Cairo University

Department of
Microbiology and
Immunology

Faculty of Pharmacy

Basic Microbiology and Immunology

(MICRO 402)
Lecture Notes
for
Third Year Pharmacy Students

General Microbiology

Microbial Genetics

Edition 2015

Immunology

Microbiology and Immunology

Preface

Preface
About This Book:
This book includes lecture notes for the General Microbiology and Immunology
course (Micro402) offered to third year students a the Faculty of Pharmacy, Cairo University.
Students are encouraged to read the appropriate chapters ahead of the lectures to get
prepared for better understanding.
Organization:
The book is divided into three major parts or modules, covering three different areas
of concentration. Part I deals with the principles and foundations of microbiology: its
history, origins, and the basic concepts of microbial classification, identification, structure,
nutrition, and metabolism. Part II focuses on microbial genetics, with emphasis on the
basics of molecular biology, microbial genetics, and microbial genomics and metagenomics.
Part III represents a comprehensive overview of basic and applied immunology.
What do Pharmacy Students Need to Know about Microbiology and Immunology?
Microbiology, the study of microscopic living organisms, or the biology of microbes, is
becoming one of the cutting edge sciences as we enter the XXIst century. In the current
general pharmacy program offered by Cairo University, undergraduate students have to
study six microbiologyrelated courses. Why is microbiology important to pharmacy
students, and what is the importance of this general course, in particular?
-

This course is almost the only biology course, offered in the general program, that
offers thorough explanation of the major biological concepts of diversity, natural
selection, adaptation, mutation, rapid evolution, etc.

The course is essential for understanding medical microbiology, and the information
presented are pivotal to understanding the mode of action of antibiotics and
chemotherapeutic agents, which are at the core of pharmaceutical microbiology.

The course is a good introduction to the following courses of biotechnology and

pharmaceutical microbiology as well.

Understanding the basics of molecular biology, microbial genetics, and recombinant

DNA technology is indispensable for nowadays pharmacists. This course presents a
thorough explanation of molecular biology and genetics from a microbiological
perspective.

The study of basic and applied immunology and immunological products is essential
for pharmacists who administer vaccines and those who work in vaccine
development or quality control.

This is one of the few courses covering recent advances in genomics, notably
bacterial and viral genomics.

PART I: GENERAL MICROBIOLOGY

Acknowledgements and Credits

Many tables and parts of the text are taken from Todars Online Textbook of Bacteriology
(http://www.textbookofbacteriology.net), with full permission from the textbooks author.
In addition, these notes have used material from the following textbooks:
- Alcamos Fundamentals of Microbiology, 7th edition
- Brocks Biology of Microorganisms, 9th edition
- Bauman Microbiology, 2nd edition
- Hugo and Russel, Pharmaceutical Microbiology, 4th edition

Microbiology and Immunology

Preface

Part I Table of Contents

Chapter 1: The Development of Microbiology

Chapter 2: Classification and Identification of Microorganisms

I. Classification of Microorganisms
II. Identification of Microorganisms

8
20

Chapter 3: The Structure of Bacteria

23

I. Structures External to the Cell Wall

II. The Cell Wall
III. Structures Internal to The Cell Wall

23
26
30

Chapter 4: Nutritional Requirements for Microbial Growth

Introduction
I. Microbial Nutrition
II. Nutritional/Metabolic Patterns
III. Cultivating Microorganisms

39
40
40
47
49

Chapter 5: Effect of Environmental Factors on Microbial Growth

51

Chapter 6: The Diversity of Microbial Metabolism

61

I. Introduction to Metabolism
II. General Features of Metabolism
III. Catabolism
IV. Anabolism or Biosynthesis
Final Word

62
64
67
76
77

Chapter 7: Microbial Growth and Population Dynamics

I. Growth Of Microbial Populations
II. How Can Growth Be Measured?

78
79
87

ii

General Microbiology

Chapter 1: Development of Microbiology

Chapter I: The Development of Microbiology

Microbiology is the science of minute organisms, invisible to the naked eye,
named microbes or microorganisms.
150 years old.

It is a relatively recent science just over

However, long before the discovery of microorganisms, certain

processes caused by microbial activities were known to man.

Primitive biological

processes were discovered by accident and were incorporated into daily life.
Humans have made use of microbes for centuries without knowing what they were
or what they did.

Thus, in ancient times at the beginning of civilization, man

employed the processes of fermentations for souring of milk, making of bread, and
for producing alcoholic beverages and vinegar.

