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Bacteriology
Content
Content
...
ii
General introduction
...
2
Introduction
...
1
...
2
I
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Fine structure of bacteria
...
2
...
Nucleic acid and plasmid
...
2
...
Cytoplasm
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2
...
The cytoplasmic membrane
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2
...
Cell wall
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2
...
Capsule and slim layers (all called glycocalyx)
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8
I
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6
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9
I
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7
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10
I
...
Sporulation
...
13
Introduction
...
1
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13
II
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Factors affecting bacterial growth
...
2
...
Nutritional requirements
...
2
...
Physical Requirements
...
3
...
18
II
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1
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19
II
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2
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21
II
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3
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21
II
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4
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21
II
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Controlling microbial growth
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4
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Microbial death rates
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4
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Action of antimicrobial agents
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4
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Chemical agents that control microbial growth
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25
Introduction: history
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1
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26
III
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1
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27
III
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2
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27
III
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3
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27
III
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4
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29
III
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5
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31
III
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Major types of bacteria
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2
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Gram- negative bacteria
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2
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Gram-positive bacteria
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3
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31
III
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1
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31
III
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2
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32
i

III
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Extremophiles
...
33
O2 requirement
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35

...
35
IV
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Normal microbiota
...
1
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Relationships between the normal microbiota and the host
...
1
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Cooperation among microorganisms
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2
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39
IV
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1
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39
IV
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2
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39
IV
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3
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39
IV
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4
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39
IV
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5
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39
IV
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Damaging host cells
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3
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Using the host's nutrients: case of siderophores
...
3
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Direct damage
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3
...
The production of toxins
...
3
...
Plasmids, lysogeny, and pathogenicity
...
4
...
45

Course description and content
The problems and methods involved in the systematic study of bacteria will be treated
...
Characterization tests for systematic bacteriology, etiology, epidemiology,
pathogenic mechanisms, clinical symptoms, laboratory diagnosis and control of disease causing bacteria
including - Staphylococcus, Streptococcus Corynebacterium, Bacillus, Lactobacillus, Actinomyces,
Mycobacteria, Enterobacteriaceae, Bacteroides, Mycoplasma, Rickettsia and Chlamydia will be discussed in
detail
...

COURSE OBJECTIVES AND OUTCOMES: The course focuses on systematics, nature,
characteristics, isolation and identification of bacteria
...


ii

General introduction
The world of living things can be divided in the domains of procarya (bacteria-eubacteria and
archaea, virus), and eucarya
...
They
are bacteria and viruses
...
Etymologically it
means rod form
...

Many are beneficial but the few hurtful ones have kill more than weapon throughout history, and are
continuing their destruction in the modern era despite civic sanitation, water purification, immunization,
and antibiotics that have dramatically reduced the overall morbidity and the mortality due to disease
...
It is estimated that eubacterial species
on Earth number in the hundreds of thousands, of which only about 5500 have been discovered and
described in detail
...



...
Magnifications
of 500 to1000X—close to the resolution limits of light microscopy—are required to obtain useful images
of bacteria
...
1–0
...
Large bacteria such as Thiomargarita namibiensis, are extremely rare
...
Another problem is that the size of bacteria offers little
visual contrast when simply observed
...
Chemical-staining techniques
are also used, even if tough the prepared specimens are dead
...
1
...
Cocci are strictly spherical
bacteria and can be encapsulated (pneumococci)
...

Between these groups there are cocobacili or coccoid /ovoid bacteria
...


I
...
Fine structure of bacteria
I
...
1
...
In molecular terms,
chromosomes are composed of (i) large DNA molecules that store information; (ii) RNA molecules in the
process of copying information from specific genes; and (iii) proteins that repair DNA damage, duplicate
the DNA, and control patterns of gene expression
...
In many bacteria, chromosomal DNA appears to be circular, but examples of linear chromosomes
have also been found (Drlica & Bendich, 2004) it is the case of Borrelia burgdorferi, Streptomyces spp
...
An individual cell can contain
multiple identical copies of a single chromosome
...
Some Agrobacterium species contain one circular and one linear- mapping
chromosome
...

When cells contain very large plasmids, the distinction between plasmid and chromosome blurs if both
carry genes essential for cell growth
...
In E
...
The genomic sequence of many bacteria is known
...
coli comprises 4
...


Bacteriology, first part

2

Table 2: Form and arrangement of bacteria
...

Extremely
spherical Roseus, M
...
aureus
...

Pairs: diplococcic Neiseria gonorrheaa,
It is the simplest form N
...

and
Micrococciis
a
minute
sphere tetrogenus, Deinococcus radiodurans
(0
...
25µ
in Chain: streptococci
...

diameter) they lack
flagella
...

Cluster: staphylococci and sarcines
Encapsulated (pneumococci)
Straigh rods, Uniform
thickness with rounded
or pointed ends, club
form: bacilli
...
5-1
...
Diplobacillus pneumoniae
...
3–1 µm)
(Rickettsiae)
Comma shaped: Vibrio

Curved rods
...
5-3µ in diameter
...
They are nonessential genetic structures and reproduce autonomously
...
The DNA double helix (one winding/10 base pairs) is also wound
counterclockwise about its helical axis (one winding/15 helical windings)
...
Only supercoiled DNA can be replicated and transcribed
...


Bacteriology, first part

3

Figure 1: Basic bacterial cell structure
...

I
...
2
...
Bacteria have 70S ribosomes comprising 30S and 50S
subunits
...

I
...
3
...
It is basically a double layer of phospholipids
with numerous proteins integrated into its structure
...

The key ingredients of biological membranes are polar lipids, primarily phospholipids
...
The fatty acid con-tent changes in response to environmental conditions,
particularly temperature
...

Some fatty acids are branched or contain cyclopropane rings
...
To the third hydroxyl group of glycerol is attached a phosphate moiety and to
it the head group
...

Other bacteria possess more complex types of membrane lipids, although these lipids are usually much
less complex than those in the plasma membrane of animal cells
...
Other bacteria produce glycolipids, such
as monogalactosyl diglyceride
...
Their hydrocarbon chains are based on isoprenoid units and these are linked to the
glycerol backbone in an ether, rather than ester, linkage
...

Sterols, such as cholesterol in mammalian cells or ergosterol in fungi, are invariant features of membranes in eukaryal cells, in which they appear to stiffen the membrane by increasing the degree of order
of the hydrocarbon chains
...
Very complex lipids, including the very long, branched mycolic acids, are
common in Mycobacterium but occur in a very thick and rigid outer layer rather than in the cytoplasmic
membrane
...
These bacteria produce patches of membrane that are densely packed with the membrane
protein, bacteriorhodopsin, having seven transmembrane helices and covalently bound retinal as in the visual pigment in mammalian retina
...
An example of this very
simple, but not very energy-rich, process is malo-lactate fermentation in Leuconostoc
...
) ,

membrane transport, export of surface molecules, and cell
growth (movement, division and signal transduction)
...
2
...
Cell wall
The tasks of the complex bacterial cell wall are to protect the protoplasts from external noxae, to
withstand and maintain the osmotic pressure gradient between the cell interior and the extracellular
environment (with internal pressures as high as 500–2000 kPa, -2-25 atm), to give the cell its outer form
and to facilitate communication with its surroundings
...
In order to achieve this, the murein forms a closed bag-shaped
structure, called sacculus, completely wrapping up the cell
...
Importantly, the murein sacculus not only
stabilizes the cytoplasmic membrane but also maintains the specific shape of the bacterium
...
On the basis of a special staining procedure bacteria can be
subdivided in essentially two groups, the Gram-positive and the Gram-negative bacteria
...
The membrane lipoteichoic acids are anchored in the cytoplasmic
membrane, whereas the cell wall teichoic acids are covalently coupled to the murein (Fig 2)
...
Within the macroorganism, teichoic acids can activate
the alternative complement pathway and stimulate macrophages to secrete cytokines
...
Cell wall-associated proteins
frequently function as pathogenicity determinants (specific adherence; phagocyte protection)
...

b) The cell wall of Gram-negative bacteria
Here, the murein is only about 2 nm thick and contributes up to 10 % of the dry cell wall mass (Fig
...

