only a single type, either

deoxyribonucleic acid (DNA) of ribonucleic acid (RNA), rarely both.
Viral nucleic acid may be single-stranded or double stranded. Thus,
there are four possible configurations: (1) ssDNA, (2) dsDNA, (3) ssRNA,
(4) dsRNA.
b. Capsid. The viral capsid is a protective protein coat that surrounds the
nucleic acid. It consists of repeating units of proteins called
capsomeres.
Together, the nucleic acid core and the capsid is called nucleocapsid.
The nucleocapsid may be enveloped or non-enveloped (naked). The
envelope is the outer membrane layer made up of glycoproteins from the
virus and lipids derived from the host cell membrane.
The Components of Viruses.

(A) Naked viruses consist of a nucleic
acid genome (either DNA or RNA)
and a protein capsid. Capsomere
units are shown on one face of the
capsids. Spikes may be present on
the capsid.
(B) Enveloped viruses have an envelope

that surrounds the nucleocapsid.
Source: Pommerville, J. C. (2018).

Alcamo's Fundamentals of Microbiology
(11th ed.). Burlington: Jones & Bartlett
Learning.
Viruses are obligate intracellular

parasites. That is, they require a host
cell to survive and replicate. Viruses
utilize the host’s machinery to
synthesize proteins or produce
energy. Every organism on earth A. B.
(humans, animals, plants, and even
bacteria) is believed to be A. The structure of a bacteriophage.
B. A false-color transmission electron micrograph of a
susceptible to viral infection. bacteriophage.
Specifically, viruses that infect Source: Pommerville, J. C. (2018). Fundamentals of
microbiology (11th ed.). Burlington: Jones & Bartlett Learning.
bacteria are called bacteriophages (or simply phages).
Phycology (Gr. “phykes”: seaweed) is the study of the

various types of algae (L. “algae”: seaweed), hence the
science is also known as Algology. Similar with fungi, algae
is a group of unicellular and multicellular organisms which
are described as “plant-like” due to their photosynthetic
ability.
a. U n i c e l l u l a r a l g a e i n c l u d e d i a t o m s a n d
dinoflagellates which are microscopic. The typical colonial green
alga, Volvox.
Source: Carroll, K. C. (2016).
b. Multicellular algae consists of macroscopic Jawetz, Melnick & Adelberg's
seaweed which have been distinguished from medical microbiology (27th
ed.). New York: McGraw-Hill
plants by their lack of roots, leaves, or stem. Education.
Only 2 human illnesses are caused by algae:
1. Protothecosis is caused by Prototheca which is believed to be variant

of green alga Chlorella. The most common manifestation of
protothecosis is the formation of skin ulcers.
2. Paralytic shellfish poisoning has been associated

with dinoflagellates, subdivision of Pyrophyta.
Dinoflagellates produce a neurotoxin that cause
paralysis, occasionally a fatal condition, in man
following consumption of contaminated shellfish.
Danger increases during seasons favored for algal
multiplication (algal blooms). Their pigment impart
a characteristic red color to the water they
SEM of the dinoflagellate
inhabit, a phenomenon known as red tide, and is Gymnodinium (4000x).
indicative of a great abundance of neurotoxin of Source: Carroll, K. C. (2016).
Jawetz, Melnick & Adelberg's
shellfish in the region. Paralytic shellfish poisoning is medical microbiology (27th
not always associated with red tide, since algae ed.). New York: McGraw-Hill
Education.
populations too small to change the water color
are still dangerous.
Elaborate
The Historical Background of Microbiology: A Summary
We know that human pathogens have existed for thousand of years because
damages caused by them have been observed in the bones of mummies
and human fossils such as those in tuberculosis, syphilis, as well as parasitic
infections.
Although Microbiology claims very early roots, the science did not really
develop in a systematic way until the nineteenth century. In this part of the
unit module, we retrace some highlights in the history of microbiology now
and describe a few of the major contributors following the three traditional
divisions of Western history — Antiquity (Ancient Civilization), Medieval period,
and Modern period.
Ancient Civilization. In ancient Egypt and China, laws concerning public

health have already in place. People during the Classical period practice
such laws in order to prevent occurrence and spread of diseases. Some of
the practices noted include isolation of the sick, burying of waste materials,
prohibition of eating animals who died of natural causes and practice of
personal hygiene by simply washing and keeping clean.
Medieval Period. In European history, the Middle Ages, or Medieval period,
lasted from the 5th to the 15th century. There was general stagnation of
culture and learning for almost 1000 years. Knowledge about public
sanitation and transmission of disease was lost. Most people believed that
diseases were caused by curses from gods. This was followed by epidemics of
smallpox, syphilis, rabies and other diseases which prompted people to
search for explanations.
Modern Period. In contrast to the pre-modern era, Western civilization made

a gradual transition from premodernity to modernity when scientific
methods were developed which led many to believe that the use of science
would lead to all knowledge, thus throwing back the shroud of myth under
which pre-modern peoples lived. New information about the world was
d i s c o v e r e d v i a e m p i r i c a l o b s e r v a t i o n , v e r s u s t h e h i s t o r i c u s e
of reason and innate knowledge. The modern era began approximately in
the 16th century.
Even before microorganisms were seen, some investigators suspected

their existence and responsibility for disease. Among others was:

Girolamo Fracastoro (Fracastorius), an Italian

physician. During the 1500’s, he was able to observe
occurrence of epidemics of syphilis and typhus. As
such, in 1546, in his book De Contagione, he proposed
that epidemic diseases are caused by tiny particles
that transmit infection by direct or indirect contact, or
even without contact over long distances. In fact, the
name syphilis was derived from Fracastoro’s 1530 epic
poem in 3 books about a shepherd named Syphilus.
First Observation of Microorganisms
Anton van Leeuwenhoek. He was an unlikely scientist, was a

tradesman from Holland, came from a family of tradesmen. He
apprenticed as a draper (fabric merchant), learned to grind lenses
and made simple microscopes and began observing with them. In
1667, he first observed live bacteria using a simple microscope.
Leeuwenhoek discovered bacteria, protozoans, microscopic algae
and nematode. He described hundreds of what he thought were
tiny, living animals which he called “animalcules”. Using his device
he was also able to observe sperm cells, blood cells, and much
more. He opened up an entire world of microscopic life to the
awareness of scientists and in the 17th century convinced scientists
of the existence of miroorganisms. He was thus named Father of
Microbiology. However, Leeuwenhoek did not speculate on the
origin of those microorganism nor associated them with the cause
of disease.
A. B. C.
A. Anton van Leeuwenhoek (1667)

B. A replica of the microscope made and used by Leeuwenhoek.
C. Leeuwenhoek’s drawings of animalcules (bacterial cells).
Source: Pommerville, J. C. (2018). Fundamentals of microbiology (11th ed.). Burlington: Jones &
Bartlett Learning.
The Origin of Microorganisms
For several hundreds of years, many scientists and philosophers

believed that some forms of life could arise spontaneously from
nonliving matter (i.e. life could develop from non-life) they called
this hypothetical process spontaneous generation (also known as
abiogenesis).
The first serious attack on the idea of spontaneous generation was
made in 1668 by Francesco Redi, an Italian physician and poet. At
that time, it was widely held that maggots arose spontaneously in
rotting meat. Redi believed that maggots developed from eggs laid
by flies. o test his hypothesis, he set out meat in a variety of flasks,
some open to the air, some sealed completely, and others covered
with gauze. As he had expected, maggots appeared only in the
open flasks in which the flies could reach the meat and lay their
eggs. As he had expected, maggots appeared only in the open
flasks in which the flies could reach the meat and lay their eggs. In
spite of his well-executed experiment, the belief in spontaneous
generation remained strong.
Francesco Redi and his experiment to refute Spontaneous Generation.

