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Basic Microbiology and Immunology
Cell Biology and Microbiology (CBE1006-N)
Teesside University
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Microbial Genetics
Basic Microbiology and Immunology
(MICRO 402)
Lecture Notes
for
Third Year Pharmacy Students
Department of Microbiology and Immunology
Cairo University
Faculty of Pharmacy
General Microbiology Immunology
Edition 2015
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 microbiology–related 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.
Microbiology and Immunology Preface
ii
- Chapter 1: The Development of Microbiology Part I – Table of Contents
- Chapter 2: Classification and Identification of Microorganisms
- I. Classification of Microorganisms
- II. Identification of Microorganisms
- Chapter 3: The Structure of Bacteria
- I. Structures External to the Cell Wall
- II. The Cell Wall
- III. Structures Internal to The Cell Wall
- Chapter 4: Nutritional Requirements for Microbial Growth
- Introduction
- I. Microbial Nutrition
- II. Nutritional/Metabolic Patterns
- III. Cultivating Microorganisms
- Chapter 5: Effect of Environmental Factors on Microbial Growth
- Chapter 6: The Diversity of Microbial Metabolism
- I. Introduction to Metabolism
- II. General Features of Metabolism
- III. Catabolism
- IV. Anabolism or Biosynthesis
- Final Word
- Chapter 7: Microbial Growth and Population Dynamics
- I. Growth Of Microbial Populations
- II. How Can Growth Be Measured?
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’. It is a relatively recent science just over
150 years old. 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’ w hile examining a drop of rain water. Thus a new world
was discovered, and the new science now called ‘microbiology’ was born.
§
General Microbiology Chapter 1 : Development of Microbiology
§ An interesting and economically significant application of Spallanzani’s 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 Spallanzani’s 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 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 th at 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, meat- peptone agar), the isolation of pure culture technique, staining of microorganisms
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 Jenner’s 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 baker’s 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.; and U. 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. steroid biotransformations) as well as
basic materials for the food and other industries as dextrans, organic acids (e. citric acid, glutamic acid lactic acid), vitamins, and many kinds of amino acids.
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 environment s 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 Chapter 2: Classification and Identification
B. Classification Systems
B. 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. The five-kingdom classification
In the 20 th 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 Monera (bacteria).
- Kingdom Protista (unicellular algae and protozoa).
- Kingdom Fungi (mushrooms, mold and yeast).
- Kingdom Plantae (multicellular plants).
- Kingdom Animalia (multicellular animals).
Consequently, microorganisms comprised three out of the five kingdoms of Whittaker classification (Monera, Protista and Fungi).
B. Two types of cellular organizations, Prokaryotes and Eukaryotes
In the 1940’s and 1950’s 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.
General Microbiology Chapter 2: Classification and Identification
B. The three-domain system classification
In the 1970’s 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 1990’s 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 Bergey’s manual of systematic bacteriology or simply Bergey’s manual. The system of classification and identification was devised by David Hendricks Bergey in the 1920’s 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 Chapter 2: Classification and Identification
Main differences between Prokaryotic and Eukaryotic cell structures
Character Prokaryotes Eukaryotes Nucleus No nuclear envelop True nucleus, with nuclear membrane DNA structure
Single, circular chromosome
Multiple linear chromosomes in the nucleus Membranes Cell membrane only Cell and organelle membranes Organelles absent Present (Endoplasmic reticulum ‘ER’, mitochondria, golgi bodies, lysosomes) some have chloroplasts Ribosome 70S (smaller than eukaryotic ribosome), free in the cell
80S (larger than prokaryotic ribosome) free or bound to ER
Cytoskeleton Absent Present Cell wall Present, formed of peptidoglycan
Present in fungi, algae and plants formed of chitin (fungi) or cellulose Flagella Rotating movement Whipping movement Cilia absent Sometimes present Cell division Binary fission Mitosis and meiosis Reproduction Asexual Sexual and Asexual Examples Archaea, Eubacteria Fungi, Protista, Plants, Animals
General Microbiology 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. T hey play an important role in industry particularly in fermentation and production of bread. o Molds are multicellular organisms. T heir body consists of a fluffy mass of filaments called hyphae (sing., hypha). The hyphae form dense network called mycelia (sing., mycelium). o 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.
General Microbiology Chapter 2: Classification and Identification
Bacteria
Bacteria are among the most abundant organisms on earth (~10 30 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.
General Microbiology Chapter 2: Classification and Identification
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.
Basic Microbiology and Immunology
Module: Cell Biology and Microbiology (CBE1006-N)
University: Teesside University
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