The outer membrane is the salient (saillant) structural element
...
Gram- negative bacteria have a second lipid
bilayer, called the outer membrane, making the envelope of Gram- negative bacteria less permeable
compared to that of Gram-positive bacteria
...
Due to this, Gram-negative bacteria are more resistant
to many antibiotics than do Gram-positive bacteria
...
The existence of a
second permeability barrier has allows the cell to reduce the thickness of its murein to even just one
single layer and makes it possible to efficiently recycle the valuable murein turnover products that
accumulate during growth in the periplasmic space
...

— Porins, proteins that form pores in the outer membrane, allow passage of hydrophilic, low- molecularweight substances into the periplasmic space
...


Bacteriology, first part

6

— A number of Omps are transport proteins
...

Note the characteristic thin murein layer and the outer membrane connected to it by proteins
(OmpA, murein lipoprotein)
...

Its outer layer is made up of closely packed lipopolysaccharide complexes
This molecular complex, also known as endotoxin, is comprised of the lipoid A, the core polysaccharide,
and the O-specific polysaccharide chain
...
As a free substance, or bound up in the LPS complex, it
stimulates— he formation and secretion of cytokines that determine clinical endotoxin symptomatology
...
Other direct and indirect endotoxin effects include granulopoiesis stimulation, aggregation and
degeneration of thrombocytes, intravasal coagulation, a drop in blood pressure, and cachexia
...
Release of large amounts of endotoxin can lead to
septic (endotoxic) shock
...
Therefore, the parent
materials used in production of parenteral pharmaceuticals must be free of endotoxins (pyrogens)
...
g
...

Some bacteria lack rigid cell wall (Bacteria without a rigid cell wall; coccoid cells, long threads
(Mycoplasma): M
...


Bacteriology, first part

7

I
...
5
...
A slim layer can be easily wash off because it is loosely associated with the
bacterium, whereas a capsule is tightly attached to the bacterium
...
From their structure, most capsules are hydrophilic, thus
preventing bacterial desiccation
...
This gives a strong correlation between the
possession of a capsule and virulence of many organisms
...
Mutant
strains of S
...
It arrives the same for B
...
The polysaccharide capsule of Klebsiella
pneumonia also prevents phagocytosis and allows the bacterium to adhere to and colonize the respiratory
tract
...

Special case of bacterial biofilm
In nature, microorganisms may exist as single cells that float or swim independently in a liquid, or they
may attach to each other and/or some usually solid surface
...
A bacterial
biofilm is a structured community of bacterial cells embedded in a self-produce d polymer matrix and
attached to either an inert surface or living tissue
...

Biofouling is the damage caused to a surface by microorganisms attached to a surface
...
The bacteria located deep within a biofilm structure are called sessile, and can
be isolated from immune system cells, antibodies, and antibiotics
...
The slime covering a rock in a lake is a biofilm
...

EPS (exopolysaccharides) and glycocalyx are terms used to describe the polysaccharide produced by
bacterial cells
...
EPS has an important role in biofilm structure and
function and has a complex physical and chemical nature
...
Because the glycocalyx is the outermost
component of bacterial cells, this layer mediates virtually all bacterial associations with surfaces and other
cells: it dictates location, juxtaposition, and the eventual success in the ecosystem
...
The bacteria that are trapped in the common capsule use the other sugar as food and
produce an acidic waste (lactic acid) that attack the tooth enamel and gives dental carries
...
Pseudomonas aeruginosa use to produce a thick capsular polymer of alginic acid that
contribute to the difficulty of eradicating the bacterium when it colonises the lungs with cystic
fibrosis
...

Examples:- cellulose from the genus Zoogloea enmeshes the bacteria into a flock (groupe) that floats on
the surface of liquid
...


Bacteriology, first part

8

-

-

-

Comment the case of staphylococci’s proteins that bind specifically to the matrix proteins covering
foreign bodies like endoprotheses, catheters, cardiac pacemakers, etc; then proliferate and secrete
exopolysaccharides, leading to foreign body -associated infection
...
Few are truly aerobic; most are facultatively or obligately anaerobic
...
Sometimes, a particular species
will colonize a preferred habitat in the oral cavity, e
...
, Streptococcus mutans colonizes the occlusal
fissures
...
These include gram- negative
organisms (e
...
, Pseudomonas aeruginosa and Escherichia coli) and gram-positive bacteria (e
...
,
Staphylococcus aureus and S
...
The latter, which are normally found on the skin, possess a
high degree of adhesiveness to the prosthetic device surface
...
In addition,
biofilm formation can also lead to malfunction of the device and destruction of adjacent tissue
...


I
...
6
...

Swimming and swarming bacteria posses flagella: long extracellular appendages of up to ten times the
length of the bacterial body, needed for free motility
...
Flagella give bacteria the ability to move about actively
...
The basal bodies act as bushings, allowing flagellar tube to turn clockwise and counterclockwise
...
These runs and
tumbles enable a bacterium to move toward an attractant or away from a repellent
...
A flagellum has three basic parts (Figure 1)
...

Flagella constitute antigens
...

Together with the O antigens, they are use d to classify bacteria in serovars
...
They can propel bacteria at ten
times their length per second
...

Flagellation is the arrangement of flagella
...

One group of bacteria, the spirochetes, has internally located
axial filaments or endoflagella
...
They are located
above the peptidoglycan cell wall, but underneath the outer
membrane or sheath
...


amphitrichous; Borrelia burgdorferi, the causative agent of Lyme disease; Leptospira
...
The rotation
of the filaments produces a movement of the outer sheath that propels the spirochetes in a spiral motion
...
2
...
Pili and fimbriae
Many
gram- negative
bacteria
contain
hairlike
appendages that are shorter,
straighter, and thinner than
flagella and are used for
attachment and transfer of DNA
rather than for motility
...

These structures, which consist
of a protein called pilin arranged
helically around a central core,
are divided into two types,
fimbriae and pili, having very
different
functions
...
)
Fimbriae
(singular:
fimbria ) can occur at the poles
of the bacterial cell or can be
evenly distributed over the entire
surface of the cell
...

Fimbriae have a tendency to
adhere to each other and to
surfaces
...
Fimbriae can
also help bacteria adhere to
epithelial surfaces in the body
...
coli
0157
...
1–
1
...
Pili are involved in
motility and DNA transfer
...
This is called the
grappling hook model of twitching motility and results in short, jerky, intermittent movements
...

coli
...
Although the exact mechanism is conjugation
...

I
...
Sporulation
A number of Gram-positive bacteria can form a special resistant, dormant structure called an
endospore
...
The primary signal for the initiation of sporulation
or sporogenesis is nutrient starvation
...
Bacterial spores (endospores) are purely dormant life forms
(more than maize and guinea maize)
...
Since bacterial destruction is
generally made using heat, the heat resistance of these spores is their most important quality from a
medical point of view
...
The endospore is able to survive for long
periods until environmental conditions again become favourable for growth
...
Potential contributing factors to spore heat
resistance include their thick wall structures, the dehydration of the spore, and crosslinking of the proteins
by the calcium salt of pyridine-2,6-dicarboxylic acid, both of which render protein denaturing difficult
...
) it returns to the vegetative state in which spore- forming bacteria can reproduce without
taking nutrient from the environment
...

Bacteriology, first part

I
...
1
...
The
integration of the extracellular and
intracellular signals is regulated through a
multicomponent
phosphorelay
that
controls the prosphorylation of the
transcriptional regulator SpoOA
...

First, the DNA replicates and a
cytoplasmic membrane septum forms at
one end of the cell
...
Both of these membrane
layers then synthesize peptidoglycan in
the space between them to form the first
protective coat, the cortex
...
A spore coat
composed of a keratin- like protein then
forms around the cortex
...
Finally, the remainder
of the bacterium is degraded and the endospore is released
...

The ability to form endospores is found among bacteria in a number of genera, predominantly Grampositive groups, including the aerobic rod Bacillus, the microaerophilic rod Sporolactobacillus, the
anaerobic rods Clostridium and Desulfotomaculum, the coccus Sporosarcina, and the filamentous
Thermoactinomyces
...

Cysts are thick-walled structures produced by dormant members of Azotobacter, Bdellovibrio (bdellocysts), and Myxococcus (myxospores)
...
In encystment by the nitrogen-fixing Azotobacter, cell division
is followed by the formation of a thick, multilayered wall and coat that surround the resting cell
...