Source: Pommerville, J. C. (2018). Fundamentals of microbiology (11th ed.).
Burlington: Jones & Bartlett Learning.
The Theory of Spontaneous Generation was debated upon for

about two centuries (roughly from 1650 to 1850). The theory of
spontaneous generation was finally laid to rest in 1859 by a powerful
opponent in the person of the young French chemist, Louis Pasteur.
In 1864, the French Academy of Sciences sponsored a contest for
the best experiment either proving or disproving spontaneous
generation. With his experiment, Pasteur had both refuted the
theory of spontaneous generation and convincingly demonstrated
that microorganisms are everywhere - even in the air.
Other contributions of Louis Pasteur include:
a.

(1)He proposed the biological process of FERMENTATION.

French emperor, Napoleon III asked Pasteur to investigate
the diseases afflicting wine which were causing
considerable economic losses to the wine industry. In 1864,
Pasteur demonstrated that wine diseases are caused by
some bacteria (Acetobacter) which may change alcohol
into acetic acid.
(2) Pasteurization Technique. Application of mild heating to
kill spoilage- and disease-causing microorganisms. In the
classic pasteurization treatment of milk, the milk was
exposed to a temperature of about 63oC for 30 minutes,
called the holding method. Since then, this technique has
long been employed to alcoholic beverages, milk and
other dairy products.
(3) Development of Vaccines (1880 - 1890). Today, a
vaccine is described as an antigenic material used to
Above: Louis Pasteur
stimulate an individual’s immune system to develop
Below: Louis Pasteur’s immunity against a pathogen. Vaccination, on the other
“swan-necked” flask.
Source: Tortora, G. J., Funke,
hand, is the administration of a vaccine. Pasteur discovered
B. R., Case, C. L., Weber, D., the method of attenuation of microorganisms that is the
& Bair, W. (2020).
Microbiology: An introduction
basis of vaccination (chicken cholera, anthrax, rabies).
(12th ed.). Upper Saddle (4) Pasteur postulated the Germ Theory of Disease — he
River: Pearson.
concept that specific infectious disease is caused by a
specific microorganism.
The defeat of a. Non-sterile liquid is poured

spontaneous out into a flask.
generation: Pasteur’s
swan-necked flask b. The neck of the flask was
experiment. heated in a flame until it
Source: Madigan, M. T., became pliable, and bent it
Martinko, J. M., Bender, K. into the shape of an S.
S., Buckley, D. H., & Stahl,
D. A. (2015). Brock a. b. c. c.Liquid was sterilized by
Biology of heating.
Microorganisms(14th ed.).
d. The liquid cooled slowly.

Air could enter the flask, but
airborne microorganisms
could not - they would settle
by gravity in the neck. As
Pasteur had expected, no
d. microorganisms grew.
e. When Pasteur tilted the

flask so that the broth
reached the lowest point in
the neck, where any airborne
particles would have settled,
e. the broth rapidly became
cloudy with life.
Robert Koch is a German scientist and is Pasteur’s

contemporary. The following are is most notable
contributions:
(1) He studied anthrax, a disease of cattle that occasionally
occurs in humans. In his experiments, he used diseased and
healthy mice as experimental animals. He injected a small
amount of blood from a diseased mouse into a healthy
mouse and the disease anthrax was quickly transferred. He
took blood from the second mouse injected it into another,
and again obtained the characteristic disease symptoms.
Robert Koch. German
physician and microbiologist. (2) In 1881, following the formulation of media chiefly made
Source: Madigan, M. T., up of meat extract and protein digests, he developed the
Martinko, J. M., Bender, K. S.,
Buckley, D. H., & Stahl, D. A. first methods for growth of pure cultures of microorganisms for
(2015). Brock Biology of which he was named as the Father of Bacteriologic
Microorganisms(14th ed.).
Glenview, Illinois: Pearson Techniques. He was able to accomplish this feat alongside his
Education. colleagues:
Fanny Hesse - use of agar to solidify culture media
Richard Petri - fashioned the Petri dish
Paul Ehrlich - introduced the use of aniline dyes for
staining microorganisms
(3) In 1882, he discovered the bacterium that causes tuberculosis,
Mycobacterium tuberculosis.
(4) In 1884, on the basis of his other experiments, he formulated the
criteria, now known as Koch’s postulates, for proving the germ
theory of disease.
The Koch’s postulates for

proving cause and effect in
infectious diseases.
Source: Madigan, M. T., Martinko,
J. M., Bender, K. S., Buckley, D.
H., & Stahl, D. A. (2015). Brock
Biology of Microorganisms(14th
ed.). Glenview, Illinois: Pearson
Education.
Control of Infections
Before the germ theory of disease was conceptualized and given
experimental support by Robert Koch, it was widely believed that these
organisms were responsible, but definitive proof was lacking.
Discoveries in sanitation provided indirect evidence for the
importance of microorganisms in causing human diseases.
Ignaz Philipp Semmelweis is a Hungarian

physician employed in Vienna General
Hospital in Austria. During his practice in
the rain institution, he observed the high
incidence of maternal mortality (death
following delivery) due to puerperal
fever. In 1847, he proposed that the
incidence could be drastically cut by
use of hand washing standards in
obstetrical clinics. In particular, he
suggested hand washing in chlorinated
Ignaz Semmelweis (background center left) believed if lime solution. After which, the incidence
hospital staff washed their hands, cases of puerperal fever of maternal mortality declined from up
would be reduced.
Source: Pommerville, J. C. (2018). Fundamentals of to 30 % to 1 upto <5%, earning himthe
Microbiology (11th ed.). Burlington: Jones & Bartlett Learning. title “Savior of Mothers”.
Joseph Lister, an English surgeon, used

the antiseptic properties of phenol in his
pioneering technique of antiseptic
surgery. Lister decided that the wounds
themselves had to be thoroughly
cleaned. He then covered the wounds
with a piece of rag or lint covered in
phenol, or carbolic acid as he called it.
The skin irritation caused by continual
exposure to phenol eventually led to the
substitution of aseptic (ger m-free)
Joseph Lister (center). techniques in surgery.
Source: Pommerville, J. C. (2018). Fundamentals of
Microbiology (11th ed.). Burlington: Jones & Bartlett Learning.
The Birth of Immunology
Edward Jenner introduced the first successful vaccination.