These processes could not be

explained, and the mystery remained until the latter part of the 19th century when
Louis Pasteur introduced his germ theory in 1876 and identified a number of
microbes and their functions.
Before that period, much has been written about the nature of disease and
the spontaneous generation of living things. Thus, the peoples of Asia had certain
ideas on the contagiousness of some disease and they isolated those suffering from
leprosy, and Avicenna (980- 1037) thought that all infectious diseases were cause
by minute living creatures invisible to the naked eye and transmitted through air
and water. However, these were only speculations lacking experimental or
observational evidences.
The

first person

to

see

and

describe

microbes was

Antony

van

Leuwenhoek (1632- 1732), a Dutch cloth merchant living in the town of Delft,
Holland. He learned grinding tiny lenses of high magnifications (up to 300x) and
became interested in things he could see through the lenses he produced.

He

made simple microscopes, and it was in 1677 that he first saw animalcules, as he
called the microorganisms while examining a drop of rain water. Thus a new world
was discovered, and the new science now called microbiology was born.

General Microbiology 1

General Microbiology

Chapter 1: Development of Microbiology

Since no other person succeeded in using single lenses as effectively as

Leuwenhoek, the compound microscope was perfected to follow up this discovery.
When he died in 1723, his field of science went in a dormant stage for almost 150
years and was forced to wait for Louis Pasteur (1822-1895), Robert Koch (18431910), and other distinguished microbiologists of the golden age of microbiology
(1850- 1950).
Although the emergence of experimental microbiology was slow, the development
of reliable methods was very much stimulated by the prolonged and intense
controversy over the theory of spontaneous generation of life, which faced the
microbiologists. Thus, from the time of Aristotle (384-422 BC) till the middle of
the 19th century, it was widely believed that animals and other living beings could
be generated de novo from non-living matter. For animals and other visible
organisms, this idea was disproven in the 17th century when Redi demonstrated
that maggots no longer appeared in decomposing meat if it was protected from
deposition of eggs by flies. However, the idea of spontaneous generation existed
for the new world of microbes. John Needham (1713-1781), a Roman priest, was
one of the early investigators supporting the theory of spontaneous generation.
He boiled meat broth or vegetable infusions in corked flasks and found that the
infusions were putrefied upon standing.
However,

the

first

strong

laboratory

evidence

that

life

does

not

arise

spontaneously de novo was demonstrated by Lazzaro Spallanzani (1729- 1799)

who repeated the experiments of Needham and arrived at the opposite
conclusion.

He criticized Needham for using cork (a porous material) which

allowed the entrance of microorganisms from air into his boiled infusions,
especially during cooling when negative pressure developed within containers and
contaminated air was sucked into the vessels. When Spallanzani boiled the
infusions and then sealed the openings of his vessels in a flame, none of them
revealed spoilage. However, others claimed that the absence of decomposition in
these sealed vessels was due to the limited supply of air rather than to the
exclusion of air-borne contaminants. The answer to this objection was made by
A. Schroeder and Van Dusch (1853-1854) when they suggested the use of the
cotton plug, which is still widely used today. These plugs mechanically remove
air- borne microorganisms but allow the entrance of bacteria- free air required by
so many microorganisms.
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Chapter 1: Development of Microbiology

An interesting and economically significant application of Spallanzanis discovery

was made in 1810 by Nicholas Appert (1750- 1841), when the French
government (Napoleon I) offered a prize to the first person who could perfect a
useful technique for the preservation of food.

Appert developed the art of

preserving food by canning (boiling in airtight containers).

Nevertheless, the controversy continued because skeptics criticized the use of
cotton plugs by claiming that air is devitalized as it passes through these plugs.
Moreover, some investigators were unable to reproduce the stability of certain
sterilized organic infusions; unfortunately because they used infusions of hay (we
know today such material is largely contaminated by the spores of Bacillus subtilis
which are so difficult to kill by mere boiling).
The history of bacteriology is closely connected with the names of Louis Pasteur
and Robert Koch because of their ingenious work.

Pasteur led concreted attacks

in support of Spallanzanis discovery because he was convinced that microbes

were the cause of fermentations. He showed that boiled medium could remain
clear in an unsealed swan neck flask open to the air through an S-shaped
capillary tube.

Since bacteria cannot move, Pasteur reasoned that it would be

impossible for contamination of his medium to occur unless he tilted the flasks
and allowed some of the sterile liquid to come in contact with the tip of the
capillary tube containing contaminated dust particles.

Fortunately enough,

Pasteur used sugar, yeast extract, and water for his medium, which is relatively
easy medium to sterilize.
The most important experimental step in finishing this controversy was taken
when John Tyndall compared various kinds of extracts. He found that after he
had brought a bale of hay into his laboratory he could no longer repeat his earlier
success in achieving sterility by boiling; but he could repeat in a separate room.
He finally concluded that the hay has contaminated his laboratory with a kind of
living organism that could survive boiling for hours.

In the same year (1877),

Ferdinand Cohn demonstrated the resistant forms as small refractile endospores

of the hay bacillus (Bacillus subtilis).
Microbiology then developed largely through interest in three different groups of
microbes responsible for: fermentations, cycling of organic matter in nature and
for diseases of man and animals.