I
...
2
...
anthracis, spores elliptical and central, B
...
sacchari), or subapical;
distorting or undistorting
...

I
...
3
...
The ability of endospores to resist these noxious agents
may ensue from the extremely low water content inside the spore
...
Endospores are resistant to deterge nts and alcohol at
70%
...
The impermeability of the spore coat is thought to be responsible for the
endospore’s resistance to chemicals
...

 Specialized DNA-binding proteins saturate the endospore’s DNA and protect it from heat, drying,
chemicals, and radiation
...

 Finally, DNA repair enzymes contained within the endospore are able to repair damaged DNA during
germination
...
3
...
Consequence
Easy spray, crossing time, not easily eradicated
...
Russian scientists even claim to have brought
back to life bacteria that was frozen in arctic ice for a million years
...
The outbreak of the same anthrax (Bacillus anthracis, a bacterium that forms endospores
...


Bacteriology, first part

12

Chapter Two:

Nutrition growth and cultivation in
bacteria

Introduction
The ability of bacteria to thrive in specific habitats is a function of both nutritional and physical
factors
...
Thus, the relationship between bacteria and the environment, as well as between bacteria
and host, is a reflection of their specific growth requirements
...
1
...
The growth of a bacterial population occurs in a geometric or
exponential manner: with each division cycle (generation), one cell gives rise to 2 cells, then 4 cells, then
8 cells, then 16, then 32, and so forth
...
The relationship shows
that the mean generation time is constant and that the rate at which the number of bacteria increases is
proportional to the number of bacteria at any given time
...

For this reason, graphs that show the growth of bacterial cultures are plotted as the logarithm of the
number of cells
...
For example,
Clostridium perfringens, one of the fastest-growing bacteria, has an optimum generation time of about 10
minutes; Escherichia coli can double every 20 min; and the slow-growing Mycobacterium tuberculosis
has a generation time in the range of 12 to 16 h
...

When bacteria are placed in a medium that provides all
of the nutrients that are necessary for their growth, the
population exhibits four phases of growth that are
representative of a typical bacterial growth curve
...
Upon inoculation into the new medium, bacteria do not
immediately reproduce, and the population size remains
constant
...
They are
also synthesizing the enzymes and factors needed for cell
division and population growth under their new environmental
conditions
...
The population then enters the log phase, in which cell
numbers increase in a logarithmic fashion, and each cell generation occurs in the same time interval
as the preceding ones, resulting in a balanced increase in the constituents of each cell
...
Under optimum conditions, the maximum population for
some bacterial species at the end of the log phase can reach a density of 10 to 30 billion cells per
millilitre
...
The log phase of bacterial growth is followed by the stationary phase, in which the size of a
population of bacteria remains constant, even though some cells continue to divide and others begin
to die
...
The stationary phase is followed by the death phase, in which the death of cells in the population
exceeds the formation of ne w cells
...

Bacteria do not necessarily die even when starved of nutrients, and they can remain viable for long
periods of time
...
2
...
In general, however, in
order for any type of bacterial cell to grow, it requires a source of carbon and a source of energy
...

Thus, whereas the absence of a specific nutrient may not have any affect on the growth of one type of
bacteria, it may entirely prevent the growth of a different type
...

II
...
1
...
g
...
g
...
Carbon is the
element required in the greatest amount by bacteria since hydrogen and oxygen can be obtained from
water, which is a prerequisite for bacterial growth
...
One means of organizing bacteria is based on these fundamental nutritional
needs: the carbon source and the energy source
...

Organisms that use the inorganic compound carbon dioxide (CO 2 ) as their source of carbon are called
autotrophs
...
Many heterotrophs, such as Escherichia coli or
Pseudomonas aeruginosa, synthesize all of their cellular constituents from simple sugars such as glucose
because they possess the necessary biosynthetic pathways
...

There are three basic sources of energy: light, inorganic compounds, and organic compounds
...
Chemotrophs obtain their energy
from chemicals (organic and inorganic compounds); chemolithotrophs obtain their energy from reactions
with inorganic salts; and chemoheterotrophs obtain their carbon and energy from organic compounds (the
energy source may also serve as the carbon source in these organisms)
...
While carbohydrates are a common energy
source for eukaryotes, these molecules are metabolized by only a limited number of species of bacteria,
...
Low levels of phosphate in many environments, particularly in water, can be a limiting factor
for the growth of bacteria, since many bacteria cannot synthesize phosphate
...
The capability of a living organism
to incorporate nitrogen from ammonia is widespread in nature, and bacteria differ in their ability to
convert other forms of nitrogen, such as nitrate in the soil or dinitrogen gas (N 2 ) in the atmosphere, into
cell material
...
Iron is
a component of heme proteins, such as haemoglobin in red blood cells and cytochromes in electron
transfer chains, as well as many other iron-containing proteins involved in electron-transfer reactions
...
In aerobic environments at neutral pH values,
Bacteriology, first part

14

ferrous iron (Fe2+ iron in the +2 state) is oxidized to ferric iron (Fe 3+), which is virtually insoluble in
water and unable to enter cells
...
The bacteria then take up these iron- siderophore
complexes and remove the iron for their synthetic tasks
...
In anaerobic environments, iron can exist in the more soluble ferrous state and is readily available to
bacteria
...
Rickettsia and
Chlamydia, for example, grow in eukaryotic cells, and Bdellovibrio grow in bacterial cells
...
Because some bacteria may thrive only as animal or plant parasites or only in a
rich source of nutrients such as milk, they likely do not thrive as free bacteria in nature
...

II
...
2
...
As a group, bacteria display the widest variation of all organisms in their ability to inhabit
different environments
...

II
...
2
...
Oxygen
Obligate aerobes include Bacillus subtilis, Pseudomonas aeruginosa, and Thiobacillus
ferrooxidans
...
In fact, the presence of
oxygen actually poisons some of their key enzymes
...
pneumoniae) are microaerophilic
or ae rotole rant anaerobes because they grow better in low concentrations of oxygen
...

Facultative anaerobes can change their metabolic processes depending on the presence of oxygen, using
the more efficient process of respiration in the presence of oxygen and the less efficient process of
fermentation in the absence of oxygen
...
coli and S
...

The response of bacteria to oxygen is not determined simply by their metabolic needs
...
Aerobic organisms produce enzymes that detoxify these oxygen
products
...
The combined action of these enzymes to
remove hydrogen peroxide and superoxide is important because these by-products together with iron form
the extremely reactive hydroxyl radical, which is capable of killing the cell
...
Many anaerobes are hypersensitive to
oxygen, being killed upon short exposure, whereas other anaerobes, including most Clostridium species,
are more tolerant to the presence of oxygen
...
2
...
2
...

Extreme thermophile thermophiles,
mesophile,
psychotrope,
extreme
psychrotropes
Until recently the highest reported
temperature for procaryotic growth was
105°C
...
Now
thermophilic procaryotes have been
reported growing in sulfide chimneys or
“black smokers,” located along rifts and
ridges on the ocean floor, that spew
sulfide-rich superheated vent water with
temperatures above 350°C
...
The
pressure present in their habitat is
Figure 6: Approximate pH growth ranges for some sufficient to keep water liquid (at 265
atm; seawater doesn’t boil until 460°C)
...

The implications of this discovery are
many
...

In the future it may be possible to design enzymes that can operate at very high temperatures
...
For example,
the Taq polymerase from the thermophile Thermus aquaticus is used extensively in the polymerase chain
reaction
...
Thermoproteus, Hyperthermus butylicus, Thermodiscus
maritimus, Thermosphaera aggregans, Thermoproteus tenax, Pyrobaculum islandicum, Thermocladium
modesties, Thermofilum pendens
...
Pyrodictium has a temperature minimum
of 82°C, a growth optimum at 105°C, and a maximum at 110°C
...
For this reason, they are classed as thermoacidophiles, so called because they grow best at acid
pH values and high temperatures
...
They grow lithotrophically on sulphur granules in hot acid springs and soils
...
This extremely thermophilic rodshaped methanogen has been isolated from a marine
hydrothermal vent
...
Methanopyrus occupies the deepest and most
ancient branch of the euryarchaeotes
...

