Micro تفاريغ PDF

INTRODUCTION
Weam Aljbaly & Nedaá Ashour

Microbiology in the biological
world
DR. WALEED AL MOMANI, MLT, PHD

Microbiology is the study of microbes which can be observed
only with the use of various types of microscopes with only
rare exceptions
“microbiology considers to be one of the biological science, we can define it as simple

which is the science studying the organisms which can’t be observed by necked eyes or
can be seen only with the microscope”.
Dr. Waleed Al Momani

Microbiology
The general feature of microorganisms:

 Microorganisms share their small sizes; although
they are simple they can be extraordinarily
complex. (Its small size does not mean its weakness,
because it is capable of causing serious disease)



 Superficially, bacteria appear to be relatively
simple forms of life (life cycle is very simple); in
fact, they are sophisticated and highly adaptable
(they can live in any environment even in harsh one
Whether it is very hot or very cold ).
Why Study Microbiology?
 Indigenous microbiota. (the body has many organisms in or on

our bodies and we have a relationship with them which can be friendly
like normal flora or enemies like pathogenic).


 Opportunistic pathogens (or the chancers they are normal
flora convert to pathogenic at certain instances like breaking down of
immune system)




 Microbes produce oxygen (algae and cyanobacteria
a group of photosynthetic bacteria that produce
oxygen) It is considered the most important source
of oxygen




 Microbes are involved in the decomposition of dead
organisms and the waste products of living organisms

 Microbes are capable of decomposing industrial
wastes (oil spills).


 Many microbes are involved in elemental cycles, e.g.:
nitrogen cycle (microbes help in fixation nitrogen in soil which is
important in fertilization=> Agricultural importance)


 Algae and bacteria serve as food for tiny animals.


 Microbes produce substances that are of value to the
host(who can’t produce it by himself ) e.g.: E. coli (normal flora at
small intestine) produce vitamins K and B1.
 Many microbes are essential in various food and
beverage industries 



 Some bacteria and fungi produce antibiotics that
are used to treat patients with infectious diseases
(60% of medicine which is uses in the pharmacies specially the
antimicrobial are comes from the fungus & bacteria) 



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 Microbesare essential in the field of genetic
engineering. ‫االعتماد األكبر على تطور هندسة الجينات هو المايكروبات‬


 Microbes have been used as “cell models. E. coli is
one of the most studied of all microbes.
E.coil: called factory because it produces vitamins, hormones, enzymes, and
many molecules
 These organisms are studied for many reasons; one
important reason is that they cause deadly diseases.




 Pathogens cause two major types of diseases:
infectious diseases and microbial intoxications (toxic
material produced by organism).
**The diseases happen by two ways by entering the microbes
to the body or by the toxic secretion of the microbes 
3% of known microbes are capable of
causing disease and said to be pathogenic

Earliest Known Infectious
Diseases
Human pathogens have existed for thousands of

years because damage caused by them has been
observed in the bones and internal organs of mummies
and early human fossils. (e.g. observed the malignant tumor
in the skull of mummies).
** How we can determine if the resulting effect happen by bacteria

or microbe?
By genetic analyses by taking scratch from the region that have the
infection sign then do DNA extraction and sequencing then decide to
which class is followed.
Pioneers in the Science of Microbiology
The father of microbiology

 Van Leeuwenhoek: the first using
magnification glass to identify bacteria and to
describe their shapes
Van Leeuwenhoek
use this simple
one lens
microscope with a
water drop from a
lake put it under
the screws and try
to draw what he
saw

Spontaneous generation
 life can arise spontaneously from nonliving

material is called the theory of spontaneous
generation or abiogenesis.




 life can only arise from preexisting life. This is
called the theory of biogenesis

Spontaneous generation
 Francesco Redi debunk the spontaneous

generation theory by simple experiment
(Redi’s experiment was piece of beef he covered it by
a mesh to prevent microbes from reach to it so he
thinks that the beef size will be the same and not
damaged, this experiment was refused by other
scientist who believe that the mesh large enough for
tiny microbe to enter and damaged it)