From the early days of his career Edward Jenner had been
intrigued by country-lore which said that people who
caught cowpox (vaccinia virus) from their cows could not
catch smallpox (variola virus). He wondered if intentionally
giving cowpox to people would protect them against
smallpox This led him to undertake the most important
research of his life. In 1798, he published a pamphlet on his
Edward Jenner.
Source: Pommerville, J. C.
work, prominent physicians confirmed his findings within a
(2018). Fundamentals of 1.3 The
few years, his Classical
method Golden
of Age of Microbiology
vaccination (1854–1914)
spread through
Microbiology (11th ed.).
Burlington: Jones & Bartlett
Europe and abroad. He was named as the Father of
Learning. Vaccination.
Edwarddid.Jenner’s
Again, hallmarks
experiment ofwhich a scientist—keen obser- of
led to the practice
vational skills and insight—led to a therapeutic
vaccination.
One day in May 1796, a dairy maid, Sarah Nelmes came to his office
intervention against disease.
with lesions of cowpox evident on her hand. Jenner took material from the
lesionsCONCEPT
and scratched
AND(variolated)
REASONING it into theCHECKS
skin of a boy, James Phipps.
The boy1.4soonEvaluate
developedthea slight fever, but recovered.
effectiveness Six weeks
of variolation after the
and vac-
variolation he inoculated the young boy with material from a smallpox
cination as ways to produce disease resistance.
lesion. Within days, the boy developed a reaction at the site but failed to
show any sign of smallpox. He then repeated his experiments with other
children, including his own son. His therapeutic technique of vaccination
(vaccaThe Stage
= “cow”) workedIsinSet
all cases and eliminated the risks associated
with variolation
During the early years of the 1800s, several events
The last naturally occurring case of smallpox (Variola minor) was
occurred
diagnosed on 26 that
Octoberhelped
1977. set the stage for the coming
“germ revolution.” In the 1830s, advances were

made in microscope optics that allowed better reso-

lution of objects. This resulted in improved and
FIGURE 1.6 The First Vaccination against
E lie
more Metchnikoff
widespread observations (Ilya
of tinyMechnikov)
living organ-
Smallpox. Edward Jenner performed the first vaccina-
tion against smallpox. On May 14, 1796, material from a i n t r o d u c e d t h e c
isms, many of which resembled short sticks. o n c eInpfact,t of
cowpox lesion was scratched into the arm of eight-year- phagocytosis.
in 1838 the GermanItbiologist became ChristianclearEhrenberg that
old James Phipps. The vaccination protected him from blood cells were also important in
suggested these “rod-like” looking organisms be
smallpox. immunity (cellular immunity) when Elie
called bacteria (bakterion = “little rod”).
Metchnikoff discovered in 1882 that
someTheblood Swiss physician
leukocytes Jacob Henlecould reported in
engulf
Prominent physicians confirmed his findings, disease-causing 1840 that living organisms could cause
bacteria. Hedisease.
called
and within a few years, Jenner’s method of vac- these This was strengthened
cells phagocytes in 1854and by Filippo
the Pacini’s
process
cination spread through Europe and abroad. By p h
discovery of rod-shaped cholera bacteria in astool
a g o c y t o s i s ( f r o m G k . p h gein
1801, some 100,000 people in England hadinbeen meaning
samples from eating).
cholera patients. Still, scientists
Elie Metchnikoff (1845 - 1916) shown here at work his
vaccinated.
laboratory. President Thomas Jefferson wrote to debated whether bacterial organisms could cause
Source: Willey, J. M., Sherwood, L., Woolverton, C. J.,
Jenner,
Prescott, “You
L. M., have erased
& Willey, J. M.from thePrescott's
(2011). calendarmicrobiology.
of human disease because such living organisms sometimes
New York: McGraw-Hill.
afflictions one of its greatest. Yours is the comfortable were found in healthy people. Therefore, how
reflection
Property thatformankind
of and canuse
the exclusive never forget
of SLU. that you have
Reproduction, couldsystem,
storing in a retrieval these distributing,
bacterial uploading
cells possibly cause
or posting online,disease?
or 16
lived.”the prior written permission of SLU, is strictly prohibited.
without To understand clearly the nature of infectious
disease, a new conception of disease had to emerge.
de Kruif put it in Microbe Hunters, ‘‘when folks of a town began by mosquitoes while working with patients. He began to show
to turn yellow and hiccup and vomit black, by scores, by hun- symptoms in 5 days and was dead in 12 days. Thus, it became
dreds, every day—the only thing to do was to get up and get clear that mosquitoes carried the yellow fever agent. Similar
out of that town.’’ The entire canal project was in jeopardy be- experiments in which volunteers slept on sheets filthy with
cause of the disease, and the physician Walter Reed was as- vomitus of yellow fever patients demonstrated that bad air,
signed the task of controlling the disease. Reed listened to the contaminated water, sheets, and dishes were not involved. La-
advice of Dr. Carlos Finlay y Barres of Havana, Cuba, who for ter Carroll passed blood from yellow fever victims through a
years had claimed that yellow fever was carried by mosquitoes. porcelain filter and used the filtrate to inoculate three people
Reed ignored those who called Dr. Finlay a theorizing old fool who had not had yellow fever. How he got their cooperation is
and insisted yellow fever was due to swamp air. Several people, not known, but it is known that two of them died of yellow fe-
including James Carroll, Reed’s longtime associate, vol- ver. The agent that passed through the porcelain filter was
unteered to be bitten by mosquitoes known to have bitten eventually identified as a virus.
The Advent of Chemotherapy

Ehrlich’s institute. After testing hundreds of compounds
(and numbering each compound), Ehrlich found com-
The development of antibiotics began in 1917 with
the observation that certain bacteria (actinomycetes)
Chemotherapy is defined as the use of chemical agent/s drugs in

pound 418 (arsenophenylglycine) to be effective against stopped the growth of other bacteria. In 1928 Fleming
sleeping sickness and compound 606 (Salvarsan) to be (Figure 1.16) observed that a colony of Penicillium
effective against syphilis. For 40 years Salvarsan re- mold contaminating a culture of Staphylococcus bac-
the treatment of diseases. Nowadays, however, the term

mained the best available treatment for this disease.
In 1922 Alexander Fleming, a Scottish physician, dis-
teria had prevented growth of bacteria adjacent to it-
self. Although Fleming was not the first to observe this
covered that lysozyme, an enzyme found in tears, saliva, phenomenon, he was the first to recognize its potential
chemotherapy is associated with treatment of cancer.
and sweat, could kill bacteria. Lysozyme was the first
body secretion shown to have chemotherapeutic
for countering infections. However, purification of suffi-
cient quantities of the substance he called penicillin
properties. proved to be very difficult. The great need for such a
drug during World War II, money from the Rockefeller
Institute, and the hard work of the German biochemist
Paul Ehrlich. His discovery that certain dyes (aniline dyes)