Thermococcus and Pyrococcus are extreme thermophiles S° metabolisers
...
2
...
3
...
For this reason, they are classed as thermoacidophiles), acidophil, neutrophil,
basophil, no extreme basophil
...
The cytoplasmic membrane of microorganisms is relatively
impermeable to H+ and OH- ions
...

growth of some foodborne organisms
...
6
...

When
Alicyclobacillus acidocaldarius
2
...
9
above neutrality, their ability to proliferate depends
Botrytis cinerea
2
...
6
more optimum value or range
...
botulinum, Group Il
5
...
perfringens
5
...
5
entering or expel H+ ions as rapidly as they enter
...

3
...
16
require neutrality
...
plantarum
3
...
3
medium becoming less acidic, whereas those that
Listeria monocytogenes
4
...
0
lowering of pH
...
5
have optimum activity at around pH 4
...

4
...
5 cause a spontaneous adjustment
S
...
0
of pH toward neutrality when cells are grown in the
Staphylococcus aureus
4
...
Bacteria such as Clostridium
Vibrio parahaemolyticus
4
...
18
butyric acid to butanol, whereas Enterobacter
Zygosaccharomyces bailii
1
...

With respect to the transport of nutrients, the bacterial cell tends to have a residual negative charge
...
At neutral or
alkaline pH, organic acids do not enter, whereas at acid pH values, these compounds are nonionized and
can enter the negatively charged cells
...
The morphology of some microorganisms
can be affected by pH
...
0
...
2
...
4
...
They will grow at salt concentrations approaching saturation (about 36%)
...
5 M
...
Halobacterium salinarium (H
...


Bacteriology, first part

17

Figure 7 : aw for some microbes
Water activity (aw) in the environment
...

RH = 100 x a w
...


II
...
Culturing bacteria
Understanding the importance of culture media components, sterile operations, aeration, and
agitation are necessary for strains creation and maintenance, and fermenter improvement
...
This
enable the determination of the properties of specific organisms such as its metabolic characteristics or its
ability to cause a particular disease
...
It also permits to know the bacterial load
...
S
...

A culture consisting entirely of one strain of organism is called a pure or axenic culture
...
The standard method of obtaining a pure
bacterial culture is the creation of a streak plate
...


Bacteriology, first part

18

The nutrients and conditions provided in the laboratory are usually a reflection of those found in the
organism’s
natural
Table 7: Approximate minimum a w values for growth of microorganisms
habitat
...

essential
that
Give those of bacteria
appropriate steps be
taken
to
avoid
contamination
...
Any
glassware
and
equipment
used
is
sterilised before work
begins
...
The wire loops and needles used to transfer small volumes of microbial cultures
are sterilised by heating them to redness in a flame
...
It can be natural (undefined) or artificial
(define)
...
An undefined or
complex medium is one whose precise chemical composition is not known
...
Solid media are particularly
useful in the isolation of bacteria; they are also used for their long-term storage
...
It comprises a circular
dish with an overlapping lid
...
It is easily used to verify O 2 situation
...

II
...
1
...

A chemically defined medium is one whose exact chemical composition is known
...
Chemically
defined media are used for the growth of autotrophic bacteria
...
In complex media,
the energy, carbon, nitrogen, and sulfur needed for microbial growth are provided by protein
...
Partial digestion by acids and enzymes break
down proteins into smaller amino acids called peptones
...
These small peptones can be digested by bacteria
...
If a complex medium is in a liquid form it is called a
nutrient broth
...
Agar is not a nutrient; it is a solidifying agent
...
3
...
1
...
Reducing media contain ingredients like sodium thioglycolate
that attaches to dissolved oxygen and depletes the oxygen in the culture medium
...
3
...
2
...
Selective and differential media are therefore used
...
It can be specific for one or not
...
Bismuth sulfite
agar is used to isolate Salmonella typhi from faecal
(which turns pink in acid environment)
...

Peptone (17 g), proteose peptone (3 g) lactose (10
A differential medium allows colonies of a
g), bile salts (1
...
03 g), crystal violet (0
...
VRB, Chapman
(13
...
then add water to make 1 L and adjust
mannitol (7
...
1 +/− 0
...

most bacteria,) is for halophile like Staphilococcus
...
Many media act both selectively and
differentially; MacConkey agar, for example, also contains
is not required, sodium chloride is omitted
...

coli O157, an enteric pathogen
...
If coliforms are present, conditions may be suitable for the presence of enteric
pathogens, such as Salmonella
...

Differential me dia make it easy to distinguish colonies of desired organisms from nondesirable
colonies growing on the same plate
...
An example is blood agar
...
An example of this type of
bacterium is Streptococcus pyogenes, the agent that causes strep throat
...
EMB contains lactose, salts, and two dyes—eosin and methylene
blue
...
ram negative bacteria that ferment the
lactose produce acid which turns the colonies dark purple as the acid acts upon the dyes
...
Other lactose
fermenters produce larger, mucoid colonies, often purple only in their centre
...
coli colonies have a characteristic green sheen
...
coli, rapid fermentation of lactose and formation of
strong acids
...
S
...

MacConkey agar is used for the selection and recovery of Enterobacteriaceae and related gramnegative rods
...


20

bacteria
...

Hektoen enteric agar is used to increase the yield of Salmonella and Shigella species relative to
other microbiota
...

An enrichment culture uses a selective medium to encourage the growth of an organism present in
low numbers
...
Enrichment cultures are
usually liquids and provide nutrients and environmental cond itions that provide for the growth of certain
microorganisms, but not others
...
3
...
3
...
Comment all these
...
Increase in temperature generally results in reduction of time
...
°C within 48 h or 37 °c within 24 h
...

A notable new rapid method known as Bactoscan (Foss Food Technology Corp
...

Stray - pour surface - deep: explain
...
3
...
Pure cultures
Define and explain giving the way to store
...
A device called an inoculating loop is sterilized and dipped into a
culture of a microorganism (s) and then is “streaked” in a pattern over a nutrient
medium
...
The last cells that are rubbed off the loop onto the medium are
far enough apart to allow isolation of separate colonies of the original culture
...

Fig
...

II
...
3
...
Deep freezing is a process in which a pure culture of microorganisms is placed in a
suspending liquid and frozen quickly at temperatures ranging from −50 to −95°C
...

Lyophilization, or freeze drying, quick freezes suspended microorganisms at temperatures from −54
to −72°C while water is removed by using a high-pressure vacuum
...
The surrounding microbes in the sealed container can last for years
...

II
...
4
...
3
...
1
...
This method measures
the number of viable cells
...

A plate count is performed by either a pour plate method or a special plate method
...
0 ml or 0
...
Melted nutrient
agar is added, which is then gently agitated, or mixed
...
With this technique, heat-sensitive microorganisms can be damaged by the
melted agar and be unable to form colonies
...
Here a 0
...

Bacteriology, first part

21

The bacterial solution is then spread evenly over the medium
...
Here 100 milliliters of water
are passed through a thin membrane, whose pores are too small for the bacteria to pass thro ugh
...
An example of bacteria that are grown using this method is coliform bacteria, which are
indicators of faecal pollution of food or water
...
For example, a 0
...
1 immersion objective lens
...
Once the number of bacteria is obtained or determined in
several different fields, an average can be taken of the number of bacteria per viewing field
...
Because the area on the slide contained 0
...

II
...
4
...
Establishing bacte rial numbe rs by indirect methods
Not all microbial cells must be counted to establish their number
...
Turbidity is the cloudiness of
a liquid or the loss of transparency because of insoluble matter
...

In the spectrophotometer, a beam of light is transmitted through the bacteria that are suspended in
the liquid medium to a photoelectric cell
...
The change of light will register on the instrument’s scale as the percentage of
transmission
...

Another indirect way of measuring bacterial growth is to measure the metabolic activity of the
colony
...
The more bacteria we have, the more waste products
we will also have
...


II
...
Controlling microbial growth
There are many terms used to describe the fight to control microorganisms
...
Sterilization is used in preparing
cultured media and canned foods
...

Antisepsis is the reduction of pathogenic microorganisms and viruses on living tissue
...
Antisepsis is used to disinfect living tissues without
harming them
...
An
example is the bacteria Clostridium botulinum, which causes botulism
...
Examples include proper hand washing,
flame sterilization of equipment, and preparing surgical environments and instruments
...
For
example, a bactercide kills bacteria
...