 Pasteur experiment=> The father of medical
microbiology 
Swan neck experiment to determine the aerobes and anaerobes.
1- He boiling the broth (media to culture bacteria) to kill all organisms with
covered the neck of flask to prevent air connection.2- he removed the
cover and allows air’s organisms to enter without connection with broth.
3-he makes the flask tilted, the broth and organisms connect so all the
broth mix with them
In this experiment, Pasteur
identified aerobic and anaerobic.
Bacteria cannot reproduce or
multiplications unless they have
direct contact with nutrients
important for their growth,
which is what the broth
Dr. represents. So when contact
occurred, the bacteria evolved
and were able to grow.
Waleed Al Momani
Pasteur
 Pasteur introduced the terms “aerobes” and “anaerobes”



 Pasteur developed Pasteurization (boiling to high middle temperature
for few time to kill pathogens just as milk Pasteurization)



 Pasteur made significant contributions to the germ theory
(background all microbiology theory) of disease


 he discovered Anthrax ( ‫(مرض الجمرة الخبيثة‬ the pathogen
(Bacillus anthracis) the most risk microbe .
 Bacillus anthracis: ‫ من حيث الخطورة كمايكروب الذي يسبب مرض‬1‫يعتبر رقم‬
‫الجمرة الخبيثة‬



 Pasteur lead changes in hospital practices tominimize the spread
of disease by pathogens (nosocomial infection). ‫يعني المريض بروح على‬
‫المستشفى بشكي من مرض بسيط بغادر المستشفى معدي بمرض اصعب فبستر عمل استراتيجية تحد من هاي‬
‫العدوى‬



 Pasteur developed vaccines to prevent chicken cholera, anthrax,
and swine erysipelas (a skin disease). (the most important
achievement to humanity)


 Pasteur developed a vaccine to prevent rabies in dogs
He has an
important role
in microbiology,
the most
important of
which is the
Koch postulate
Robert Koch.

 Koch discovered that B. anthracis produces spores)
Which is the source of resistance in bacteria(




 Koch developed methods of cultivating bacteria
on solid media




 Koch discovered the bacterium (M. tuberculosis)
that causes tuberculosis and the bacterium (Vibrio
cholerae) that causes cholera.


 Koch’s work on tuberculin
Tuberculin; A test to detect infection with tuberculosis by injecting the
patient with a substance in the event that the cause of inflammation of a
certain diameter It indicates that the test result is positive)TB+), if there
is no inflammation , so it is negative(TB-), meaning healthy
1. The microorganism must always be
found in similarly diseased animals but
not in healthy ones.
2. The microorganism must be isolated from a

diseased animal and grown in pure culture.
3. The isolated microorganism must cause the

original disease when inoculated into a susceptible
animal.
Sick
4. The microorganism can be reisolated from the

experimentally infected animal.

Medical microbiology-past triumphs
 Golden Age of microbiology 1875-1918 )The most

important period), most pathogenic bacteria were
identified



 10 million died of small pox ( ‫)الجدري‬, as a result of
vaccination no cases have been reported since 1977 

 Note that: The vaccine is only given if it is 100% safe, for
example, the smallpox vaccine is safer than the plague
vaccine, and it is not given unless the patient is in a very
serious condition.



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 1346-1350, 1/3 of the entire population of Europe
died from bubonic plague (‫) الطاعون‬




 The discovery of antibiotic and vaccine provided
an important weapon against bacterial diseases
In 1964, the surgeon general of the United States delivered a speech to
Congress: “It is time to close the book on infectious diseases,” he said. “The war
against pestilence is over.”
In 1998, Surgeon General David Satcher had a different message. The Miami
Herald reported his speech with this headline: “Infectious Diseases a Rising Peril;
Death Rates in U.S. Up 58% Since 1980.”

