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MODULE:
MICROBIOLOGY
Contributor Modul :
Prof. Dr. dr. Sanarto Santoso, DTM&H., Sp.MK (K)
dr. Roekistiningsih, MS, Sp.MK(K)
dr. Dewi Santosaningsih, M.Kes
Dr. dr. Dwi Yuni Nur Hidayati, M.Kes
Tutor :
Prof. Dr. dr. Sanarto Santoso, DTM&H., Sp.MK(K)
Prof. Dr. dr. Noorhamdani AS, DMM., Sp.MK(K)
Prof. Dr. dr. Sumarno, DMM., Sp.MK(K)
dr.Roekistiningsih, MS, Sp.MK(K)
Dr. dra. Sri Winarsih, Apt., M.Si
Dr. dr. Dwi Yuni Nur Hidayati, M.Kes
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
BIOLOGY OF MICROBES
MODULE 1
MICROBIOLOGY
Sub-module :
Basic Bacteriology
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Direction:
The module-task should be written, done by the student individually prior before the
small group discussion. To work with the module, the student may refer to the
references as mentioned in the last part of this book.
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Part A
The Microbial World
Overview
For many people, the words germ, microbe, and microorganism bring to mind a
group of tiny creatures that do no quite fit any of the categories in that old question,
Is it animal, vegetable, or mineral? Microorganisms are minute living things that
individually are too small to be seen with the naked eye. The group includes bacteria,
fungi, protozoa, and microscopic algae. It also includes viruses, those noncellular
entities sometimes regarded as being at the border of life and nonlife.
We tend to associate these small organisms only with uncomfortable infections.
However the majority of microorganisms make crucial contributions to the welfare of
the worlds inhabitants by helping to maintain the balance of living organisms and
chemicals in our environment.
Today we understand that microorganisms are found almost everywhere. Yet
not long ago, before the invention of the microscope, microbes were unknown to
scientists. Thousands of people died in devastating epidemics, the causes of which
were not understood. Food spoilage often could not be controlled, and entire families
died because vaccinations and antibiotics were not available to fight infections.
We can get an idea of how our current concepts of microbiology developed by
looking at a few of the historic milestones in microbiology that have changed our
lives. Now that we have generally examined how microbes relate to our everyday
lives, we will take a look at how the field of microbiology developed from its beginning
hundreds of years ago to its current high-technology state.
Learning objectives
1. List several ways in which microbes affect our lives.
2. Explain the importance of observations made by Hooke and van
Leeuwenhoek.
3. Compare the theories of spontaneous generation and biogenesis.
4. Identify the contributions to microbiology made by Pasteur.
5. Identify the importance of Kochs Postulates.
Module task
1.Briefly state the role played by microorganisms in each of the following :
a. Normal microbiota
b. Human insulin production
c. Vaccine production
Jelaskan peran mikroorganisme dalam hal di bawah ini :
a. Flora normal
b. Produksi insulin manusia
c. Produksi vaksin
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Part B
Classification of Microorganisms
Overview
The science of classification, especially the classification of living forms, is
called taxonomy, from the Greek words for law and order. The objective of taxonomy
is to classify living organisms-that is, to establish the relationship between one group
of organisms and another and to differentiate between them. A taxonomic system
enables us to classify organisms that have not yet been studied in detail; that is, a
previously unknown organism can be identified and then grouped or classified with
other organisms that have similar characteristics.
Taxonomy also provides a common reference for identifying organisms already
classified. For example, when a bacterium suspected of causing a specific disease is
isolated from a patient, characteristics of that isolate are matched to lists of
characteristics of previously classified bacteria to identify the isolate. After the
bacterium has been identified, drugs can be selected that affect that bacterium.
Finally, taxonomy is a basic and necessary tool for scientists, as it provides a
universal language of communication. Modern taxonomy is an exciting and dynamic
field; new techniques in molecular biology and genetics are providing new insights
into classification and evolution.
Learning objectives
1. Define taxonomy
2. List the characteristics of the Kingdom Procaryotes that differentiate it from
other kingdoms.