These developments gave rise to industrial,

General Microbiology 3

General Microbiology

Chapter 1: Development of Microbiology

agricultural and medical microbiology, respectively. The studies of fermentations

came earliest and contributed too much for the development of biochemistry. It
was fortunate for microbiology that not all investigators during the golden era of
fundamental discoveries devoted their energies to exactly the same problems.
Thus, with the development of microbiology attempts were made to apply this
science to the practical problems being faced at that time.
The name of the great French scientist chemist and microbiologist, Louis Pasteur
(1822-1895) is linked with the most important discoveries in the field of
microbiology and thus deserved to be the Father of Microbiology.

As a

professor at the University of Lille, in the heart of the wine industry in France, he
has been asked by Napoleon I to study a serious wine problem that was
threatening the wine industry in France and no one seemed able to correct. He
stressed that spoilage of wine could be directly attributed to the action of certain
microbes that produced undesirable end products and diseased the wines. By
selectively heating the fresh grape juice after it was bottled, he prevented such
spoilage. This heating has been given the name pasteurization. He concluded
that fermentations were due to living organisms and that different kinds of
microbes were associated with different kinds of fermentations.

When Pasteur

subsequently turned his attention to disease, he suggested that infection was due
to organisms.

Thus, in 1865, Pasteur discovered a protozoan that was

threatening to ruin the European silkworm industry and by excluding the

diseased worms, he could maintain a healthy stock.
In addition, the investigations of Pasteur on the causative agents on chicken
cholera, anthrax, and rabies formed the bases for the use of protective vaccines.
Moreover, the works of Pasteur drew the attention of many scientists to the study
of important problems and encouraged this new science (microbiology) to
flourish.

Thus, the English surgeon Joseph Lister introduced into surgery the

principle of antiseptics (disinfection of wounds with chemical agents) to combat

supportive processes in wounds.
Of great importance in the progress of microbiology were also the discoveries
made by the German scientist Robert Koch (1843- 1910). He and his students
introduced solid nutrient media (potatoes, gelatin, coagulated serum, meatpeptone agar), the isolation of pure culture technique, staining of microorganisms
General Microbiology 4

General Microbiology

Chapter 1: Development of Microbiology

with aniline dyes, the oil immersion system, and microphotography into
laboratory techniques. Koch established the aetiology of anthrax, discovered the
causative agents of tuberculosis and cholera, and obtained tuberculin from
tubercle bacilli. Koch also formulated his famous Kochs postulates to prove the
causative agents of disease. Thus, before an organism could be said to be the
cause of a specific disease, the agent must fulfill the following postulates:
1) The suspected organism must be found in every case of the disease.
2) The organisms must be isolated in pure culture from every case of the
disease.
3) The pure culture must be capable of reproducing the original disease in
its typical clinical form when introduced into susceptible animals.
4) The same organism must be re-isolated from the injected test animal.

These postulates were proposed before the discovery of viruses and other strict
parasites, which cannot grow on inanimate media, and subsequently Kochs
postulate cannot be fulfilled for every disease.
In addition to the above-mentioned discoveries of Koch, he developed a large
school of microbiology and among his students were Friedrich Loeffler, Emil
Behring, G. Gaffky, and many others. Loeffler discovered the causative organism
of diphtheria and advanced the hypothesis that diphtheria organisms, though
localized in the throat, made a poison that escaped from the cells and diffused to
other parts of the body causing death.

Behring was the first to introduce

antitoxic sera to cure diseases. He used antidiphtheritic serum to cure diphtheria

in 1891 and from this date the production of antitoxic sera for several diseases
was developed.
Immunity studies have had their origin in1796 with the pioneer work of the
English physician Edward Jenner (1749- 1823). He learned from his patients in
farm country that milkmaids who contracted cowpox were resistant to the
dreadful smallpox, and, he postulated that there must be a relation between the
two diseases.

In his famous experiment in 1796, Jenner scratched a farm boy

with a needle bearing fluid from a sore of a milkmaid who had cowpox. When the
boy later exposed to smallpox, he resisted the disease.

Jenner introduced the

word vaccine (which means cow in Latin) and the technique of vaccination against
smallpox by rubbing the cowpox vaccine into scarified skin of humans.
General Microbiology 5

The

General Microbiology

Chapter 1: Development of Microbiology

cowpox and smallpox viruses are so similar that vaccination with the cowpox
virus stimulates the immune system to react against if it is exposed to smallpox.
However, relatively little was done with this revolutionary discovery until about
1880 when Pasteur discovered a useful vaccine for chicken cholera and applied
the word vaccination in the honors of Jenners studies. Pasteur then introduced
the protective vaccines against rabies and anthrax.
These research efforts were paralleled with the early work on genetics by Gregor
Mendel in mid 1800s and the beginning of the industrialization of the
fermentation processes (the practical side of biotechnology).