Medical microbiology- future challenges
 The importance of medical microbiology as an active field

of research



 750 million cases of infectious diseases occur in the USA
leading to 200 000 deaths annually and results in tens
of billions of dollars in health care costs alone ‫يعني االمراض‬
‫ المعدية تسبب خسائر بشرية و اقتصادية‬



 Respiratory infections (as cavid 19) and diarrheal
diseases are the leading causes of illness and deaths



Diseases that were attributed to other causes have now been
shown to be caused by microorganisms i.e peptic ulcer ( ‫قرحة‬
‫ بسبب )المعدة‬%90 ‫ كان يعتقد ان سببها العصبية الزائدة او شرب الكحول لكن اثبت ان‬microor
Cell Structure and Taxonomy
Ammar M Battah
Edited by : Lubna AL-RAwabdeh
Cell Structure and Taxonomy
DR. WALEED AL MOMANI, MLT,

PHD

Introduction
Two major categories of microbes:
Acellular microbes (infectious particles)

.self-replication ‫ ﻷﻧﮭﻢ ﻣﺎ ﺑﺤﻘﻘﻮا ﺷﺮط ال‬Microorganisms ‫ ﻻ ﺗﺼﻨﻒ ﺿﻤﻦ ال‬A cellular microbes -
Because they depend on the host cell’s metabolic machinery
Cellular microbes (microorganisms).
G Self replicate... they depend on their own machinery

Microbes
Acellular Cellular
(Infectious agent )
Viroid
Prions
viruses
Prokaryotes
Eukaryotes
These can cause remarkable diseases
Archaea Algae
Bacteria Protozoa
Cyanobacteria Fungi

Objectives
1. To learn about the structure of microorganisms
2. Discuss the ways in which microbes and their cells reproduce

and how microorganisms are classified.

One cell can produce an organism
e
A cell is defined as the fundamental unit of any living
organism
Metabolism refers to all of the chemical reactions that occur

within a cell ‫ﻗﺪرة اﻟﺨﻠﯿﺔ اﻟﺒﻜﺘﯿﺮﯾﺔ ﻋﻠﻰ إﻧﺘﺎج اﻟﻄﺎﻗﺔ و اﺳﺘﮭﻼﻛﮭﺎ وﯾﻨﺘﺞ ﻋﻨﮭﺎ ﺑﻨﺎء اﻟﺨﻠﯿﺔ‬
. Fundamental unit ‫ ھﻲ ال‬organism ‫ ﻗﺪﯾﻤﺎ ً ﻗﺒﻞ إﻛﺘﺸﺎف اﻟﺨﻠﯿﺔ ﻛﺎﻧﻮا ﯾﺤﻜﻮا إﻧﮫ ال‬-
.Cells - tissue - organ - system - Organism : ‫ اﻟﺘﺴﻠﺴﻞ ﻷي ﻛﺎﺋﻦ ﺣﻲ اﻵن‬-
. Development to organism ‫ ﻷﻧﮭﺎ ﻗﺎدرة ﻋﻠﻰ‬Fundmental unit ‫ و ﺗﺴﻤﻰ ب‬Single cell ‫ ﻣﻌﻈﻢ اﻟﻤﺎﯾﻜﺮوﺑﺎت ﺑﺘﻜﻮن‬-
. ‫ اﻟﺘﻲ ﺗﺤﺪث ﻓﯿﮭﺎ‬Motabolism ‫ ﺑﺘﻌﺘﻤﺪ اﻟﺨﻠﯿﺔ ﻓﻲ ﺗﻄﻮرھﺎ ﻋﻠﻰ اﻟﻤﺎدة اﻟﻮراﺛﯿﺔ اﻟﺨﺎﺻﺔ ﺑﮭﺎ إﺿﺎﻓﺔ إﻟﻰ ال‬-
Note: metabolism is divided to anabolism and catabolism

Catabolism is break down molecules where as anabolism construct molecules from small units .

Pro section mean pre nucleus
\
EU section mean true nucleus
Eukaryotic cells possess a true nucleus, whereas prokaryotic

cells do not.
The main difference is the presence of the plasmic organs within a cell
Bacteria and Archaea, are called prokaryotes or prokaryotic

cells.