For the same reason, these germicides are also used in preserving specimens in laboratories
...
Examples of these chemical agents are phenols, alcohols, aldehydes,
and surfactants
...
This area of the skin is degermed by using an alcohol wipe or a piece of cotton swab soaked
with alcohol
...

Bacteriology, first part

22

Pasteurization, uses heat to kill pathogens and reduce the number of food spoilage microorganisms
in foods and beverages
...

Sanitation is the treatment to remove or lower microbial counts on objects such as eating and
drinking utensils to meet public health standards
...
Bacterostatic, or any word with the suffix static or -stasis—indicate the inhibition of a particular type of microorganism
...
Germistatic agents include refrigeration, freezing, and some
chemicals
...
4
...
Microbial death rates
Microbial death is the term used to describe the permanent loss of a microorganism’s ability to
reproduce under normal environmental conditions
...
The effectiveness of antimicrobial treatments is influenced
by the number of microbes that are present
...

Environmental influences, such as the presence of blood, saliva, or faecal matter, inhibits the action of
chemical antimicrobials
...
Many chemical
antimicrobials need longer exposure times to be effective in the death of more resistant microorganisms
or endospores
...
4
...
Action of antimicrobial agents
There are two categories that chemical and physical antimicrobial agents fall into: those that affect
the cell walls and those that affect cellular metabolism and reproduction
...
The function of a protein depends on its three-dimensional shape
...
This affects
the function of the protein and ultimately bringing death to the cell
...
the cell can no longer replicate or synthesize enzymes, which are important in
cell metabolism
...
4
...
Chemical agents that control microbial growth
Commonly used chemical agents include phenols, phenolics, glutaraldehyde, and formaldehyde
...
4
...
1
...
Phenolics disrupt the plasma
by denaturing proteins; they also disrupt the plasma membrane of the cell
...
However, they, are not effective against
fungal spores or bacterial endospores
...
Alcohols denature proteins and disrupt cytoplasmic membranes
...

II
...
3
...
Halogens
They are nonmetallic, highly resistive chemical elements, any of the five electronegative elements,
namely fluorine, chlorine, iodine, bromine or astatine
...
Halogen-containing
antimicrobial agents include iodine, which inhibits protein function
...
Other halogen agents include: • Chlorine (Cl2 ), Chlorine dioxide (ClO2),
Chloroamines, Bromine, Oxidizing agents
...
4
...
3
...
They inhibit microbial growth because they denature enzymes and alter the threedimensional shapes of proteins that inhibit or eliminate the protein’s function
...

Bacteriology, first part

23

II
...
3
...
Glutaraldehyde and formaldehyde
Aldehydes function in microbial growth by denaturing proteins and inactivating nucleic acids
...
Glutaraldehyde is used in a 2 %
solution to kill bacteria, fungi, and viruses on medical and dental equipment
...
Formalin is used
in disinfecting dialysis machines, surgical equipment, and embalming bodies after death
...
4
...
5
...
Examples are household soaps and detergents
...
Organisms that have similar
characteristics are presumed to have a natural relationship and therefore are placed in the same group
...
Taxonomy has three components:
• Classification
...
These groups are also called taxa
...
The name given to each organism
...

• Identification
...

Taxonomy is a subset of systemics
...
Using techniques from other sciences such as
biochemistry, ecology, epidemiology, molecular biology, morphology, and physiology, biologists are able
to identify characteristics of an organism
...
Wolfe,
proposed a new
six-kingdom
taxonomy
...

(anaerobes that live
in swamps,
marshes, and in the intestines of mammals);
• Protista (unicellular eukaryotes and algae);
• Fungi (multicellular forms and single-cell yeasts);
• Plantae;
• Animalia
...

Today organisms are grouped into three categories called domains that are represented as Bacteria,
Archaea, and Eukarya
...
The term
Bacteriology, first part

25

Archaebacteria refers to the ancient origin of this group of bacteria that appears to have diverged from
Eubacteria
...

1) Domain Bacteria (Eubacteria) who have a cell wall composed of peptidoglycan and muramic acid,
2) Domain Archaea (Archaebacteria) who lack muramic acid in the cell walls;
3) Domain Eukarya (eukaryotes) (Protista, Fungi, Plantae, Animalia)
...
Most prokaryotes are bacteria
...
The precise different types of bacteria that inhabit Earth is unknown
because of the extraordinary metabolic diversity among prokaryotes, which is reflected in the countless
different types of bacteria
...


III
...
Approaches to bacterial classification
It is difficult to classify microscopic organisms, especially bacteria base on their morphology, because
many of them have similar structures
...
Nor does the presence of specific structures such as
flagella, endospores, or capsules allow identification of particular species
...
Staining reactions, especially the Gram stain, were among the first properties other than
morphology to be used to classify bacteria
...
These features
include properties of DNA and proteins
...
1 and 3
...
3
...
A bacterial strain consists of descendants of a single isolation in pure
culture
...
In recent years, similarities of DN A and proteins
Bacteriology, first part

26

among organisms have proved a reliable means of assigning a strain to an existing species or establishing
the basis for a new species
...
This problem is well highlighted by the fact that organisms
are sometimes moved from one category to another, and their official names are sometimes changed
...
Its genus name was changed to Francisella after DNA hybridization
studies revealed that hybridization between its DNA and that of Pasteurella species did not occur
...
Efforts are being made to classify
bacteria by evolutionary relationships, too, but these efforts are hampered by the incompleteness of the
fossil record and by the limited information gleaned from what fossils have been found
...
These
two groups are obligate intracellular parasites
...
Mycop lasmas lack cell
walls and form colonies that look like eggs fried sunny-side up
...
Also interesting are the Ureaplasmas, also with unusual cell
walls and/or cell membranes (table 3
...

table 3
...
Today the classification of bacteria is grounded primarily in genetics
...

III
...
1
...
Although
phenetic studies can reveal possible evolutionary relationships, they are not dependent on phylogenetic
analysis
...

III
...
2
...
It is the grouping by numerical methods of taxonomic units into taxa on the basis of their
character states
...
The results of numerical taxonomic
analysis are often summarized with a treelike diagram called a dendrogram
...
1
...
Phylogenetic / phyletic classification
These are systems based on evolutionary relationships rather than general resemblance (the term
phylogeny refers to the evolutionary development of a species)
...
The direct comparison of
genetic material and gene products such as RNA and proteins overcomes many of these problems
...
2: Criteria for Bacteria classification
...
3: Specific biochemical tests sometimes used in identifying bacteria
...
1
...
Classification by genetic dive rgence
Genetic approaches to the classification of bacteria are aimed at identifying a degree of relatedness
between organisms to obtain a more fundamental measure of the time elapsed since two organisms
diverged from a common ancestor
...
The 16S rRNA gene is present in all bacteria, and a related form occurs in all cells
...

coli is 1,542 nucleotides long, and some of its regions are double- stranded, while other regions are single- stranded
...
Other positions change very slowly, allowing much broader taxonomic levels to be
distinguished
...
The assumption that the rate at which base changes occur and are
established within a species is constant is unlikely to be true
...

The radical differences between Archaea (Archaeabacteria) and Eubacteria, which are evident in the
composition of their lipids and cell walls and in the utilization of different metabolic pathways, enzymes,
and enzyme cofactors, are also reflected in the rRNA sequences
...
– In the other hand since lithotrophy
seems widely distributed among bacterial organisms before photosynthesis developed, t he Archaea may
came from a different line of descent than Eubacteria
...
Rather, it uses a single protein, bacteriorhodopsin, in
which light energy is absorbed by retinal, a form of vitamin A, to activate a proton (hydrogen ion)
...
For example, Mycoplasma, which appear to be
different from other bacteria actually are related to some Gram-positive clostridia on the basis of their
nucleic acid sequences
...
In fact, there are many groupings of bacteria that are
not supported by RNA sequence analysis
...
DNA contains four purine and pyrimidine bases: adenine (A), guanine (G), cytosine (C),
and thymine (T)
...
Thus the (G _ C)/(A_T)
ratio or G _ C content, the percent of G _ C in DNA, reflects the base sequence and varies with sequence
changes as follows:

...
Although the G+C content can be ascertained after hy drolysis of DNA and analysis of its
bases with high-performance liquid chromatography (HPLC), physical methods are easier and more often used
...
4: Representative G _ C Contents of Microorganisms

Bacteriology, first part

30

III
...
5
...
Bergey's Manual of Determinative
Bacteriology (9th ed
...
in 1923) does not classify bacteria according to evolutionary relatedness
but instead provides identification (determinative) schemes based on such criteria as cell wall composition,
morphology, differential staining, oxygen requirements, and biochemical testing
...


