‫ميحرلا نمحرلا هللا مسب‬

ORAL
MICROBIOLOGY
lecture 1

INTRODUCTION
Prof. Mohamed Shohayeb

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Oral Microbiology:
• Oral microbiology is the study of the microorganisms of the
oral cavity and their interactions with the host.
What we will study?
1. Basic knowledge about microbes and their diversity
and basic structures.
2. Dental infections, dental caries and immunology.
3. Infection control
4. Antimicrobial chemotherapy
Reference Book
Samaranayake, L. (2018). Essential microbiology for dentistry-E-Book. Elsevier
Health Sciences.

2
 Classification of organisms
Based on genetic relatedness, forms of life fall into three
domains.

The evolution of
life was described
by Charles
Darwin In 1859.
But the Qur’an
pointed to it
1more than 14
centuries ago.
But with the will of
Allah and not
spontaneously.

َ ‫علَ ٰى ك ُِل‬
‫ش ْيء‬ َ َّ ‫ئ النَّشْأَةَ ْاْل ِخ َرةَ ۚ ِإ َّن‬
َ ‫َّللا‬ ُ ‫ش‬
ِ ‫َّللاُ يُن‬ َ ‫ف بَدَأَ ا ْل َخ ْل‬
َّ ‫ق ۚ ث ُ َّم‬ ُ ‫ض فَان‬
َ ‫ظ ُروا َك ْي‬ ِ ‫يروا فِي ْاْل َ ْر‬
ُ ‫س‬ِ ‫قُ ْل‬
)20 ‫قَدِير (العنكبوت‬ 3
Classification of organisms
• Bacteria comprise the vast majority pathogens
humans.
• Archaea and Bacteria are also known as prokaryotes.
Archaea rarely cause human disease and live in
extreme environments (e.g. high temperature).
• Viruses are not included in this classification, because
they are particles. They are genetic material (DNA or
RNA) and there is no cytoplasm. They use the
biochemical machinery of the host.

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Reproduction
• Bacteria reproduce by binary fission (divides
into two similar cells).
• Fungi reproduce by sexual and asexual spore
formation.
• Viruses reproduce copies of their nucleic acid and
proteins. Then they reassemble to produce other
viruse particles.

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 Prokaryotic and Eukaryotic cells
Prokaryotes (Archaea & and Bacteria)
Bacteria:
The genome (chromosome) is a single,
circular molecule of double-stranded
DNA, with no nuclear membrane. They
may have (smaller, single or multiple
circular DNA molecules called plasmids.
Eukaryotes
Like Fungi, protozoa and humans.
Eukaryotes have a nucleus
(surrounded by a membrane) and
organelles such as mitochondria,
ribosomes and complex endoplasmic
reticulum
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 Shape, size and arrangement of Bacteria
• The shape of a bacterium is
determined by its rigid cell wall.
• The size of bacteria ranges
from about 0.2 to 5 μm.
• Bacteria are classified by
shape into three basic groups:
1. cocci (spherical)
2. bacilli (rod shaped)
3. spirochaetes (helical).

• Some bacteria have variable

shapes, appearing as both
coccal and bacillary forms, and
are called pleomorphic.
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Structure
Bacteria have a rigid cell wall that
protects a fluid protoplast, which
includes a cytoplasmic membrane
and various other components.

Structures external to the cell wall

Flagella
• Flagella are filaments that act as propellers.
• They are composed of a protein subunit called, flagellin.
• Spirochaetes move by axial filament, which wraps around
the cell.

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Fimbriae and pili
• Fimbriae and pili are hair-like filaments,
shorter than flagella.
• Pili are typically longer and thicker than fimbriae. They are
composed of subunits of a protein, pilin.
• They mediate the adhesion of bacteria to receptors on the
human cell surface.
• The sex pilus forms the attachment between the male (donor)
and the female (recipient) bacteria during conjugation.
Glycocalyx (slime layer)
• It is a polysaccharide coating the bacterial
outer surfaces.
• It allows the bacteria to adhere firmly to various
structures. They contribute to the formation of
biofilms on teeth, heart valves and catheters.
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Capsule
It is composed of polysaccharide, and sometimes protein. The
sugar components of the polysaccharide vary in different
bacterial species.
The capsule is important because:
• It mediates the adhesion of bacteria
to human tissues or prosthesis such
as dentures or implants.
• It hinders or inhibits phagocytosis; hence factor.
• It helps in laboratory identification of organisms (in the
presence of antiserum against the capsular polysaccharide.
• Its polysaccharides are used as antigens in certain vaccines
(e.g., polysaccharide vaccine of Streptococcus pneumoniae)
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Cell envelope
The cell envelope consists of the cell wall and the cell
membrane.
The cell wall
It is a peptidoglycan layer. It is thicker in Gram-positive
bacteria than in Gram-negative bacteria.