Ernst Chain, the Australian pathologist Howard Florey,
and researchers at Oxford University accomplished the
task. Penicillin became available as a safe and versatile
stained microorganisms but not animal cells suggested that

chemotherapeutic agent for use in humans.
While this work was going on, sulfa drugs were
being developed. In 1935, prontosil rubrum, a reddish
dyes or other chemicals might selectively kill microbial cells.
dye containing a sulfonamide chemical group, was used
in treating streptococcal infections. Further study showed
This led him to search for the “magic bullet” a chemical

that sulfonamides were converted in the body to sulfa-
nilamides; much subsequent work was devoted to devel-
oping drugs containing sulfanilamide. The German
that would destroy specific bacteria without damaging

chemist Gerhard Domagk played an important role in
this work, and one of the drugs, prontosil, saved the life
of his daughter. In 1939 he was awarded a Nobel Prize
surrounding tissues. In 1908, he found a chemotherapeutic

for his work, but Hitler refused to allow him to make
the trip to receive it. Extensions of Domagk’s work led
agent, called salvarsan (now known as arsphenamine), an

to the development of isoniazid, an effective agent
against tuberculosis. Both sulfa drugs and isoniazid are
still used today.
arsenic derivative used in the treatment of syphilis. He

The development of antibiotics resumed with the
Figure 1.15 Paul Ehrlich. Ehrlich was a pioneer in the work of Selman Waksman, who was born in Ukraine
Paul Ehrlich.
development of chemotherapy for infectious disease. (! Bettmann/ and moved to the United States in 1910. Inspired by the
Corbis)
S o u r c e : W i l l e y, J . M . , coined the term chemotherapy and headed the world’s
1939 discovery, by the French microbiologist Rene
Sherwood, L., Woolverton, C. first institute concerned with the development of drugs to
J., Prescott, L. M., & Willey, J.
M . ( 2 0 11 ) . P r e s c o t t ' s treat disease.
microbiology. New York:
McGraw-Hill.
Alexander Flemming in 1929 observed that a colony of

Penicillium mold contaminating a culture of
Staphylococcus bacteria had prevented growth of
bacteria adjacent to itself. he was not the first to observe
this phenomenon, but he was the first to recognize its
potential for countering infections. Penicillin became
available as a safe and versatile chemotherapeutic agent
for use in humans.
These, to name a few, are among the most notable contributions that
paved way to the advances and branching of the diverse science of
what we know now as Microbiology.
For further details and more detailed insights in the History of Microbiology,
you may refer to https://lib.guides.umbc.edu/c.php?
g=836720&p=6561140#s-lg-box-wrapper-24463621.
MLS 223.1.1. Evaluate
Matching type. Select which among the options given in column B best
matches the description in each item in column A. (5 points)
A B
1. A discipline of microbiology which centers on the A. Pasteurization
study of animal-like, unicellular, non-photosynthetic
microorganisms that lack cell wall.
2. A technique employed to kill spoilage- and disease- B. Chemotherapy
causing microorganisms by application of mild heating.
3. The administration an antigenic material to stimulate C. Bacteriology

an individual’s immune system to develop immunity
against a pathogen.
4. This process involves the use of chemical agent/s or D. Vaccination
drugs in the treatment of diseases.
5. The study of the structure, functions, and activities of E. Protozoology

bacteria.

References:
Carroll, K. C. (2016). Jawetz, Melnick & Adelberg's medical microbiology (27th

ed.). New York: McGraw-Hill Education.
Madigan, M. T., Martinko, J. M., Bender, K. S., Buckley, D. H., & Stahl, D. A. (2015).
Brock Biology of Microorganisms(14th ed.). Glenview, Illinois: Pearson
Education.
Melnick, J. L., Jawetz, E., Adelberg, E. A., & Riedel, S. (2020). Jawetz, Melnick y
Adelberg Microbiología médica. México: McGraw-Hill.
Pommerville, J. C. (2018). Alcamo's Fundamentals of Microbiology (11th ed.).

Procop, G. W., Church, D. L., Hall, G. S., Janda, W. M., Koneman, E. W.,
Schreckenberger, P. C., & Woods, G. L. (2017). Color Atlas and Textbook of
Diagnostic Microbiology (7th ed.). Philadelphia: Wolters Kluwer Health.
Talaro, K. P., & Chess, B. (2018). Foundations in Microbiology (10th ed.). McGraw
Hill.
Tortora, G. J., Funke, B. R., Case, C. L., Weber, D., & Bair, W. (2020). Microbiology:
An introduction (12th ed.). Upper Saddle River: Pearson.
Willey, J. M., Sherwood, L., Woolverton, C. J., Prescott, L. M., & Willey, J. M. (2011).
Prescott's microbiology. New York: McGraw-Hill.
MODULE 1
Unit 2:
Scope and Relevance of Microbiology
1. Outline the development of microbiology as a science.

2. Relate the practical uses of microorganisms.
Engage
Microbiology is said to be one of the most rewarding of professions because it

gives its practitioners the opportunity to be in contact with all the other natural
sciences and thus to contribute in many different ways to the betterment of
human life. From your previous courses, studies or readings, can recall any
microorganism that may have a positive contribution to man or to the
environment?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
_____________________________________________________________________________.
Explore
Through the years, microbiologists have made great strides in discovering

how microorganisms function, and application of this knowledge has greatly
advanced human health and welfare. Besides understanding microorganisms
as agents of disease, microbiology has made great advances in understanding
the important roles microorganisms play in food and agriculture, and

microbiologists have been able to exploit microbial activities to produce
valuable human products, generate energy, and clean up the environment.
These discoveries and application new knowledge have thus broadened the
scope of Microbiology as a science.
While pathogens and infectious disease remain a major threat to
humanity, and combating these harmful organisms remains a major focus of
microbiology, most microorganisms are not harmful to humans. In fact, most
microorganisms are beneficial, and in many cases are even essential to human
welfare and the functioning of the planet.
Explain
Medical Microbiology involves the study of pathogens, the

nature and development of diseases that they cause (i.e.
pathogenesis), and the body’s defenses against such
diseases. Further, the field of medical microbiology is
concerned with transmission of pathogens, disease-
prevention measures, aseptic techniques, treatment of
infectious diseases, and immunology.
Medical microbiology also delves into the fields of
epidemiology and immunology. Epidemiology studies the
factors that determine the occurrence and distribution of A clinical laboratory
diseases. Immunology on the other hand is concerned with worker.
how the immune system protects the body from pathogens Source: Madigan, M. T.,
and the response of infectious agents. Martinko, J. M., Bender,
K. S., Buckley, D. H., &
A branch of medical microbiology, called clinical or Stahl, D. A. (2015).
diagnostic microbiology, is concerned with the laboratory Brock biology of
diagnosis of infectious diseases of humans. Clinical microorganisms. Boston:
microbiology laboratories isolate and identify pathogenic Pearson.
microbes and suggest possible treatment to clinicians.
The science of Veterinary Microbiology centers on the spread and control of

infectious diseases among animals. Zoonoses or zoonotic diseases which are
infectious diseases of humans acquired from animals, is another area of major
importance in veterinary microbiology.
Agricultural Microbiology studies the harmful and beneficial roles of microbes in

plants and crops; in the production of foods from plants and crops; in soil
formation and fertility; in carbon, nitrogen, phosphorus, and sulfur cycles; and in

the digestive processes of cows and other ruminants. A significant breakthrough

in the field is the discovery of the role of nitrogen-fixing and nitrifying bacteria in
soil fertility.
Nitrogen-fixing bacteria (e.g. Rhizobia species) in the root nodules of legumes