III
...
Major types of bacteria
David Bergey classify Bacteria into 24 phyla, more than 30 classes (32), some subclasses, around
75 orders (76), many suborders, around 210 families (212), some of which have just a genus, like some
orders have a family, some classes an order and some phyla a class
...
It also sustains the
wideness of environment and adaptations
...
It is also easy to see just by the
names that not all extremophiles are Archaea
...
2
...
Gram-negative bacteria
Gram- negative bacteria have only a thin peptidoglycan layer in their cells walls
...
There are a number of different kinds of Gram- negative bacteria, many
of which are pathogenic in humans, including E
...
Coliforms are a group of
bacteria that comprise all aerobic and facultatively anaerobic, gram- negative, non–spore- forming rods
able to ferment lactose and produce acid and gas at 32°Cor 35°C within 48 h
...
2
...
Gram-positive bacteria
Refer to chapter one and course of General Microbiology
...
3
...
The name was subsequently changed to Archaea
...

Further molecular analysis has shown that domain Archaea consists of two major subdivisions, the
Crenarchaeota and the Euryarchaeota, and two minor ancient lineages, the Korarchaeota and the
Nanoarchaeota
...
The first has one class, 4 orders and 6 families
...
With genetic research going on, this
classification is continuously adjusted
...
3
...
Habitats of the Archaea
Archaea define the limit of life on earth
...

Bacteriology, first part

31

Although many of the cultured Archaea are extremophiles, these organisms in their respective extreme
habitats represent only a minority of the total diversity of the Archaea domain
...

Culture- independent studies have shown that Archaea are abundant and fulfill important ecological roles
in cold and temperate ecosystems
...
In the phylum
Euryarchaeota, uncultivated organisms in deep-sea marine sediments are responsible for the removal of
methane, a potent green- house gas,
...

The cultured representatives of the Crenarchaeota are from high- temperature environments, such as hot
springs and submarine hydrothermal vents
...

Organisms in the lineages Korarchaeota and Nanoarchaeota also inhabit high-temperature environments;
however, the NNanoarchaea are highly unusual because they grow and divide on the surface of another
archaea, Ignicoccus
...
Members of the Korarchaeota and
Nanoarchaeota have not been detected in pure culture; rather, they have been detected only in mixed
laboratory cultures
...

Archaea are also found living in association with eukaryotes; for example, methanogenic Archaea are
present in the digestive systems of some animals, including humans
...

III
...
2
...
Major examples of these traits include:
1
...
Various types of
cell walls exist in the Archaea
...

2
...
In contrast, the Archaea have ether bonds connecting fatty
acids to molecules of glycerol
...

3
...
Bacteria
contain a simple RNA polymerase consisting of four polypeptides
...
For example, the
RNA polymerases of Archaea contain more than eight polypeptides
...

4
...
A prominent difference is that bacteria have an initiator tRNA
(transfer RNA) that has a modified methionine, whereas eukaryotes and Archaea have an initiator
tRNA with an unmodified methionine
...
Metabolis m: various types of metabolism exist in both Archaea and bacteria that do not exist in
eukaryotes, including nitrogen fixation, denitrification, chemolithotrophy, and hyperthermophilic
growth
...
Classical photosynthesis using chlorophyll has not been found in any archaea
...
4
...
They are primarily prokaryotic (Archaea
and Bacteria), with few eukaryotic examples
...
The
organisms may be described as acidophilic (optimal growth between pH 1 and pH 5); alkaliphilic
(optimal growth above pH 9); halophilic (optimal growth in environments with high concentrations of
salt); thermophilic (optimal growth between 60 and 80 °C); hyper thermophilic (optimal growth above 80
°C); psychrophilic (optimal growth at 15 °C or lower, with a maximum tolerant temperature of 20 °C and
minimal growth at or below 0 °C); piezophilic, or barophilic (optimal growth at high hydrostatic
pressure); oligotrophic (growth in nutritionally limited environments); endolithic (growth within rock or
within pores of mineral grains); and xerophilic (growth in dry conditions, with low water availability)
...

Other classification
O2 re quirement
Different atmospheres will also benefit different organisms :
• Obligate aerobes - these carry out aerobic respiration and therefore require oxygen from the atmosphere
...

• Strict anaerobes - unable to grow and reproduce in the presence of oxygen, and usually die if oxygen is present
...
e
...

• Facultative anaerobes - can grow with or without the presence of oxygen
...

• Microaerophilic - obligate aerobes which only require a tiny amount of oxygen
...


Bacteriology, first part

33

Figure 3
...

These relationships
were
determined
from rRNA sequence
comparisons
...
J
...
R
...
“Ribosomal RNA:
A Key to Phylogeny” in The
FASEB Journal, 7:113–123,
1993
...
Introduction
A rather delicate balance exists between our defences and the pathogenic mechanisms of
microorganisms
...
After the disease has become
established, an infected person may recover completely, suffer temporary or permanent damage, or die
...
It is first concerned with the cause,
or aetiology, of disease
...

Third, pathology is concerned with the structural and functional changes brought about by disease and
with their final effects on the body
...
Disease is an abnormal state in which part
or all of the body is not properly adjusted or incapable of performing its normal functions
...
The presence of a particular type of bacterium in a part of
the body where it is not normally found is also called an infection - and may lead to disease
...
coli are normally present in the healthy intestine, their infection of the
urinary tract usually results in disease
...
In fact, less than 200 bacteria are harmful to human and his activity
...
Therefore, before we discuss the role of microorganisms in causing
disease, let's examine the relationship of the microorganisms to the healthy human body
...
1
...
Animals, including humans, are generally free of microbes in uterus
...
Just before a
woman gives birth, lactobacilli in her vagina multiply rapidly
...
More microorganisms are introduced to the newborn's body from the environment
when breathing begins and feeding starts
...
coli and other bacteria acquired from foods begin
to inhabit the large intestine
...
Many other usually harmless microorganisms establish themselves inside other parts of the
normal adult body and on its surface
...
10 13 body cells, yet harbours an
estimated 1
...

The microorganisms that establish more or less permanent residence (colonize) but that do not
produce disease under normal conditions are members of the body's normal microbiota, or normal flora
...

Microorganisms are not found throughout the entire human body but are localized in certain regions
(Table 4
...
Nutrients, physical and chemical factors, defences of the host, and mechanical factors
determine the distribution and composition of the normal microbiota (comment)
...
1
...
Relationships between the normal microbiota and the host
Once established, the normal microbiota can benefit the host by preventing the overgrowth of
harmful microorganisms
...

One consequence of this competition is that the normal microbiota protects the host against colonization
by potentially pathogenic microbes by competing for nutrients, producing substances harmful to the
invading microbes, and affecting conditions such as pH and available oxygen
...

Bacteriology, first part

35

For examples:
(1)
...
The
presence of normal microbiota inhibits the over-growth of the yeast Candida albicans, which can grow
when the balance between normal microbiota and pathogens is upset and when pH is altered
...
albicans can flourish and become the dominant microorganism
there
...

(2)
...
coli cells produce bacteriocins, proteins that inhibit the growth of other
bacteria of the same or closely related species, such as pathogenic Salmonella and Shigella
...
Bacteriocins are used in medical microbiology to help identify different strains of bacteria
...
The normal microbiota of the large intestine inhibit Clostridium difficile
...
difficile can become a problem
...

The relationship between the normal microbiota and the host is called symbiosis, a relationship
between two organisms in which at least one organism is dependent on the other (Figure 4
...

IV
...
1
...
Symbiosis
IV
...
1
...
1
...

Many of the microorganisms that make
up
our
normal
microbiota
are
commensals;
these
include
the
corynebacteria that inhabit the surface of
the eye and certain saprophytic
Figure 4
...

mycobacteria that inhabit the ear and
external genitals
...

IV
...
1
...
2
...
For example, the large intestine
contains bacteria, such as E
...