Breweries and

distilleries became big industries and bakers yeast was produced in specialized
factories. During this period microbes have become the basis of great industries.
It began with the production of industrial chemicals and antibiotics by
fermentation under the pressure of World War I and World War II, respectively.
Thus, in 1914, H. Weizman introduced the manufacture of acetone (as essential
ingredient of explosives) by fermentation in the U.K.; and U.S.A. contributed its
facilities for large-scale production (rows of 50,000 gallon tank fermenters, the
largest in the history).

Although Alexander Fleming published his famous

discovery of penicillin in 1929, he abandoned his research due to the instability of

penicillin. In 1938, Florey and Chain (Oxford University) purified small quantities
of penicillin and demonstrated its therapeutic value for humans and animals but it
remained difficult and expensive to produce the drug in any quantity.

The

problems of large scale production of penicillin were resolved under the pressure
of Word War II, namely, the pressing need to produce this drug for treating battle
casualties.
Today, fermentation is carried out in huge vessels, 150 cubic meters or more,
using highly developed computer control of temperature, pH, aeration, and
stirring to give the optimum conditions for production.

Careful selection of

production strains of microbes and improved methods of extraction and

purification have increased yields many times over the last 70 years or so. These
traditional techniques are used to produce yeast, alcohol, antibiotics, enzymes,
vaccines and drugs of many kinds (e.g. steroid biotransformations) as well as
basic materials for the food and other industries as dextrans, organic acids (e.g.
citric acid, glutamic acid lactic acid), vitamins, and many kinds of amino acids.

General Microbiology 6

General Microbiology

Chapter 1: Development of Microbiology

A new era of microbiology began with the development of and advances in

recombinant DNA technology in 1973. The technology permitted human genes to
be cut and inserted into microorganisms thus enabling them to manufacture the
gene products far more efficiently than traditional methods of extraction from
animal or human tissues. These techniques used to rearrange the genetic code to
produce an organism with new desirable characteristics such as the ability to
produce certain substance are often referred to as genetic engineering.

The

genetic is concerned with gene or part of DNA that code for the desired
characteristic and engineering refers to cutting out that part of the DNA from
one organism and joining or grafting it into the DNA of another organism (cutting
and splicing)
It was so spectacular that these processes are described nowadays as modern or
new biotechnology to distinguish them from all the previous conventional ones.
Recombinant DNA technology is reshaping medicine and the pharmaceutical
industry; it was used to produce many therapeutic products such as insulin for
human use in 1982 followed by human growth hormone, interferon, blood
clotting factors and many other products. It also allowed the development of more
effective and safer vaccines (compared to those produced by traditional methods)
which use genetically engineered surface antigens rather than whole viruses.
Great potentials lie in gene therapy, which consists of the insertion of genetic
material into cells to prevent, control or cure disease. It includes repairing or
replacing defective genes and making tumors more susceptible to other kinds of
treatment.

Recombinant DNA technology also offers forensic, agricultural and

environmental applications and raises important safety and ethical questions

Finally, another new era and a new golden age of microbiology has started near
the end of the 20th century and the start of the current millennium. A genomic
revolution is being driven by the advances in DNA sequencing, and new
technologies have emerged, such as metagenomics, or the study of microbial life
in different environments by directly sequencing DNA. Today, the Human
Microbiome Project, the Earth Microbiome Project, and other genomic-based
projects are changing the way we understand microbes, our planet, and even
ourselves. Details on these technologies are presented at the end of Part II of this
book.

General Microbiology 7

General Microbiology

Chapter 2: Classification and Identification

Chapter 2: Classification and

Identification of Microorganisms
I. Classification of Microorganisms
A. Nomenclature
All organisms have a double name usually from Latin or Greek stems. The
name consists of two parts, the first part is the genus name to which the
microorganism belongs and the second part is the species name which is usually a
descriptive adjective that further describes the genus name. This system of
nomenclature is called the binomial system (binomial = two names), it was first
suggested by Carolus Linnaeus and it gives scientists throughout the world a
universal system of naming microorganisms to avoid any confusion. When the name
is written, the first letter in the genus name is capitalized while the remainder of
the genus name and the species name is written in lowercase letters. Both names
have to be italicized or underlined when printed.
Examples:

Escherichia coli or Escherichia coli refers to a species of bacteria that inhabit

the intestines. The genus name is after Theodor Escherich (the scientist who
discovered it) while the species name refers to where the bacteria is located
(the colon).

Staphylococcus aureus or Staphylococcus aureus refers to a species of

bacteria that forms grape like clusters of spherical cells. The genus name is
after the words (staphyle=grape and coccus=sphere) while the species name
(aureus = golden yellow) refers to the color of the colonies these bacteria
form when they grows on solid media.