\
Viruses are composed of only a few genes protected by a
Enos
protein coat, and sometimes may contain one or a few
enzymes. .‫ أﺣﯿﺎﻧﺎ ً ﺑﺘﻜﻮن ﻣﻦ ﺟﯿﻨﺎت ﻣﻐﻄﯿﺔ ﺑﻄﺒﻘﺔ ﻣﻦ اﻟﺒﺮوﺗﯿﻨﺎت و ﻗﺪ ﯾﺤﺘﻮي ﻋﻠﻰ إﻧﺰﯾﻤﺎت‬،‫ اﻟﻔﯿﺮوس ﻣﺎ ﺑﺘﻜﻮن ﻣﻦ ﺧﻼﯾﺎ‬-
Viruses depend on the energy and metabolic machinery of a

host cell to reproduce. Note: the viruses can’t replicate unless it enter in the host
. ‫و اﻟﺴﺒﺐ ھﻮ أن اﻟﻔﺎﯾﺮوس ﺑﻌﺘﻤﺪ ﻋﻠﻰ اﻟﻜﺎﺋﻦ اﻟﺬي ﯾﺪﺧﻠﮫ ﻟﻠﺤﺼﻮل ﻋﻠﻰ طﺎﻗﺔ ﻋﺸﺎن ھﯿﻚ ﻟﻤﺎ ﺑﺪي أﺿﺎﻋﻒ اﻟﻔﺎﯾﺮوس ﺑﺎﻟﻤﺨﺘﺒﺮ ﺑﺤﻄﮫ ﺑﺨﻠﯿﺔ ﺣﯿﺔ‬
Because viruses are acellular (not composed of cells), they are

placed in a completely separate category.

Health care professionals, should learn differences in the
structure of various cells to:
1. identify organisms To know the infectious agent that cause infectious disease
2. understand differences in their metabolism.
‫ﻣﻌﺮﻓﺔ ﺗﺮﻛﯿﺐ اﻟﺨﻼﯾﺎ ﺑﺴﺎﻋﺪﻧﺎ ﻋﻠﻰ ﻓﮭﻢ اﻹﺧﺘﻼف ﺑﯿﻦ و اﻹﺧﺘﻼف ﺑﯿﻦ وظﺎﺋﻔﮭﺎ‬
These factors must be known before one can determine or

explain why antimicrobial agents (drugs) attack and destroy
pathogens, but do not harm human cells.
Anti microbial agents ‫أﺣﺪ اﻷﻣﺜﻠﺔ ﻋﻠﻰ ﻓﺎﺋﺪة ﻣﻌﺮﻓﺔ ﻓﺮق اﻟﺘﺮﻛﯿﺐ ﺑﯿﻦ اﻟﺨﻼﯾﺎ ھﻲ‬
Anti-microbial agent: Kill microorganism or stops their growth by selective toxicity , where as it doesn’t
effect on host cell of eukaryotic

Eukaryotic Cell Structure
*g wb-
Prokaryotic d I
oIjldrgi-sd-a@K-m-jsd.d
l Hh I em
Dr. Waleed Al Momani A typical eukaryotic animal cell

Cell wall
Present Absent
I -
Plants l -
Animals
2- Algae 2- Protozoa
3- Fungi 3- mycoplasma
4- Most bacteria
↳ ‫ ﺑﻌﺾ أﻧﻮاع اﻟﺒﻜﺘﯿﺮﯾﺎ ﻻ ﺗﺤﺘﻮي ﻋﻠﻰ‬Cell wall