3. List the major characteristics used to differentiate among kingdoms in the
five-kingdom system
Module task :
1.List and define the five kingdoms used in the five-kingdom system of classification.
Sebut dan jelaskan lima kingdom yang digunakan dalam klasifikasi dengan sistem
lima kingdom.
2.List the ten bases for the classification of microorganisms. Separate your list into
those test used primarily for taxonomic classification and those used primarily for
identification of microorganisms already classified.
Sebutkan 10 dasar klasifikasi mikroorganisma sesuai table di bawah ini.
Taxonomic classification
Identification of microorganisms
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Part C
Microbial Morphology and Ultrastructure
Overview
Despite their complexity and variety, all living cells can be divided into two
groups, procaryotes and eucaryotes, based on their ultrastructure as seen with the
electron microscope. Plants and animals are entirely composed of eucaryotic cells. In
the microbial world, bacteria and cyanobacteria are procaryotes. Other cellular
microbes fungi (yeast and molds), protozoa, and algae-eucaryotes.
Learning objectives
1. Identify the three basic shapes of bacteria.
2. Describe the structure and function of the glycocalyx, flagella, axial filaments,
fimbriae, and pili.
3. Compare and contrast the cell walls of gram-positive bacteria and gramnegative bacteria.
4. Describe the functions of endospores, sporulation, and endospore
germination.
Module task
1. Draw the structure of bacterial cell.
Gambar struktur sel bakteri.
2. Match the structures to their functions.
Cocokkan struktur di bawah ini dengan fungsinya.
1.
2.
3.
4.
5.
6.
7.
8.
________
________
________
________
________
________
________
________
Cell wall
Endospore
Fimbriae
Flagella
Glycocalix
Pili
Plasma membrane
Ribosomes
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c. Coccus
5.Endospore formation is called ____(a)_________. It is initiated by
_______(b)__________. Formation of a new cell from an endospore is called
__________(c)______________.
This
process
is
initiated
by
______(d)___________.
Pembentukan endopora disebut ___(a)___________. Diawali oleh proses
_______(b)____________. Pembentukan sel baru dari suatu endospora disebut
___________(c)________________.
Proses
ini
diawali
oleh
___________(d)________.
6. Diagram cross sections of gram positive and gram negative bacterium cell walls.
Gambar potongan melintang dinding sel bakteri gram positif dan gram negatif.
Gram Positive
Bacteria
Gram Negative
Bacteria
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BIOLOGY OF MICROBES
MODULE 2
MICROBIOLOGY
Sub-module :
Bacterial Growth & Metabolism
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Learning objectives
1. List the requirements for microbial growth into physical aspect and chemical
requirements, the growth of bacterial culture, measurement of microbial
growth.
2. List all chemical reactions within living organism, enzyme by living cells,
energy production ,carbohydrat metabolism, lipid and protein metabolism
Module tasks
1. Fill in the table below with the carbon source and energy source of each type
of organism
Organism
Photoautotroph
Photoheterotroph
Chemoautotroph
Chemoheterotroph
Carbon source
Energy source
2.
3.
4.
5.
Draw typical bacterial growth curve. Label and define each of the phases.
Explain five bacterial categories based on organisms oxygen requirement
Most bacteria grow best at pH ..
Methods of measuring microbial bacterial growth and categorize each as
either a direct or an indirect methode
6. Mention factors influencing activity enzymatic
7. Explain microorganisms use two general processes cellular respiration and
fermentation to produce energy from glucose
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References
Tortora, GJ., Funke BR., Case CL, 1998, Microbiology an introduction 6th ed,
Benjamin/Cummings Publishing, USA
Brooks, GF., Butel, JS., Morse, SA., 2001, Jawetz, Melnick, & Adelbers Medical
Microbiology 21st ed, Appleton & Lange, USA
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BIOLOGY OF MICROBES
MODULE 4
MICROBIOLOGY
Sub-module :
Bacterial Genetics & Genetic Engineering
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Microbial Genetics
Overview
Virtually all the microbial traits are controlled or influenced by heredity. The
inherited traits of microbes include thair shape and structural features, their
metabolism, their ability to interact with other organisms perhaps causing disease.