Scientists usually abbreviate the binomial names by writing only the first letter of
the genus name together with the full species name. This abbreviation should also
be italicized or underlined. Thus, Escherichia coli becomes E. coli or E. coli and
Staphylococcus aureus becomes S. aureus or S. aureus.

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Chapter 2: Classification and Identification

B. Classification Systems
B.1. The three-kingdom classification
In 1866 the German scientist Ernst H. Haeckel proposed a new system to
separate microorganisms and distinguish them from the plant and animal kingdoms
which were the only two divisions known at that time. Haeckel grouped all
microorganisms including bacteria, protozoa, algae and fungi in a new third
kingdom known as Protista. At that time there was a plethora (excess) of newly
identified microorganisms as a result of both Pasteur and Koch work and the new
kingdom Protista came to include all the newly discovered microorganisms that
share plant and animal characteristics but were not plants or animals.
B.2. The five-kingdom classification
In the 20th century, advances in cell biology led scientists to question the two- or
three- kingdom classification. In 1969 Robert H. Whittaker proposed a system that
classified all living organisms into five kingdoms.

Kingdom
Kingdom
Kingdom
Kingdom
Kingdom

Monera (bacteria).
Protista (unicellular algae and protozoa).
Fungi (mushrooms, mold and yeast).
Plantae (multicellular plants).
Animalia (multicellular animals).

Consequently, microorganisms comprised three out of the five kingdoms of

Whittaker classification (Monera, Protista and Fungi).
B.3. Two types of cellular organizations, Prokaryotes and Eukaryotes
In the 1940s and 1950s the electron microscope was being developed and
was able to magnify objects and cells thousands of times more than a typical light
microscope. With the electron microscope, bacteria were seen as being cellular like
other microbes, plant and animals. However, their cells were organized in a
fundamentally different way from other organisms. Plant and Animal cells had a cell
nucleus that houses the genetic material in the form of chromosomes and this
structure is physically separated from other cellular structures by a membrane
envelop. This type of cellular organization is called eukaryotic (having true nucleus)
(eu=true; karyon=kernel, nucleus). Microscopic observation of protista and fungi
also revealed that their cells had a eukaryotic organization (true nucleus). Bacteria
on the other hand lack the presence of a true nucleus as the genetic material in the
form of the bacterial chromosome is not surrounded by a membrane. Bacteria is
therefore classified as prokaryotes meaning it has a primitive cellular organization
as (pro=primitive). Eukaryotic cells, including eukaryotic microbes, have a variety of
structurally discrete compartments called organelles (endoplasmic reticulum, golgi
apparatus, lysosomes and mitochondria).These organelles are absent from
prokaryotic cells. Therefore and based on the Whittaker five-kingdom classification
only one kingdom (Monera) is prokaryotic while the four other kindgdoms (Protista,
Fungi, Plantae, and Animalia) are eukaryotic.

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Chapter 2: Classification and Identification

B.4. The three-domain system classification

In the 1970s and with the advent of new techniques in molecular biology
and biochemistry Carl Woese proposed the three-domain system or suprkingdooms
for classification of living organisms.

Domain Archaea
Domain Eubacteria
Domain Eukarya

The Archaea included a group of bacteria that were formally known as

archaebacteria (archae=old) and were known for their ability to live under harsh
environmental conditions that were dominant in early stages of life. The Eubacteria
(true bacteria) included all other types of bacteria (Similar to kingdom Monera but
without the archaebacteria). The separation between these two types of bacteria as
distinct domains was based on the differences in the composition of their cell walls,
lipid composition of their membranes, the sequence of their ribosomal RNA (the
RNA component of the ribosome), and their sensitivity to different antibiotics.
These differences were only discovered after the advances in molecular biology
techniques at that time and were confirmed with more studies that were done in the
1990s when it became feasible to know the complete sequence of DNA of many
bacterial species. The third and last domain: domain Eukarya comprised the four
remaining kingdoms of Whittaker (Protista, Fungi, Plantae and Animalia).
Consequently, the first two domains (Archaea and Eubacteria) are Prokaryotes while
the last domain (Eukarya) is Eukaryotic.
Bacterial taxonomy on the molecular level
Because of the important position that bacteria occupy in microbiology and
because bacterial taxonomy has been through complex systems, there exists a
guide which includes the official listings of all recognized bacteria. This guide is
known as Bergeys manual of systematic bacteriology or simply Bergeys manual.
The system of classification and identification was devised by David Hendricks
Bergey in the 1920s.The manual has been updated in several editions and is a
complete guide for the identification and classification of bacteria and now has
information about each organism on the molecular level.