Cell wall bacteria ‫ ھﺬا اﻟﻨﻮع ﯾﺴﻤﻰ‬Mycoplasma

Prokaryotic Cell Structure
Prokaryotic cells are about 10 times smaller than eukaryotic

cells
Reproduction of prokaryotic cells is by binary fission

2
Asexual reproduction by a separation
of the body to two identical body.
All bacteria are prokaryotes It’s important to survive the kind of my crops.
Embedded within the cytoplasm of prokaryotic cells are a

chromosome, ribosomes, and other cytoplasmic particles
Nucleus, nuclear envelope, organelles in cytoplasm ‫ ﺗﺨﻠﻮ ﻣﻦ‬The prokaryotic cells
. ‫ ﻣﺜﻞ اﻟﻜﺮوﻣﻮﺳﻮﻣﺎت و اﻟﺮاﯾﺒﻮﺳﻮﻣﺎت‬particles‫ﻣﺎﻋﺪا ﺑﻌﺾ ال‬

Unlike eukaryotic cells, the cytoplasm of prokaryotic cells is
not filled with internal membranes.
① ②
The cytoplasm is surrounded by a cell membrane, a cell wall
(usually), and sometimes a capsule or slime layer.
③

Cell Membrane
Chemically, the cell membrane consists of proteins and

phospholipids
mainfunction
of cell membrane
↳
Selective permeability
Many enzymes are attached to the cell membrane, and

various metabolic reactions take place there
Mesosomes—are foldings of the cell membranes—where

cellular respiration takes place in bacteria
‫ )ﻷﻧﮭﺎ ﻻ ﺗﺤﺘﻮي ﻋﻠﻰ ﻣﯿﺘﻮﻛﻮﻧﺪرﯾﺎ ( ﺣﯿﺚ أﻧﮭﺎ ﺗﺤﺘﻮي ﻋﻠﻰ‬Mesosomes ‫ ﺗﺤﺪﯾﺪاً ال‬Cell membrane ‫اﻟﺨﻠﯿﺔ ﺑﺘﺤﺼﻞ ﻋﻠﻰ طﺎﻗﺔ ﻣﻦ ال‬
Cytochrome oxidase enzymes ‫ ھﺬه اﻹﻧﺰﯾﻤﺎت ﺗﺴﻤﻰ‬، ‫اﻧﺰﯾﻤﺎت ﺗﺴﺎھﻢ ﻓﻲ إﻧﺘﺎج اﻟﻄﺎﻗﺔ ﻋﻦ طﺮﯾﻖ ﻧﻘﻞ اﻹﻟﻜﺘﺮوﻧﺎت‬

Chromosome
The prokaryotic c h r omo s ome usually consists of a single,

long, supercoiled, circular DNA molecule, which serves as the
control center of the bacterial cell ‫اﻟﻤﺴﺆول ﻋﻦ ﻛﻞ اﻟﻤﻮاﺻﻔﺎت اﻟﺠﯿﻨﯿﺔ ﻟﻠﺨﻠﯿﺔ‬
The chromosome is suspended or embedded in the

cytoplasm.
The DNA-occupied space within a bacterial cell is sometimes

referred to as the bacterial nucleoid
Chromatin body ‫ أو‬Nucleoid ‫ ﻣﻮﺟﻮد ﺑﻤﻨﻄﻘﺔ ﺗﺴﻤﻰ‬DNA ‫ال‬

‫‪Plasmids = a small, circular molecules of double-stranded‬‬
‫‪DNA that are not part of the chromosome may also be‬‬
‫‪present in the cytoplasm of prokaryotic cells‬‬
‫‪ The plasmid -‬ھﻮ ﻣﺎدة زي اﻟﻜﺮوﻣﻮﺳﻮم و ﻟﻜﻨﮫ ﺑﺘﻮاﺟﺪ ﻓﻲ ال ‪ Cytoplasm‬و ﻟﯿﺲ ﺟﺰء ﻣﻦ اﻟﻜﺮوﻣﻮﺳﻮم ‪.‬‬
‫ﻣﻮﺟﻮد ﻓﻲ ﺑﻌﺾ أﻧﻮاع اﻟﺨﻠﯿﺔ و ﻟﯿﺴﺖ ﺟﻤﯿﻌﮭﺎ ‪ ،‬ﯾﺒﻠﻎ ﺣﺠﻤﮭﺎ ‪ 0.1 - 10 %‬ﻣﻦ ﺣﺠﻢ اﻟﻜﺮوﻣﻮﺳﻮم ‪.‬‬
‫ﻓﻮاﺋﺪه ﻟﻠﺨﻠﯿﺔ‬
‫‪ -١‬ﺗﻌﻄﻲ ﺑﻌﺾ اﻟﻤﻮاﺻﻔﺎت ﻏﯿﺮ اﻟﻤﻮﺟﻮدة ﻓﯿﮭﺎ و ذﻟﻚ ﻋﻦ طﺮﯾﻖ ﻧﻘﻞ اﻟﻤﺎدة اﻟﻮراﺛﯿﺔ ﻣﻦ ﺧﻠﯿﺔ ﺑﻜﺘﯿﺮﯾﺔ أﺧﺮى ‪Toxgen‬‬
‫و ﺗﻨﺘﻘﻞ ﻋﻦ طﺮﯾﻖ ﻣﻮاد ﺗﺴﻤﻰ ‪. Sex pilus‬‬
‫‪. Unit-microbial resistance -٢‬‬
‫‪Dr. Waleed Al Momani‬‬