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Outer membrane
• The Gram-negative organisms have an outer membrane
composed of lipopolysaccharide (LPS), lipoprotein and
phospholipid. The Gram-positive bacteria have no LPS in
their cell walls).
• Between the outer membrane and the cytoplasmic
membrane of
Gram-negative
bacteria is a
periplasmic
space.
• The LPS of
Gram-negative
bacteria is called
the endotoxin. It
causes fever and
shock.
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Cytoplasmic membrane
The cytoplasmic membrane is composed of a phospholipid
bilayer similar in appearance to that of eukaryotic cells. It
contains no sterols, like eukaryotic cells.
The membrane has the following major functions:
■ Active transport and selective diffusion of molecules in and
out of the cell
■ Electron transport and oxidative phosphorylation, in
aerobic species which is responsible for ATP formation.
■ synthesis of cell wall precursors
■ secretion of enzymes and toxins
■ has receptors of the chemotactic and sensory systems.

13
Cytoplasm
The cytoplasm contains nuclear material, ribosomes,
cytoplasmic inclusions and ions.
Nuclear material or nucleoid
Bacterial DNA comprises a single, supercoiled, circular
chromosome. It undergoes semiconservative replication.
Ribosomes
Ribosomes are 70S, compared with
eukaryotic ribosomes of 80S. They are
the basis of action of some antibiotics
that inhibit protein synthesis.
Cytoplasmic inclusions
like polysaccharide and β-
hydroxybutyrate serve as
sources of stored energy. 14
Bacterial spores
• Spores are formed in response to adverse conditions by
the bacteria that belong to the genus Bacillus (which
includes the agent of anthrax) and the genus Clostridium
(which includes the agents of tetanus and botulism).
• Spores are resistant
to heat, dehydration,
radiation and
chemicals.
• They are metabolically
inert and can remain
dormant for many
years.

15
Bacterial physiology
Growth 3. Inorganic ions
• Bacteria manufactures their Nitrogen, Sulphur, phosphate,
proteins, lipids, nucleic acid, etc. magnesium, potassium and several
trace elements are required for
1. Oxygen and hydrogen
bacterial growth.
• Both O2 and H2 are obtained from
water. 4. Organic nutrients
• Aerobic bacteria requires oxygen.
• Anaerobic bacteria is inhibited by • Organic nutrients are essential in
oxygen. some bacterial species:
• Carbohydrates are energy source
2. Carbon
and as substrate for other
• Autotrophs:CO2 is the carbon
source. substances.
• Heterotrophs: Complex organic • Amino acids, vitamins, purines and
substances are the source of pyrimidines are needed for some
energy. bacteria.
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Reproduction
• Bacteria reproduce by binary fission. The parent cell divides
to form a progeny of two cells.
• The doubling or mean generation time of bacteria may vary,
(e.g. 20 min for Escherichia coli, 24 h for Mycobacterium
tuberculosis).
• Factors that affect the doubling time include the amount of
nutrients, the temperature and the pH of the environment.

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Bacterial growth cycle
The growth cycle of a bacterium has four main phases.
1. Lag phase: lasts for a few minutes to many hours. It is a
period of adaptation with vigorous metabolic activity.
2. Log (logarithmic, exponential) phase: rapid cell division
occurs, determined by the environmental conditions.
3. Stationary phase: this is reached when nutrient depletion
or toxic products cause growth to slow until the number of
new cells produced balances the number of cells that die.
4. Decline or death phase: this is a decline in the number of
live bacteria.