General Microbiology 10

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Chapter 2: Classification and Identification

Whittaker five-kingdom classification

Woese three-domain classification

General Microbiology 11

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Chapter 2: Classification and Identification

Main differences between Prokaryotic and Eukaryotic cell structures

Character
Nucleus

Prokaryotes
No nuclear envelop

DNA
structure
Membranes

Single, circular
chromosome
Cell membrane only

Organelles

absent

Ribosome

70S (smaller than

eukaryotic ribosome),
free in the cell
Absent
Present, formed of
peptidoglycan

Cytoskeleton
Cell wall
Flagella
Cilia
Cell division
Reproduction
Examples

Rotating movement
absent
Binary fission
Asexual
Archaea, Eubacteria

Eukaryotes
True nucleus, with nuclear
membrane
Multiple linear chromosomes
in the nucleus
Cell and organelle
membranes
Present (Endoplasmic
reticulum ER, mitochondria,
golgi bodies, lysosomes)
some have chloroplasts
80S (larger than prokaryotic
ribosome) free or bound to ER
Present
Present in fungi, algae and
plants formed of chitin (fungi)
or cellulose
Whipping movement
Sometimes present
Mitosis and meiosis
Sexual and Asexual
Fungi, Protista, Plants,
Animals

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Chapter 2: Classification and Identification

C. Various groups of microorganisms

Fungi

Fungi are eukaryotic microorganisms; their cells wall contains the

polysaccharide chitin which distinguishes them from plant cells.

Fungi do not carry out photosynthesis, but absorb and use preformed organic
matter from the environment as their nutritional source. This is another
difference that fungi have from plant cells that carry out photosynthesis. They
grow best in warm, moist places.

Fungi are divided into two main groups: the unicellular fungi (yeast) and
multicellular fungi (molds), again both types of cells are eukaryotic.
o

Yeasts are unicellular organisms larger than bacteria. They play an important role
in industry particularly in fermentation and production of bread.

Molds are multicellular organisms. Their body consists of a fluffy mass of

filaments called hyphae (sing., hypha). The hyphae form dense network called
mycelia (sing., mycelium).
The hyphae can have cross walls or septa (sing., septum) that divide the
cytoplasm within the hypha into separate cells, such fungi are described as
septate. The septa are incomplete as there are pores within the septa to allow the
contents of the cell cytoplasm to mix with the adjacent ones freely. Other types of
fungi do not have these septa and are (non septate).

Among The important fungi to humans are those that produce antibiotics such
as the fungus Penicillium, a mold that produces penicillin.

Some types of fungi play an important role in decomposing organic matter,

few species do not wait for an organism to die and consequently cause disease
to humans and also to plants.

Among the diseases caused to humans by fungi are candidiasis, which is a

skin infection caused by Candida albicans, and dermatophytosis which is a
fungal infection of the hair, skin and nails caused by certain species of the
genus Trichophyton, Microsporum or Epidermophyton.

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Chapter 2: Classification and Identification

Algae

Algae are eukaryotic organisms that carry out photosynthesis but are
different from plants.

Two types of unicellular algae, the diatoms and dinoflagellates, play an

important role in marine life as they both make up the phytoplankton which is
a major food source for marine and aquatic animals.

Both types of algae carry out photosynthesis and trap the suns energy to
manufacture carbohydrates, which are passed to other aquatic organisms in
the food chain.

The cell wall of diatoms is impregnated with silicon dioxide, which is a glasslike substance. When they die these glassy remains accumulate on the seafloor
as diatomaceous earth, which is extracted and used in filtering devices and as
mild abrasives in toothpastes.

The cells wall of dinophlagellates is encased in hard cellulose shells.

Protozoa

Protozoa are eukaryotic single-celled microorganism. Most of them lack cell

walls, move freely, and ingest food particles.

Digested food particles enter the food vacuoles, which are then joined by
lysosomes where digestive enzymes digest the food. Nutrients are absorbed
from the food vacuole, and any waste is eliminated.

Many protozoa decompose dead organisms and recycle nutrients.

Some species are important links in the food chain as they help other
organisms break down complex molecules into simple ones that can be
utilized. For example: some protozoa live in the intestine of grass-feeding
animals and help break down cellulose.

Protozoa have a different assortment of shapes, sizes and structural

components, but they are classified according to their movement mechanisms
into four groups (amoebas, flagellates, ciliates, and sporozoa).
o

Amoebas move by psuedopods (false feet), example: Entamoeba

histolytica which causes diarrhea.

Flagellates move by a whip like flagella, example: Euglena which lives

in fresh water ponds and can carry out photosynthesis.

Ciliates move by hair like structures (cilia) that protrude from all
around the body, example: Paramecium.

Sporozoa: No psuedopods, flagella, or cilia, examples: Plasmodium

which causes malaria and Toxoplasma which causes toxoplasmosis.

General Microbiology 14

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Chapter 2: Classification and Identification

Bacteria

Bacteria are among the most abundant organisms on earth (~1030 cells)

The term bacteria is a plural form of the Latin word bacterium meaning
staff or rod.