(e.g., peas and peanuts) convert nitrogen gas from air into ammonia (the
process is known as nitrogen-fixation) which is then converted into nitrites and
nitrates by nitrifying bacteria in soil (nitrification) used by plants to build plant
proteins, thereby reducing the need for fertilizers.
Steps in the formation of a root nodule in a legume infected by Rhizobium. Formation of a bacteroid state is a prerequisite for
nitrogen fixation.
Source: Madigan, M. T., Martinko, J. M., Bender, K. S., Buckley, D. H., & Stahl, D. A. (2015). Brock biology of microorganisms. Boston:
Pearson.
Food Microbiology and Dairy Microbiology
Food microbiology is primarily concerned with the role of microorganisms

in food production such as in the manufacture of dairy products (e.g.,
cheese and yogurt); breads; alcoholic beverages (e.g., beer, wine); plant
products (e.g., soy sauce, pickles); and fish products (e.g., fish sauces).
Food microbiology also explores on the use of microorganisms as food
source. Such is the case for those referred to as single cell protein (SCP) —
a food substitute consisting of microbial cells (e.g., Spirulina).
Food microbiologists employ various food preservation methods such as

the use of heat, cold, radiation, and chemical preservatives to prevent
food spoilage and food poisoning. Food poisoning associated with
microorganisms may be of 2 mechanisms:
a. Food-borne infection results when the contaminating organism

infects the person who ingests the contaminated food.
b. Food intoxication occurs when toxin formed in food by microbial

growth and is ingested with the food. Toxins produced in the food
can be associated with live microbial cells or can be released from
the lysed bacterial cells.
Scientists specializing in Dairy Microbiology oversees the grading,

pasteurization and processing of milk to prevent contamination, spoilage
and transmission of diseases from environmental sources.
A Food Microbiologist in a dairy farm overseeing automated pasteurization of products.

Source: Retrieved from https://kkandp.com/2020/04/28/wrights-dairy-farm-and-bakery on 28 December 2021.
Sanitary Microbiology involves the study and detection of

risks associated with the production, manufacture or
consumption of foods and water to ensure that microbial
pathogens are not transferred to man. Sanitary
microbiologists guarantee public safety by purification
and processing of water supplies to ensure that no
pathogens are carried to consumer by drinking water and
by inspection of food processing installations and eating
establishments to ensure that proper food handling
procedures are being enforced. Additionally, sanitary
microbiologists monitor processing and disposal of
garbage and sewage wastes.
By performing well-developed and standardized methods, Detection of fecal coliform

sanitary microbiologists assess water quality to ensure its in water samples.
Source: Madigan, M. T.,
suitability for consumption. A widely used indicator for Martinko, J. M., Bender, K. S.,
microbial water contamination is the coliform group of Buckley, D. H., & Stahl, D. A.
(2015). Brock biology of
microorganisms. Boston:
Pearson.
bacteria. Coliforms are useful because many of them inhabit the intestinal tract
of humans and other animals. Thus, the presence of coliforms in water indicates
likely fecal contamination. Water samples are collected and analyzed in water
testing laboratories to rule out or detect and confirm the presence of coliform
group of bacteria.
Industrial Microbiology encompasses the monitoring and

maintenance of essential microorganisms for commercial
enterprises. Business and industries depend on
microorganisms to harvest desired products on a large scale
production. Products produced by or derived from
microorganisms that have been made available for public
consumption include antibiotics, vaccines, enzymes, amino
acids, vitamins, beer, wine and other alcoholic beverages.
The activities of industrial microbiologists do not only involve

identification of microbes of use to industry. Rather, they Humulin (Human Insulin) is
produced by insertion of
also engineer microbes with desirable traits and devise insulin producing gene
systems for culturing them and isolating the products they from human pancreas to the
chromosome of e. coli.
make, a sub discipline of industrial microbiology known as Source: Retrieved from
biotechnology. Biotechnology includes any technique that https://www.toppr.com/ask/
question/human-insulin-is-
uses living orgs or substances produced by these orgs to being-commercially-produced-
make or modify a product, to improve plant or animals or from-a-transgenic-species/.
to develop microorganisms for specific purpose.
Microbial Ecology (also known as Environmental Microbiology) is the study of

the interrelationships among microorganisms and other microorganisms and the
environment. It relates primarily to the overall microbial processes that occur in
soil, water, or food, as examples. Microbial ecologists examine natural microbial
communities that may exist in soils, waters, or in association with other organisms,
including humans. They study the global and local contributions of
microorganisms to the carbon, nitrogen, and sulfur cycles.
The field of environmental microbiology has become important because of an

increased concern about the environment, particularly about pollution. The
analysis of the effects of pollution on microorganisms is important because of
the impact these organisms have on the environment. The field of
environmental microbiology is further subdivided into soil microbiology and
aquatic microbiology.
Soil Microbiology centers on the role of microorganisms in the

Biogeochemical Cycle. The biogeochemical cycle refers to the recycling
of chemical elements by microorganisms for use by other microorganisms

which is perhaps the most important role of soil microbes. Soil microbes
decompose organic matter and transform C-, N-, S- & P-containing
compounds into usable forms.
All organisms need nitrogen to synthesize protein, nucleic acids, and other
nitrogen- containing compounds. During nitrogen cycle, nitrogen in the
atmosphere goes through fixation, nitrification, and denitrification. Nitrates
assimilated into plants and animals after nitrificatlon go through
decomposition, ammonification, and then nitrification again.
The nitrogen cycle.

biology of microorganisms.
Boston: Pearson.
Aquatic Microbiology deals with the study of microorganisms and their

activities in natural waters which include lakes, ponds, streams, rivers,
estuaries and sea. One important concern in the field is microbial pollution
of water, as one form of water pollution. Environmental microbiologists
that specialize in this field are concerned about water and sewage
treatment. The purification of waste water is partially accomplished by
bacteria in the holding tanks of sewage disposal plants, where feces,
garbage, and other organic materials are collected and reduced to
harmless waste.
The most dangerous form of water pollution occurs when feces enter the
water supply. Many diseases are perpetuated by the fecal-oral route of
transmission, in which a pathogen is shed in human or animal feces,
contaminates water, and is ingested. Examples of such diseases are
typhoid fever and cholera, caused by bacteria that are shed only in
human feces.
The possible routes of

transmission fecal-oral diseases
in the environment.
Source: Melnick, J. L., Jawetz, E.,
Adelberg, E. A., & Riedel, S.
(2020). Jawetz, Melnick y Adelberg
Microbiología médica. México:
McGraw-Hill.
Bioremediation involves the use of microbes for treatment o f wastes and