Probiotics are live microbial cultures applied to or ingested that are intended to exert a beneficial
effect
...
Ingesting certain lactic acid bacteria (LAB) can alleviate diarrhoea and
prevent colonization by Salmonella enterica during antibiotic therapy (explain)
...


Bacteriology, first part

36

Table 4
...

Region
Principal Components
Comment
Most of the microbes in direct contact with skin do
Propionibacterium, Staphylococcus,
not become residents because secretions from
Corynebacterium, Micrococcus,
sweat and oil glands have antimicrobial properties
...
Moreover, the low pH
Pityrosporum; Candida, Malassezia
of the skin inhibits many microbes
...

Staphylococcus epidermidis, S
...
Propionibacterium,
mucous membrane, contains basically the same
(Conjuncttva) Corynebacterium, streptococci,
microbiota found on the skin
...
aureus, S
...

potential pathogens, their ability to cause disease
throat (Upper epidermidis, S
...

Respiratory
Streptococcus pneumoniae,

Nasal secretions kill or inhibit many
System)
Haemophilus, and Neisseria in the
microbes, and mucus and ciliary action remove
throat
many microbes,
• Abundant moisture, warmth
...
Veillonella, environment that supports very large and diverse
Neisseria, Haemophifis,
microbial populations on the tongue, cheeks
...
and gums
...
Corynebacterium,
• However, biting
...

Escherichia coli, Bacteroides
...
Bifidobacterium,
because of its available moisture and nutrients
...

• The lower urethra in both sexes has a resident
population; the vagina has its acid-tolerant
Staphylococcus
...

Bacteroides, aerobic diphtheroids,
Urinary and
• Mucus and periodic shedding of the lining
Pseudomonas, Klebsiella, and Proteus
Reproductive
prevent microbes from attaching to the lining:
in urethra; lactobacilli, Streptococcus,
Systems
urine flow mechanically removes microbes, and
Clostridium, Candida albicans
the pH of urine and urea are antimicrobial
...

IV
...
1
...
3
...
For example, given the proper circumstances, a mutualistic organism, such as E
...
coli is generally harmless as long as it remains in the large intestine; but if it gains access to
other body sites, such as the urinary bladder, lungs, spinal cord, or wounds, it may cause urinary tract infect ions, pulmonary
infections, meningit is, or abscesses, respectively
...
coli are called opportunistic pathogens
...
For example, microbes leaving normally on
the skin and that gain access through broken skin or mucous membranes can cause opportunistic
infections
...
-AIDS is often accompanied by a common opportunistic infection,
pneumocystis pneumonia, caused by the opportunistic organism Pneumocystis jirovecii
...
Opportunistic pathogens possess other features that contribute
to their ability to cause disease
...
Some opportunistic pathogens may be found in locations in or
on the body that are somewhat protected from the body's defences, and some are resistant to antibiotics
...
Among the pathogens that are frequently
carried in healthy individuals are Neisseria meningitidis, which often resides benignly in the respiratory
tract, can cause meningitis; Streptococcus pneumoniae, a normal resident of the nose and throat, can
cause a type of pneumonia
...
1
...
2
...
Many disease-causing bacteria are parasites and considered pathogens
...

IV
...
1
...
1
...
gaining access to the body by direct deposition into the tissues beneath
the skin or into mucous membranes when these barriers are penetrated or injured, is called the parentenal
route (injections, bites, cuts, wounds, surgery, etc)
...
For
example, Salmonella typhi, produce all the signs and symptoms of the disease when swallowed, but if the
same bacteria are rubbed on the skin, just a slight inflammation can occurs
...
Some
bacteria, such as Yersinia pestis, the microorganism that causes plague, and Bacillus anthracis can initiate
disease from more than one portal of entry
...
1
...
2
...
Numbe rs of invading bacteria
If only a few microbes enter the body, they will probably be over-come by the host's defences
...
Thus, the likelihood of
disease increases as the number of pathogens increases
...

IV
...
1
...
3
...
For most pathogens, this attachment, called adherence (or adhesion), is a necessary step in
pathogenicity
...
Adhesins may be located on a microbe's glycocalyx or on other microbial
surface structures, such as pili, fimbriae, and flagella
...
1
...
Cooperation among microorganisms
It is not only competition among microbes that can cause disease; cooperation among microbes can
also be a factor in causing disease
...

Bacteriology, first part

38

IV
...
Penetration into host defences
Although some pathogens can cause damage on the surface of tissues, most must penetrate tissues
to cause disease
...

IV
...
1
...
However, the human body can produce antibodies against the
capsule, and when these antibodies are present on the capsule surface, the encapsulated bacteria are easily
destroyed by phagocytosis
...
Also have virulence determine by capsule
...
2
...
Cell walls
The cell walls of certain bacteria contain chemical substances that contribute to virulence
...
The M protein mediates attachment of the bacterium to epithelial
cells of the host and helps the bacterium resist phagoc ytosis by white blood cells
...
These bacteria use fimbriae and an outer
membrane protein called Opa to attach to host cells
...
The waxy
lipid (mycolic acid) that makes up the cell wall of Mycobacterium tuberculosis also increases virulence
by resisting digestion by phagocytes, and can even multiply inside phagocytes
...
2
...
Enzymes
The virulence of some bacteria is aided by the production of e xtracellular enzymes (exoenzymes)
and related substances
...

Coagulases are bacterial enzymes that coagulate (clot) the fibrinogen in blood changing it to fibrin
...
The fibrin clot may protect the bacterium from phagocytosis and isolate it from other
defenses of the host
...

Bacterial kinases are bacterial enzymes that break down fibrin and thus digest clots formed by the
body to isolate the infection
...

Hyaluronidase is another enzyme secreted by certain bacteria, such as streptococci
...
This digesting action is thought to be involved in the tissue blackening of infected
wounds and to help the microorganism spread from its initial site of infection
...

Other enzymes are collagenase, produced by several species of Clostridium; IgA proteases, that can
destroy these antibodies
...
gonorrhoeae has this ability, as do N
...

IV
...
4
...
Thus, by
the time the body mounts an immune response against a pathogen, the pathogen has already altered its
antigens and is unaffected by the antibodies
...
gonorrhoeae has several copies of the Opa-encoding
gene, resulting in cells with different antigens and in cells that express different antigens over time
...
2
...
Penetration into the host cell cytoskeleton
As previously noted, microbes attach to host cells by adhesins
...


Bacteriology, first part

39

Salmonella strains and E
...
This leads to
dramatic changes in the membrane at the point of contact
...
For example, when S
...
This effect, called
membrane ruffling (creusement), is the result of disruption in the cytoskeleton of the host cell
...

Once inside the host cell, certain bacteria such as Shigella and Listeria species can use actin to
propel themselves through the host cell cytoplasm and from one host cell to another
...
3
...
2: Structure of
enterobactin, one type of
bacterial siderophore
...
3
...
Using the host's nutrients: case of siderophores
Iron is required for the growth of most pathogenic bacteria
...
To obtain free iron, some pathogens secrete proteins called
siderophores, and release them into the medium where they take the
iron away from iron-transport proteins by binding the iron even more
tightly
...
Then the iron is
brought into the bacterium
...

As an alternative to iron acquisition by siderophores, some pathogens have receptors that bind
directly to iron-transport proteins and haemoglobin
...
Some bacteria produce toxins that kill host cells, releasing their iron and thereby making it
available to the bacteria
...
3
...
Direct damage
Pathogens can cause direct damage as the pathogens use the host cell for nutrients and produce
waste products
...
Then, the
released pathogens can spread to other tissues in even greater numbers
...
coli,
Shigella, Salmonella, and Neisseria gonorrhoeae, can induce host epithelial cells to engulf them by a
process that resembles phagocytosis
...
Some bacteria can also penetrate host cells by excreting enzymes and by their own motility; such
penetration can itself damage the host cell
...

IV
...
3
...
They are often the
primary factor contributing to the pathogenic properties of those microbes
...
Toxins transported by the blood or lymph can
cause serious, and sometimes fatal, effects
...
Toxins can also inhibit protein synthesis, destroy blood cells and blood vessels, and
disrupt the nervous system by causing spasms
...
The term toxaemia refers to the presence of toxins in
the blood
...