There may be more than 10 million species of bacteria.

Bacteria are single-celled and they are divided into two main domains: the
Archaea and Eubacteria. Both groups are more metabolically diverse than any
other microbes.

Bacteria come in three different shapes: bacillus (rod shaped), coccus

(spherical) and spirillum (spiral).

Most bacteria absorb their food from the environment but some of them
(Cyanobacteria) can carry out photosynthesis.

Bacteria more than any other organism have adapted to the diverse
environments on earth. They inhibit air, soil and water and they exist with
large numbers on the surfaces of all plants and animals.

Bacteria can be isolated from arctic ice, thermal hot springs, animal tissues
and even outer space.

Certain types of bacteria can withstand the powerful activity of digestive

enzymes the crushing pressure of deep oceans and the acidity found in
volcanic ash. Others can withstand boiling water, extremely dry conditions and
some can survive in oxygen-free environment.

Bacteria have so completely colonized every part of the earth that the mass of
bacterial cells is estimated to outweigh the mass of all plants and animals
combined.

The vast majority of bacteria play a positive role in nature; they break down
remains of dead organisms and recycle the carbon, digest sewage into simple
chemicals, extract nitrogen from air and make it available for plants for
protein production and produce foods for human consumption like cheese and
yogurts and products for industrial technology. It is safe to say that life as we
know it would be impossible without bacteria.

Some bacteria (disease causing bacteria or pathogenic bacteria) are harmful as

certain species multiply within the human body where they disrupt tissues or
produce toxins that result in human disease (Typhoid, Plague, Tuberculosis
and Cholera just to name a few). Other bacteria infect animal herds and plant
crops.

The diseases bacteria cause will be handled in the Medical Microbiology

course next semester.

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Special types of bacteria

Rickettsiae
First described by Howard Taylor Ricketts in 1909.
Very tiny nonmotile organisms can be barely seen with the light microscope.
Must be grown on living tissues such as fertilized eggs.
They are transmitted among humans by arthropods like ticks and lice.-They
cause a number of important diseases like Typhus fever and Rocky Mountain
spotted fever.

Chlamydiae
Very tiny organisms- half the size of rickettsiae.
Cannot be seen with the light microscope and must be grown in living cells.
They can cause pneumonia (chlamydial pneumonia) and Chlamydial urethritis
(sexually transmitted disease).

Mycoplasma
The smallest of all types of bacteria.
Can be cultivated on artificial media in the laboratory.
Prokaryotic but lacks the presence of a true cell wall which is present in all
other bacteria.
Certain species of mycoplasma can cause pneumonia.

Cyanobacteria

Cyanobacteria were once known as blue green algae but are now grouped
among bacteria due to the structural and biochemical similarities to typical
bacteria.
Cyanobacteria still have a major difference from typical bacteria which is
their ability to carry our photosynthesis similar to unicellular algae; this
character makes them unique among prokaryotes.
Cyanobacteria possess light trapping pigments that function in
photosynthesis. The pigments are usually blue or green but some are yellow,
black or even red.
The periodic redness of the Red Sea (hence the name) is due to the presence
of cyanobacteria whose members contain large amounts of red pigments.

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Non-cellular microscopic life forms

Viruses

Viruses are the most abundant life forms on this planet (~ 1031 viral particles)
Viruses are structurally simpler than other microbes because they are not
made of cells.
Viruses are smaller than the tiniest bacteria and can only be seen by electron
microscope.
They are neither prokaryotes nor eukaryotes.
They have a core of nucleic acids (DNA or RNA) surrounded by a protein coat
or shell (capsid).
As independent entities they do not grow or show any metabolic activity. They
only replicate when they are inside a living cell.
When a virus penetrates a host cell its genetic material is released inside the
cell.
The virus utilizes the cell enzymes and structures and replicates itself
hundreds of times thus, destroying the cell.
Newly formed viruses attack neighboring cells and repeat the cycle where the
virus particles replicate inside the host cells leading to their destruction and
forming more virus particles until the whole tissue is destroyed.
Viruses cause many disease in humans among them are (AIDS, SARS, Bird flu).
Certain types of viruses attack bacteria they are known as bacteriophages or
simply phages.