to to detoxify or degrade pollutants such as those coming from industrial
plants or oil spills in waters. Scientists in this field use microorganisms as
“natural pollution fighter” to clean up industrial and toxic wastes in the
environment.
Oil spills from wrecked tankers represent some of the most dramatic
examples of chemical pollution. The economic losses from contaminated
fisheries and beaches can be enormous. Bioremediation may be
employed by use of microbes that can gradually but completely degrade
organic pollutants (e.g., petroleum) to carbon dioxide . Such was the
case when Pseudomonas species were used in the Exxon Valdez oil spill
that occurred in Alaska in 1989. Pseudomonas species degrade oil for
their carbon and energy requirement. However, petroleum hydrocarbons
are deficient in essential elements, such as nitrogen and phosphorus.
Bioremediation of oil spills is greatly enhanced if the microbes used are
provided with “fertilizer” (i.e. plant fertilizers) containing nitrogen and
phosphorus, a process also referred to as bioaugmentation. Simply,
bioaugmentation involves addition of nutrients to speed up

bioremediation.
Bioremediation of an oil spill in

Alaska. The portion of beach on
the left is uncleaned, the beach
on the right has been treated with
application of fertilizer.

biology of microorganisms.
Boston: Pearson.
Elaborate
Throughout the discussion in this module unit, one may conclude that science of
microbiology revolves around two interconnected themes: (1) understanding
the nature and functioning of the microbial world, and (2) applying our
understanding of the microbial world for the benefit of humankind and our
planet.
Studies in microbiology have led to greater understanding of many theoretical
biological principles. Perhaps one of the most advanced contribution of
microbes to man is by providing insight on how scientists, particularly geneticists,
can provide cure to some diseases which were before deemed as
“untreatable”.
Microbial Physiology and Genetics provides a clear understanding of the

function of microorganisms, the structure of DNA, and the science of genetics,
the study of heredity. Scientists specializing in the field focuses on the nature of
genetic information and how it regulates the development and function of cells
and organisms. Included in this field are genetic.
Genetic Engineering refers to gene manipulation to produce a desired

gene product. It involves the transfer and insertion of genes from one cell
to another, so that when the cell receives a new gene, it can produce the
gene product that is coded by that gene (also known as Recombinant
DNA Technology). In the performance of such procedure, the recipient
cells chosen are those that are easily cultured in order to facilitate the
large production of important gene products. Hence, during genetic
engineering, microorganisms are commonly used as biological factories.

Examples of such advances include the use of genetically engineered
bacteria, E. coli, in the production of insulin and interferons.
Production of insulin through recombinant DNA technology.

Source: Retrieved from https://ib.bioninja.com.au/standard-level/topic-3-genetics/35-genetic-modification-and/gene-
transfer.html 28 December 2021.
Microbial genetics involves the study of microbial DNA, chromosomes, plasmids,

and genes which has been very helpful in understanding the structure and
function of genes (i.e., DNA). The field of microbial genetics has made a great
impact on how some diseases may be treated by the process known today as
gene therapy. Gene therapy is another interesting and exciting outcome of
recombinant DNA technology. It involves treating disease by replacing
abnormal genes or providing missing genes. Disease treatment is facilitated by
insertion of normally functioning genes into a cell to correct problems
associated with abnormally functioning genes. This technique uses harmless virus
to carry the missing or new gene and insert it into the chromosome.

Multiple choice. Select a single, best answer. (5 points)
1. A subdivision of Microbiology which focuses on the isolation and

identification of bacterial pathogens.
A. Immunology C. Epidemiology
B. Clinical Microbiology D. Veterinary Microbiology
2. A process which involves recycling of chemical elements by microorganisms

that in turn benefit other microorganisms.
A. Bioremediation C. Biogeochemical Cycle
B. Bioaugmentation D. Sanitation
3. This results from ingestion of microbe - contaminated food and subsequent

growth of the contaminating organism within a host.
A. Food poisoning C. Food intoxication
B. Food spoilage D. Food-borne infection
4. This procedure results to a change in the genetic make up of an organism

due to transfer and insertion of genetic material from another microbe or
cell.
A. Genetic engineering C. Gene mapping
B. Gene therapy D. Gene translocation
5. Scientists in this area of microbiology focus on the issue of microbial pollution

of drinking water.
A. Sanitary Microbiology C. Industrial Microbiology
B. Food Microbiology D. Agricultural Microbiology

References:

Education.

Hill.
MODULE 1
Unit 3:
Microbial Taxonomy: Classification, Nomenclature, and Identification
1. Define taxonomy and outline the various levels in the taxonomic classification
scheme to show how microbes are organized.
2. Describe the binomial system of nomenclature and show how microbial names
are written.
Engage
Taxonomy (Gk. taxis = arrangement; nomos = name), is a branch of biology that

is concerned with the classification of all living organisms in ordered system that
indicates a natural relationship. A systematic approach is employed in which
organisms are characterized, named, and classified according to defined
criteria. In bacterial taxonomy, bacteria are grouped into categories, or taxa
(singular: taxon) with precise names, to show degrees of similarities among them
hence enabling microbiologists to communicate with each other in an efficient
manner. Example, Escherichia coli which is a member of the normal intestinal
flora of man belongs in the same family as the pathogenic Klebsiella
pneumoniae. Can you cite a criterion to rationalize their grouping?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
_____________________________________________________________________________.
Explore
Taxonomy is the area of biologic science comprising three distinct, but highly
interrelated, disciplines that include classification, nomenclature and
identification.
Classification is the categorization of organisms into related group or

taxon. The arrangement of organisms into groups are primarily based on
similar characteristics, evolutionary similarity or common ancestry.
Nomenclature (L. nomen = name; clare = to call), refers to the naming of

an organism by international rules according to its characteristics. The
rules and guidelines that govern the assigning of names to specific
organisms are established by a recognized group of medical
professionals. This rules provide accepted labels by which organisms can
be universally recognized.
Identification involves the process of discovering and recording the traits

of organisms so that they may be confirmed as belonging to a previously
established taxon. In a clinical laboratory setting, it is the practical use of a
classification scheme to isolate and identify the causative agent of a
disease.
Explain
Classification systems are needed to organize all of life into a system that
everyone recognizes, to show evolutionary or other relationships between
organisms. Similar with the field of microbiology, the classification of bacteria
also have a long history which originated in the 1700’s.
Carl von Linné (Linnaeus; 1707 - 1778), a Swedish

botanist, was the first to classify organisms based on early
descriptions of organisms as either animals (Kingdom
Animalia) or plants (Kingdom Plantae). It is for this reason
that he is know as the “Father of Taxonomy”. In his honor,
the first classification system was referred to as the
Linnean taxonomy.
Early biologists found it convenient to classify organisms into these 2

kingdoms, as to many people today, this grouping still seems perfectly
adequate. But with advancement in science, after thorough examination, is
was later found to be too simplified and unsatisfactory.
Ernst Haeckel (1866) was the first to create a natural

kingdom for microscopic organisms which have been
discovered nearly 2 centuries before by Leeuwenhoek
(1667) thereby introducing the so-called three-kingdom
classification. The third group to which these
microorganisms were grouped under was called
Kingdom Protista.
The development of the electron microscope in the 1950s revealed a

fundamental dichotomy among the microscopic Protista. That is, some of
these organisms possess membrane bound nucleus but are lacking of
membrane-bound organelles.
Robert H. Whittaker (1969), an ecologist working at