IV
...
3
...
Exotoxins
Exotoxins are soluble proteins produced by microorganisms
that can enter a host cell and catalyze the covalent modification of
a cellular component(s) to alter the host-cell physiology
...
3: Exotoxin production
...
3)
...
Bacteria that produce exotoxins may be Grampositive or Gram- negative
...

Many exotoxins can be chemically modified to toxoids that no longer expresses cytotoxicity, but may retain
immunogenicity
...
Exotoxins have also been used as therapeutic agents to
correct various disorders, including the treatment of muscle spasms by botulinum to xin
...
In addition, bacterial to xins have been used as research tools to assist in defining
various eukaryotic metabolic pathways, such as G-protein-mediated signal transduction
...
One is the type of host cell that is
attacked
...
Some exotoxins are named for the diseases with which they are associated
...
Other
exotoxins are named for the specific bacterium that produces them, for example
...

The ability of a bacterial pathogen to cause disease frequently requires the production of exotoxins,
but the mere ability to produce a toxin is not sufficient to cause disease
...
Administration of micrograms of purified cholera toxin to human
volunteers elicits a diarrhoeal disease that mimics the magnitude of the natural infection
...
cholerae have been isolated and shown to lack specific
biological properties, such as motility or chemotaxis
...
anthracis have been
isolated and shown to lack the ability to produce a polyglutamic acid capsule
...

Exotoxins are divided into three principal types on the basis of their structure and function: ( 1) A-B
toxins, (2) membrane-disrupting toxins
...

IV
...
1
...
A-B toxins
A-B toxins consist of two parts designated A and B, both of which are polypeptides
...
The A part is the active (enzyme) component, and the B part is the binding
component
...
Then, the B part is release and the A portion inhibits protein synthesis
...

Botulinum toxin is a neurotoxin produced by Clostridium botulinum that acts at the neuromuscular
junction and inhibits the release of acetylcholine, thus preventing the transmission of impulses
from the nerve cell to the muscle
...
There are several types of
botulinum toxins, each with its potency
...

Cholera toxin is an A-B enterotoxin
...
3
...
2
...
Some
do this by forming protein channels in the plasma membrane (Staphylococcus aureus); others disrupt the
phospholipid portion of the membrane (Clostridium perfringens)
...
They act by
forming protein channels
...

Most leukocidins are produced by staphylococci and streptococci
...
Important producers of
haemolysins include staphylococci and streptococci
...

IV
...
1
...
Superantigens
Superantigens are proteinic antigens that provoke a very intense immune response
...
In response to superantigens, T cells are stimulated to release
enormous amounts of cytokines
...

Streptococcus pyogenes has the genetic material to synthesize three types of cytotoxins, designated A, B, and C
...
Scarlet fever, caused by S
...

Staphylococcus aureus produces a superantigen that affects the intestines in the same way as vibrio enteroto xin
...

aureus also produces a superantigen that results in the symptoms associated with toxic shock syndrome
...
3
...
2
...
4)
...
that Gram - negative bacteria have an outer
Bacteriology, first part
Figure 4
...


42

membrane surrounding the peptidoglycan layer of the cell wall
...
The lipid portion of
LPS, called lipid A, is the endotoxin: they are lipopolysaccharides, released when Gram-negative
bacteria die and their membrane lysed
...

Table 4
...

Disease

Bacterium

Type of Exotoxin

Botulis m

Clostridium
botulinum

A-B

Tetanus

Clostridium tetani

A-B

Diphtheria
Scalded skin
syndrome

Corynebacterium
diphtheriae
Staphylococcus
aureus

Cholera

A-B
A-B

Mechanism
Neurotoxin prevents the transmission of nerve impu lses:
flaccid paralysis results
...

Cytotoxin inhib its protein synthesis, especially in nerve,
heart, and kidney cells
...

Enteroto xin causes secretion of large amounts of fluids and
electrolytes that result in diarrhoea
...


A-B

Enteroto xin causes secretion of large amounts of fluids and
electrolytes that result in diarrhoea
...
The A
proteins cause shock and reduce the immune response
...


Clostridium
difficile

Membrane-d isrupting

Staphylococcus
aureus

Superantigen

Staphylococcus
aureus

Superantigen

Enteroto xin causes secretion of fluids and electrolytes that
results in diarrhoea: cytotoxin disrupts host cytoskeleton
...

Toxin causes secretion of flu ids and electrolytes from
capillaries that decreases blood volume and lo wers blood
pressure
...
3: Comparing exotoxin and endotoxin
...
usually with two parts (A- B)

Gram-negative bacteria
Present in LPS of outer memb rane of cell wall
and released with destruction of cell or during
cell division
...


Toxicity

Specific fo r a part icular cell structure or function
in the host (main ly affects cell functions
...

and gastrointestinal tract)
...

High

Fever-production

No

Immunology

Can be converted to toxoids to immunize against
toxin: neutralized by antito xin
...


Pharmacology
Heat stability

Bacteriology, first part

General, such as fever, weaknesses, aches, and
shock: all produce the same effects
...

Low
Yes
Not easily neutralized by antito xin: therefore,
effective to xoids cannot be made to immun ize
against toxin
...

Typhoid fever, urinary t ract infect ions, and
men ingococcal men ingitis
...
Endotoxins exert their effects by stimulating macrophages to release cytokines in very
high concentrations
...
All endotoxins produce the same signs and symptoms, regardless
of the species of microorganism, although not to the same degree
...
5)
...
Another consequence of endotoxins is the activation of
blood -clotting proteins, causing the formation of small blood clots
...
This condition is referred to as disseminated intravascular coagulation (DIC)
...
Gram- negative bacteria cause endotoxic shock
...

-

Phagocytosis of Gram bacteria causes the phagocytes to secrete tumor necrosis factor (TNF ), sometimes
called cachectin (comment)
...
O ne effect of TNF is damage to blood capillaries; their permeability is increased, and
they lose large amounts of flu id
...

Low blood pressure has serious effects on the kidneys, lungs, and gastrointestinal tract
...
These, in turn, cause a weakening of the blood-brain barrier that normally protects the central nervous system
from infection
...
In developed contries, 1/3 of the patients die within a month, and nearly half die within 6 months
...


Representative microorganisms that produce endotoxins are Salmonella typhi, Proteus spp
...


Figure 4
...

A macrophage ingests a Gram- negative bacterium; The bacterium is degraded in a vacuole,
releasing endotoxins that induce the macrophage to produce cytokines IL-1 and TNF·
...
The cytokines induce the hypothalamus to produce prostaglandins, which reset the body's
“thermostat” to a higher temperature, producing fever
...
3
...
Plas mids, lysogeny, and pathogenicity
One group of plasmids, called R (resistance) factors, is responsible for the resistance of some
microorganisms to antibiotics
...

Examples of virulence factors that are encoded by plasmid genes are tetanus neurotoxin, heat-labile
enterotoxin, and staphylococcal enterotoxin
...
coli
...
Such a state is called lysogeny,
and cells containing a prophage are said to be lysogenic
...
Such a
change in the characteristics of a microbe due to a prophage is called lysogenic conversion
...
In addition,
lysogenic cells are of medical importance because some bacterial pathogenesis is caused by the prophages
they contain
...

The gene for Shiga toxin in E
...
Pathogenic strains of Vibrio cholerae carry
lysogenic phages
...
cholerae strains, increasing the
number of pathogenic bacteria
...
4
...
Infectious diseases are caused by organisms
...

I
...

2
...

3
...

4
...

Analyse it and bring out some exceptions
...
For example, some microbes have unique culture requirements
...
Mycobacterium leprae, has also never
been grown on artificial media
...
These limits have caused the modification of the postulate
and the use of alternative methods of culturing and detecting certain microbes
...
For example, the pathogens responsible for diphtheria and
tetanus cause distinguishing signs and symptoms that no other microbe can produce
...
But some infectious diseases are
not as clear-cut and provide another exception to Koch's postulates
...
Thus, it is often difficult to know which particular microorganism is causing a disease
...

Still another exception to Koch's postulates results because some pathogens can cause several
disease conditions
...
Streptococcus pyogenes can cause sore throat, scarlet fever, skin infections
(such as erysipelas), and osteomyelitis (inflammation of bone), among other diseases
...
For example, some
agents that cause disease in humans have no other known host
...
He promised their freedom
if they lived
...


Bacteriology, first part

45



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