Individual organisms transmit these chaeacteristics to their offspring through genes,
the units of hereditary material that contain the information that determines these
characteristics.
Genetics is the study of what genes are, how they carry information, how their
information is expressed, and how they replicated and passed to subsequent
generations or other organisms.
An understanding of genetics is key to grasping a number of concepts in
microbiology. For example, many antibiotics act by inhibiting steps in protein
synthesis. Knowing how biological information flows from genes to proteins can help
us understand how some antibiotics work, thereby enabling to develop new weapons
against disease.
Researchers are trying to solve the difficult medical problem of microbes
developing antibiotic resistance. A microorganism can become resistant to antibiotics
in any of several ways, all of which depend on genetic information. Resistant
microbes have somehow obtained gene or set of genes that will prevent the action of
antibiotic.
Emerging diseases provide another example of the importance of
understanding genetics. New diseases are the result of genetic changes in some
existing organism. Currently, biologists are using genetics to discover relatedness
among organisms and how life evolved on Earth.
Learning Objectives
1. Describe how DNA serves as genetic information
2. Describe the process of DNA replication and protein synthesis
3. Explain the regulation of gene expression in bacteria by induction, and
repression.
4. Clasify and describe mutations by type
5. Differentiate between horizontal and vertical gene transfer
6. Describe the function of plasmids and transposons
Modul Tasks
1.
2.
Page
3.
4.
5.
6.
7.
Outline how you would find a morphologic mutant and a biochemical mutant
8.
9.
10. Define plasmids and transposons, and their role in antibiotic resistamce
References
Brooks G.F., Butel J.S., Morse S.A., 2004. Jawetz, Melnick, & Adelbergs Medical
Microbiology, 23rd ed. The McGraw-Hill Companies, Inc. p 96 - 118
Tortora G.J., Funke B.R., Case C.L., 2004. Microbiology an Introduction, 8 th ed,
Pearson Benjamin Cummings. p 210 247.
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BIOLOGY OF MICROBES
MODULE 5
MICROBIOLOGY
Sub-module :
The Control of Microbial Growth
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Page
BIOLOGY OF MICROBES
MODULE 6
MICROBIOLOGY
Sub-module :
Antimicrobial Agents
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Antimicrobial agents
Introduction
When the bodys normal defense cannot prevent or overcome a disease, it is often
treated with chemical drugs (chemotherapy). Like disinfectants, antimicrobial
drugs/agents act by interfering with the growth of microbes. But unlike disinfectants,
they must often act within the host. Therefore, their effects on the cells and tissues of
the host are important. The ideal antimicrobial drugs kill the harmful microbes without
damaging the host; this is the principle of selective toxicity.
Antibiotics were one of the most important discoveries in the modern medicine.
Abdominal wounds or ruptured appendix represented nearly certain death from
infection. The use of antimicrobial agents such penicillin and sulfonamide in the
treatment of some infections resulted in rapid cures.
Today, we are seeing these advances are threatened by the development of
resistance of microbes to these drugs.
Learning objectives
Identify the contribution of Ehrlich and Fleming to chemotherapy
Define these terms: spectrum of activity, broad spectrum versus narrow
spectrum
Identify five modes of action of antimicrobial drugs
Compare synergism and antagonism in the drugs combination
List the commonly used antibacterial drugs
Explain the modes of action of antifungal agents
Explain the modes of action of antiviral drugs
Describe tests for microbial susceptibility to antimicrobial agents
Describe the mechanisms of drug resistance
Module task
1. What characteristics would an ideal chemotherapeutic agent have?
2. Both human cells and pathogens synthesize proteins in the ribosomal sites.
How can antimicrobial agents that target this process be safe to use in
humans?