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Bacterial growth curve
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Growth regulation
Bacterial growth is essentially regulated by:
Intracellular factors include:
■ End product inhibition ■ Catabolite repression
Extracellular factors include:
Temperature:
• Mesophiles, which grow well between 25° and 40°C (that
grow best at body temperature)
• Thermophiles, which grow between 55° and 80°C
• Psychrophiles, which grow at temperatures below 20°C.
pH:
It should be around pH 7.2–7.4 (i.e., physiological pH). Some
bacteria (e.g., lactobacilli) can grow in carious cavities where
the pH may be as low as 5.0. 20
Aerobic and anaerobic growth
bacteria can be classified as follows:
■ obligate (strict) aerobes, which require oxygen to grow.
because their adenosine triphosphate (ATP)-generating
system is dependent on oxygen as the hydrogen acceptor.
■ obligate (strict) anaerobes, which cannot grow in the
presence of oxygen because they lack either superoxide
dismutase or catalase, or both (e.g., Porphyromonas
gingivalis)
■ facultative anaerobes, which use oxygen to generate
energy by respiration if it is present, but can use the
fermentation pathway to synthesize ATP in the absence of
sufficient oxygen (e.g., mutans streptococci)
■ microaerophiles, that grow best at a low oxygen
concentration (e.g., Campylobacter fetus). 21
Bacterial genetics
• All inherited characteristics are encoded
in DNA, except in RNA viruses.
The bacterial chromosome
• The bacterial chromosome contains the
genetic information that defines all the
characteristics of the organism.
• It is a single, continuous double-
stranded DNA with a closed, circular
structure attached to the cell membrane
of the organism.
Replication
• Replication is semiconservative.
• It is synchronous with cell division. Each
cell receives a full complement of DNA
from the mother cell.
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Genetic variation in bacteria
Genetic variation can occur as a result of mutation or gene
transfer.
Mutation
A mutation is a change in the base sequence of DNA, as a
consequence of which different amino acids are incorporated into
a protein.
Gene transfer in bacteria
The transfer of genetic information can occur by: Conjugation,
Transduction and Transformation

1. Transformation 2. Conjugation 3.Transduction

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Plasmids
• Extrachromosomal, double-stranded circular DNA molecules.
They replicate independently of the chromosome.
• Transmissible plasmids can be transferred from cell to cell by
conjugation and transformation.
• Plasmids may carry drug-resistance
genes.

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Polymerase chain reaction (PCR)
• A short region of a DNA molecule or a single gene is
synthesized in vitro by a DNA polymerase enzyme.
• This technique could be used to identify bacteria and
viruses from the oral cavity.

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Mycology
• Mycology is the study of fungi (Myco = fungus).
• Some fungi have the ability to infect plants and animals.
General properties
• They are Eukaryotes.
• They have ergosterol in their membranes and a rigid cell wall made of
chitin.
• Non-motile and chemoheterotrophs (org. comp. are source of energy
and carbon).
• Osmiotrophic (tolerate high osmotic pressure).
• They are saprophytes or parasites.
• Molds are aerobic, and yeasts are facultative anaerobes.
• They reproduce asexually and or sexually by spores.
• Food storage is generally as lipids or glycogen.
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Classification based on morphology:
1. Molds (filamentous fungi).
2. Yeasts (single cells that forms bud)
3. Dimorphic (two morphological forms at
different environmental conditions.

Reproduction
• Sexual reproduction
• Asexual reproduction

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VIROLOGY
• Viruses can cause severe acute oral and orofacial disease, produce
systemic infections and be transmitted to patients and dental staff.
• They are small in size (10–100 nm)
• Viruses are small obligate intracellular parasites.
• Viruses may contain either RNA or DNA genome surrounded by a
protective protein coat.
• Viruses are unable to generate energy.
• Viruses are propagated in host cells supplying the complex
metabolic and biosynthetic machinery.
• A complete virus particle is called a virion.
• The main function of the virion is to deliver its DNA or RNA genome
into the host cell so that the genome can be expressed.
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 VIROLOGY (cont.) capsid

Structure and Function

• The viral genome, is packaged inside a
symmetric protein capsid (naked
virus).
In enveloped viruses, the capsid is
Naked Virus
surrounded by a lipid bilayer .
capsid
• the capsid protects the viral genome .
• During infection the capsid or spikes
attach the virion to specific receptors
on the host cell.
• Capsid proteins are coded for by the
virus genome. Enveloped virus
• Capsids consist of only one or more
structural protein species.
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 spikes

Structural components and symmetry

 2- Life cycle of eukaryotic viruses
• The life cycle is basically the same as that of
bacteriophage.
• In case of enveloped viruses penetration takes place
through fusion or engulfment.

Entry by fusion with host CM.

Entry by engulfment. 31
LIFE CYCLE OF EUKARYOTIC VIRUSES (cont.)

• Finally the mature virus or VIRIONS are released into

the environment to begin the cycle again.
• Release involves lysis or budding
• In enveloped viruses budding involves involves taking a
portion of the cell membrane .
• In both cases cells eventually die.

Release of virus by budding 32

PRIONS
• Prions are infectious proteins. They are able to convert a
"normal" protein into a non-functional "prion protein".
• As the number of prions increases in brain they eventually
kill the victim.
• There is no treatment for prion diseases and they lead to
death.
• Prions are not destroyed by autoclaving, cooking
temperatures, most disinfectants or being buried in the
soil for months.
• They cause the following diseases:
1. KURU which infects its victims when they eat the brain
tissue of their enemies (tribes in Africa).
2. MAD COW DISEASE.
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