Cornell University refined the existing three-kingdom
classification of organisms into five kingdoms. Whittaker’s
five-kingdom classification include Animalia, Plantae,
Protista (protozoans and single-celled algae), Fungi
(Mycetae), and Monera (Prokaryotae).
There were 3 major criteria used to classify organisms into each kingdom:
1. Cell Type. Organisms are classified as either possessing eukaryotic or

prokaryotic types of cells. Eukaryotic organisms (eukaryotes) possess
a membrane-bound nucleus [Gk. eu = true or normal; karyon = nut
or kernel (referring to the nucleus)]. Animals, plants, algae,
protozoa, and fungi were classified as eukaryotes. Prokaryotic
organisms (prokaryotes) on the other hand, lack nuclear membrane
and other membrane-bound organelles. All bacteria are classified
as prokaryotes; hence, kingdom Monera is also known as Kingdom
Prokaryotae.

2. Cellular Organization. Microbes are classified as either colonial or

solitary; unicellular or multicellular. That is, whether an organism live
in a colony (colonial) such as in the case of bacteria; or alone
(solitary), similar with the protozoa. Whether an organism consists of
a single cell (unicellular, e.g., bacterium), or made up of several
cells (multicellular such as plants and animals), was also a basis for
placing them in a particular group.
3. Nutritional Type. This pertains to an organism’s manner or way of

food procurement from its immediate environment; its energy
source; and its carbon source.
a. Food procurement. Microorganisms procure food differently.

Some microbes obtain food by ingestion either by way of
mouth or a similar apparatus. A few protozoans for example
possess a specialized “cell mouth” called cytostome through
which food passes. Another group of protozoans, the
amoebas, are able to extend part of their cytoplasm and
surround a nearby food particle thereby “ingesting” it. Other
microbes such as the fungi feed by absorption of ready-
made nutrients form their environment.
b. Energy source. Generally, based on their source of energy,

organisms may either be a phototroph (i.e., it obtains energy
from sunlight by photosynthesis); or chemotroph which
obtains energy by oxidation of organic or inorganic chemical
components.
c. Carbon source. Depending on their carbon source, organisms

may either be autotrophs or heterotrophs. Autotrophs utilize
the only inorganic carbon-containing compound, carbon
dioxide as their sole carbon source. They are capable of
synthesizing their own cellular materials from carbon dioxide,
hence are known as “self-feeder”(auto = self; troph =
feeding). Heterotrophs require organic compounds as carbon
source. Being unable to manufacture their own food, they
rely on other sources of organic carbon for biosynthesis. For
this reason, they are called “feeders on others” (hetero =
other; troph = feeding). The parasites and saprophytes (or
saprobes) are also heterotrophs but differ in terms of their
organic carbon source. The parasites feed on the living tissues
or body fluids of their host, whereas the saprobes derive
organic carbon from dead, decaying matter.

When combining their source of energy and carbon,

organisms are classified as photoautotrophs,
photoheterotrophs, chemoautotrophs, or chemoheterotrophs.
Eukaryotes include organisms that belong under the kingdoms

Animalia, Plantae, Fungi, and Protista. The Kingdom Animalia consists
of multicellular, chemoheterotrophs that procure food mainly by
ingestion. The Kingdom Plantae include multicellular organisms that are
absorptive and photoautotrophic. Fungi are multicellular (except for
yeast) organisms which are absorptive and are generally chem-
heterotrophs. Grouped under Kingdom Protista are organisms that
have either a single cell or no distinct tissues and organs, such as
protozoa and algae. Algae are absorptive, photoautotrophic
organisms, whereas protozoa are generally ingestive
chemoheterophic organisms.
Prokaryotes include the bacteria and archeae. Both of which are

unicellular, absorptive organisms, which are diverse in terms of their
carbon and energy source.
The 5 - Kingdom classification.

Source: Talaro, K. P., & Chess, B. (2018). Foundations in
Microbiology (10th ed.). McGraw Hill.
Taxonomy was not exempted from rapid advancements that came after
the discovery of DNA as the chief component of the genetic material. At
that time, two classification systems was introduced and became widely
accepted. Organisms were then classified by either of the following:
1. Phenetic System of Classification. Organisms are classified based

on similarities of observable traits or characteristics. This system was
widely used for bacterial classification. Bacteria were grouped
according to their similarities in morphology (cell shapes, grouping);
staining property; physiologic requirements (temperature, oxygen,
pH); metabolism, and ecology.
2. Phylogenetic Classification System is based on the concept of

evolutionary relationships among types of organisms.
Carl Woese (1978). Ribosomes provide a method for

comparing cells since they are present in all cells. Carl
Woese studied and compared the rRNA (ribosomal
ribonucleic acid) sequences (16S) in different cell types
and found that there are three distinctly different cell
groups: the eukaryotes, and two different types of
prokaryotes — the bacteria and archaea. He then
proposed elevating the three cell types to a level above
kingdom, called domain. Hence, the three-domain
system for classifying organisms includes the Domain
Bacteria, Domain Archaea, and the Domain Eukarya.
The 3-Domain System which was proposed by Carl Woese in

1978 forms the “Tree of Life”.
Source: Pommerville, J. C. (2018). Alcamo's Fundamentals of
Microbiology (11th ed.). Burlington: Jones & Bartlett Learning.

Notes of interest.
The Domain is a relatively new level in the classification hierarchy. It was erected mainly to preserve the
kingdoms as we know them. The former kingdom Monera, which included all prokaryotes (lacking a nucleus),
was recently split into two domains, the Domain Bacteria, which includes the true bacteria, and the Domain
Archaea, a group of organisms completely unlike the bacteria, except for the lack of a nucleus.
A taxonomy has an overlapping

hierarchy that forms levels of rank or
category similar to an organization chart.
Each rank contains microorganisms that
have similar characteristics. A rank can
also have other ranks that contain
microorganisms.
Microorganisms that belong to a
lower rank have characteristics that are
associated with a higher rank to which
the lower rank belongs. However,
characteristics of microorganisms of a
lower rank are not found in
microorganisms that belong to the same
higher rank as the lower-rank
microorganism.
In the taxonomy of prokaryotes,
the most commonly used rank (in order
from most general to most specific) is: The Taxonomic Classification of Man.
Source: Talaro, K. P., & Chess, B. (2018). Foundations in
Domain Microbiology (10th ed.). McGraw Hill.
Kingdom
Phyla (sing. Phylum)
Class
Order
Family
Genus (pl. Genera)
Species
The basic taxonomic group in microbial taxonomy is the species.