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Prions

Prions are considered to be infectious protein structures. They are composed

solely of proteins and contain no nucleic acids.
They cause mad cow disease or bovine spongiform encephalopathy (BCE) in
cows (bovine). They cause scrapie in sheep and goats which is a similar
neurological degenerative disease.
They cause Creutzfeldt-Jacob disease in humans which is also a neurological
degenerative disease.
All these diseases belong to a rare group of diseases called transmissible
spongiform encephalopathy (TSEs) as they can be transmitted among
animals of the same species as well as other animals in different species and
to humans.
Some theories hypothesize that infection is due to the presence of two types
of prion protein the normal PrPC and the abnormal PrPSC which has a defective
shape.
The normal prion protein is present in normal brain cells while the abnormal
one is present in the infected cells and is believed to be the causative agent of
the disease.
With PrPSC (abnormal shape) proteins cannot organize well in the cell
membrane and the cell eventually dies.
The defective protein binds to normal ones causing them to change their
shape and become defective and so on that is how the disease spreads
without the need of DNA or any genetic materials.
Infection occurs after eating products contaminated with the defective protein
PrPSC as it can cross the blood brain barrier and reaches the brain where it can
remain dormant for up to 10 years. Once active, the disease runs its course in
less than one year.
It is still not clear how the abnormal protein (PrPSC ) causes the clinical
symptoms of the disease or the deadly pathogenesis that result.

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Microorganisms

Classification

Distinguishing character

Bacteria

Prokaryotic

Extremely abundant, microscopic. Many play

positive role in nature, some cause diseases.
Special types such as rickettsiae and
chlamydiae multiply only in host cells,
mycoplasma do not have a cell wall and
cyanobacteria can carry out photosynthesis

Fungi

Eukaryotic

Unicellular (yeast) or multicellular (molds)

which are filamentous. Unique cell wall
(Chitin), not photosynthetic

Protozoa

Eukaryotic

Animal-like, classified by type of motion, no

cell wall not photosynthetic

Unicellular Algae

Eukaryotic

Plant-like, photosynthetic, usually marine

forms include diatoms and dinoflagellates

Viruses

Acellular

Ultramicroscopic, non-cellular inert particles

formed of DNA or RNA, enclosed in protein
capsule, cannot replicate except in living
cells.

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II. Identification of Microorganisms

A. Size, shape and arrangement of bacterial cells
Most bacteria range from 0.2-2 m in diameter and from 2-8 m in length.
Bacteria can have three basic shapes:
Bacillus (pl., bacilli): rod shaped.
Coccus (pl., cocci): spherical.
Spirals.

Rod shaped bacteria (Bacilli)

Bacilli have a cylindrical shape.

The cylindrical cell may be as long as 20 m or as short as 0.5 m.
Some bacilli are slender such as those of Salmonella typhi that cause typhoid
fever, others such as those of Bacillus anthracis (which causes anthrax) are
rectangular with square ends and others as those of Corynebacterium
diphtheriae (which causes diphtheria) are club shaped.
Most rods are singly arranged, but Sometimes the bacilli form long chains
called streptobacilli as (strepto=chain).

Spherical shaped bacteria (cocci)

Spherical bacteria tend to be small usually 0.5 to 1 m in diameter.

They are usually rounded but sometimes thy may be oval, elongated or
indented on one side.
Many bacterial species that are cocci stay together after cellular division
resulting in a cellular arrangement characteristic of the organism.
The cocci that remain in pairs after division are called diplococci examples
are Niesseria gonorrhea (the causative agent of gonorrhea) and N. meningitis
(the causative organism of meningitis).
Cocci that remain in chains are called streptococci as
Streptococcus pyogenes, which causes throat infections, and S. lactis, which
is harmless and is used in manufacture of yogurt.
When four cocci form a square, the arrangement is known as tetrad.
A cube like packet of eight cocci is known as Sarcina as Micrococcus luteus,
a common inhabitant of the skin.
Other cocci may divide irregularly and forma a cluster of grapelike cluster of
cells known as Staphylococcus. Example is Staphylococcus aureus the
causative bacterium for certain type of food poisoning and skin infections.

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Spirals and other shapes

The third most common shape is the spiral.

The spiral can be of three different shapes (vibrios, spirilla, and spirochetes).
Curved rods that resemble commas are known as vibrios. An example is
Vibrio cholerae, the causative agent of cholera.
Spiral bacteria with a helical shape, a thick rigid cell wall and flagella that
assist in movement are known as spirilla (sing., spirillum).
-Spiral bacteria with thin flexible cell wall and no real flagella are known as
spirochetes. Movement of spirochetes occurs by contraction of an axial
filament that runs through the length of the cell. An example is the
bacterium Treponema pallidum the causative agent of syphilis.

Other shapes
In addition to the usual bacilli, cocci and spiral shaped bacteria, some types
of bacteria have branching filaments such as (Nocardia), others may have
square, star, or irregular shapes.

Different shapes of bacteria

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B. Bacteria form colonies on solid culture media

Bacterial cells divide very rapidly (E.coli divides every 20 minutes). A single
cell can produce millions of cells if the conditions are favorable. This collection of
identical cells arising from the division of one single cell is called a clone. If these
cells are grown on a solid medium (nutrient agar plates), the cells grow close to
each other and the large number of cells produced becomes visible in the form of a
colony.
Bacterial colonies have distinct shapes, sizes and morphological characters
that help in the identification of bacteria.

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