3. Why are antiviral drugs difficult to develop?
4. Compare and contrast the actions of polyenes, azoles, allylamines, and
polymyxin!
5. What is the difference in drug action of synergists compared with that of
antagonists? Give examples of each!
6. What is the definition of cross resistance?
7. Mention the mechanism of action of the followings:
a. Penicillin
c. Sulfonamide
b. Fluoroquinolone
d. Macrolide
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BIOLOGY OF MICROBES
MODULE 7
MICROBIOLOGY
Sub-module :
General Properties of Viruses
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Learning Objective
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Outline
Viral structure
Nucleic acid
Capsid and envelope
General morphology
Taxonomy of viruses
The isolation, cultivation, and identification of viruses
Growing bacteriophage and animal viruses in the laboratory
Viral identification
Viral multiplication
Multiplication of bacteriophage and animal viruses
Task
1.
2.
3.
4.
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BIOLOGY OF MICROBES
MODULE 8
MICROBIOLOGY
Sub-module :
General Properties of Fungi
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Learning objectives
Mention at least three characteristics that distinguish fungi from other groups of
Eukaryotes
List five ways in which fungi are beneficial
Distinguish among septate hyphae, nonseptate hyphae, and mycelia
Describe asexual and sexual reproduction in fungi
List three basic types af asexual spores found in molds
Compare the division of fungi with respect to the formation of sexual spores
Outline/Overview
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Task
1.
2.
3.
4.
5.
References:
1. Brooks GF, JS Butel, SA Morse: Jawetz, Melnick, & Adelbergs Medical
Microbiology, 23rd edition; chapter 45, 2004
2. Tortora GJ, BR Funke, CL Case: Microbiology An Introduction, 6th edition,
chapter 12, 2001
3. Mims C, HM Dockrell, RV Goering, I Roitt, D Wakelin, M Zuckerman: Medical
Microbiology, 3rd edition, chapter 4, 2004
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BIOLOGY OF MICROBES
MODULE 9
MICROBIOLOGY
Sub-module :
The Host - Parasite Relationship
FOR STUDENT
LABORATORY OF MICROBIOLOGY
MEDICAL FACULTY
BRAWIJAYA UNIVERSITY
2014
Page
Overview
After understanding the structure and functions of microbes and some idea of
the variety of microorganisms that exists, we can consider how the human body and
microorganisms interact in term of health and science. A balance exists between host
defense mechanisms and the pathogenic mechanisms of microbes. When our
defenses resist these pathogenic capabilities, we maintain our health; whereas the
pathogens capabilities overcome our defenses, disease result.
Pathogenicity is the ability to cause disease, and virulence is the degree or
extent of pathogenicity. To cause disease, most pathogens must gain access to the
host, adhere to host tissues, penetrate or evade host defense, and damage the host
tissues. Some microbes do not cause disease by directly damaging host tissues, but
the disease is due to the accumulation of microbial waste products.
If only a few microbes enter the host body, they will probably be overcome by
the hosts defense. However, if large numbers of microbes enter our body, the stage
may set for diseases, the virulence of microbes is often expressed as the Infectious
Dose 50 (ID50).
Humans are generally free of microbes in utero. At birth, normal and
characteristic microbial populations begin to establish themselves. After birth, E. coli
and other bacteria acquired from foods begin to inhabit the colon. Many other usually
harmless microbes establish themselves inside other parts of normal adult body, and
its surface. These are called as normal microbiota or normal flora.
Normal cells, tissues, organ, and system of the host body have got some
defense mechanism against the microbial invasions. Broadly we classify them into
two groups:
Nonspecific defense mechanisms
Specific defense mechanisms
Learning objectives
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Module Tasks
1. Compare pathogenicity and virulence!
2. Describe how hemolysins, leukocidins, coagulases, kinases, hyaluronidases,
siderophores might contribute to pathogenicity.
3. Which of the following genera is the most infectious? Explain your answer.
Genus
Salmonella
Legionella
Treponema
Shigella
ID50
105 cells
1 cell
50 cells
200 cells
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