Taxonomists working with higher organisms define their species differently than
microbiologists. Species in higher organisms is defined as a group of
interbreeding or potentially interbreeding natural population.
Species among bacteria, however, is defined as a group of bacterial cells
with shared characteristics, or a collection of strains, a group of bacterial cells
that descend from a single parent cell, and differs slightly from other cells within
the same species.

Bacterial strains can also be further differentiated as to their physiology,

morphology, pathology, and on the basis of their surface antigens. A biovar is
strain that differs physiologically or biochemically from other strains. A
morphovar (or morphotypes) are those strains that differ morphologically.
Serovars (also referred as serotypes) are those strains that have antigenic
properties that differ from other strains. A pathovar on the other hand, is a
bacterial strain or set of strains that differ from other strains on the basis of
distinctive pathogenicity.
Nomenclature is the assignment of names to taxonomic groups. Bacteria are

named according to rules established by International Code of Nomenclature. A
standard reference is used for bacterial taxonomy which is the Bergey’s Manual
of Systematic Bacteriology. It is considered as the authority on bacterial
taxonomy, with the published classification, and approved names of all
bacteria which is also a practical aid for bacterial identification.
Each taxon is given latinized names with suffixes to indicate a particular

taxonomic group. These are the endings that are used for various taxonomic
levels. Proper use of these endings allows other people to tell what group of
organisms you’re talking about.
Taxon Suffix Example
Domain Bacteria
Kingdom -ae
Phylum Proteobacteria
Class / Division -es Gammaproteobacteria
Order -ales Enterobacterales

Family -aceae Enterobacteriaceae
Tribe -eae
Genus Escherichia
Species E. coli
At present, the trend is to place emphasis on the Genus and species, aka
Binomial System of Nomenclature, whereby each group of organism is given 2
names, the genus name and the species epithet, which comprise the scientific
name (e.g., E. coli). In relation to this, rules regarding how scientific names of
organisms should be written or appear in print were laid out.

1. The first letter of the Genus/generic name is ALWAYS capitalized. The

first letter of the species epithet is NEVER a capital letter.
2. When appearing in print, scientific names MUST BE italicized or

underlined.
3. Scientific names are often shortened by abbreviating the genus name

with a single capital letter.
4. Some bacteria are given common name/s – trivial names which may
be:
a. descriptive of the organism’s morphology, habitat or attribute
E.g.
Vibrio cholerae - “vibrio” = comma-shaped
Staphylococcus epidermidis -
“staphylo” = clusters; “coccus” = spheres
Escherichia coli - “colon bacillus”
b. honorary of the organism’s discoverer

E.g.
Mycobacterium tuberculosis - Koch’s bacillus
Klebsiella pneumoniae - Friedlander’s bacillus

Elaborate
Identification is the process of observing and classifying organisms into a

standard group that is recognized throughout the biological community. In the
aspect of Clinical Bacteriology, pathogenic bacteria in patient specimens are
identified by growing them in pure cultures in clinical laboratories. A standard
reference to aid in the identification of unknown bacteria, the Bergey’s Manual
of Determinative Bacteriology was published by the Committee on
Characterization and Classification of the Society of American Bacteriologists.
The book consists of a systematic guide on the phenotypic characterization of
bacterial isolates. The outline of process includes inoculation, incubation,
isolation, inspection, and identification of specific species.
An outline of the typical processes scientists perform for bacterial identification.

Source: Pommerville, J. C. (2018). Alcamo's Fundamentals of Microbiology (11th ed.). Burlington: Jones & Bartlett Learning.
True or False. For each item, write “true” if the statement is correct and “false”
for an incorrect statement.
1. Bergey's Manual of Determinative Bacteriology is the standard reference

on bacterial classification.
2. According to binomial system of nomenclature, each organism is assigned

two names, a scientific name and a common name.
3. Organic compounds provide nutrients for chemoheterotrophs.
4. A genus consists of one or more lower ranks called species.
5. Both archaea and bacteria consist of prokaryotic cells.

 
 

References:

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MODULE 1 IN

Department of Medical Laboratory Science

At the end of the module, you should be able to:

1. outline the development of microbiology as a science with emphasis on the

4. describe the binomial system of nomenclature and show how microbial

Unit Learning Outcomes:

The Diversity of the Microbial World.

Most often, the word microorganism, microbes, or germs gives a negative

Microbiology Disciplines by Organism or Agent Studied.

a. Eubacteria or “true bacteria”, to which disease-

The current science of bacteriology includes the study of Archaebacteria

b. Multicellular - molds, consists of fundamental unit

Parasitology studies certain organisms — parasites, that live at the expense of

Protozoology is the science of protozoa which is a group of animal-like,

b. Flagellum (pl. flagella) (L. whiplike) is a long, whiplike appendage seen

A fourth major group of protozoa, the sporozoa, particularly those

a. Nucleic acid. Of which, viruses posses only a single type, either

The Components of Viruses.

(B) Enveloped viruses have an envelope

Source: Pommerville, J. C. (2018).

Viruses are obligate intracellular

bacteria are called bacteriophages (or simply phages).

Phycology (Gr. “phykes”: seaweed) is the study of the

Only 2 human illnesses are caused by algae:

1. Protothecosis is caused by Prototheca which is believed to be variant

2. Paralytic shellfish poisoning has been associated

The Historical Background of Microbiology: A Summary

Ancient Civilization. In ancient Egypt and China, laws concerning public

Modern Period. In contrast to the pre-modern era, Western civilization made

Even before microorganisms were seen, some investigators suspected

Girolamo Fracastoro (Fracastorius), an Italian

First Observation of Microorganisms

Anton van Leeuwenhoek. He was an unlikely scientist, was a

A. Anton van Leeuwenhoek (1667)

The Origin of Microorganisms

For several hundreds of years, many scientists and philosophers

Francesco Redi and his experiment to refute Spontaneous Generation.

The Theory of Spontaneous Generation was debated upon for

(1)He proposed the biological process of FERMENTATION.

The defeat of a. Non-sterile liquid is poured

d. The liquid cooled slowly.

e. When Pasteur tilted the

Robert Koch is a German scientist and is Pasteur’s

The Koch’s postulates for

Ignaz Philipp Semmelweis is a Hungarian

Joseph Lister, an English surgeon, used

The Birth of Immunology

Edward Jenner introduced the first successful vaccination.

made in microscope optics that allowed better reso-

The Advent of Chemotherapy

Chemotherapy is defined as the use of chemical agent/s drugs in

the treatment of diseases. Nowadays, however, the term

Paul Ehrlich. His discovery that certain dyes (aniline dyes)

stained microorganisms but not animal cells suggested that

This led him to search for the “magic bullet” a chemical

that would destroy specific bacteria without damaging

surrounding tissues. In 1908, he found a chemotherapeutic

agent, called salvarsan (now known as arsphenamine), an

arsenic derivative used in the treatment of syphilis. He

Alexander Flemming in 1929 observed that a colony of

MLS 223.1.1. Evaluate

3. The administration an antigenic material to stimulate C. Bacteriology

5. The study of the structure, functions, and activities of E. Protozoology

Carroll, K. C. (2016). Jawetz, Melnick & Adelberg's medical microbiology (27th