Cytoplasm
The cytoplasm of prokaryotic cells consists of water, enzymes,

dissolved oxygen (in some bacteria), waste products, essential
t f L-
nutrients, proteins, carbohydrates, and lipids—a complex

mixture of all the materials required by the cell for its
metabolic functions.

Cytoplasmic Particles
Prokaryotic ribosomes are smaller than eukaryotic

ribosomes, they are the sites of protein synthesis.
A 70S prokaryotic ribosome is composed of a 30S subunit

and a 50S subunit ، ‫ ھﻲ ﻣﺜﻞ وﺣﺪة ﻗﯿﺎس ﻟﻠﺮاﯾﺒﻮﺳﻮم و ﻣﺎ اﻟﮭﺎ دﺧﻞ ﺑﺤﺴﺎﺑﺎت اﻷرﻗﺎم‬70s ‫اﻵن ھﻮن وﺣﺪة ال‬
، Small subunit or ribosome ‫ ﺑﺘﺮﻣﺰ ﻟﻞ‬30s ‫ال‬
.Large subunit or ribosome ‫ ﺑﺘﺮﻣﺰ ﻟﻞ‬50s ‫ال‬
. Small & Large subunit ‫ﯾﻌﻨﻲ ﺑﺤﻜﻲ اﻧﮫ اﻟﺮاﯾﺒﻮﺳﻮم ﺑﺘﻜﻮن ﻣﻦ‬
Cytoplasmic granules occur in certain species of bacteria.

↳ ‫ و ھﻲ ﻣﺨﺰن ﻟﻠﻤﻮاد اﻹﺿﺎﻓﯿﺔ اﻟﺘﻲ ﺗﺤﺘﺎﺟﮭﺎ اﻟﺒﻜﺘﯿﺮﯾﺎ ﻓﯿﻤﺎ ﺑﻌﺪ‬، ‫ھﻲ أھﻢ ﻣﻜﻮن ﻣﻮﺟﻮد ﻓﻲ اﻟﺴﯿﺘﻮﺑﻼزم ﻟﻠﺨﻠﯿﺔ اﻟﺒﻜﺘﯿﺮﯾﺔ‬
The granules may consist of starch, lipids, sulfur, iron, or

other stored substances.

Bacterial Cell Wall
The structure of bacterial cell walls is different from the eukaryotic cell
walls
Save the shape of bacteria cell
Functions—rigidity, strength, and protection / Organelle inside cell
Peptidoglycan is the major constituent of most bacterial cell walls (also

known as murein)
Peptidoglycan is only found in bacteria.
The thickness of the cell wall and its exact composition vary with the
species of bacteria
Depends on number layer of peptidoglycan in the cell

The two major content of peptidoglycan ,
and linkage by glycosidic bonds
These amino acid is link with N-acytelmuramic acid

and it 3-5 amino acid, peptidoglycan is one of the
most sources of D amino acid in nature .

‫ طﺒﻘﺔ‬30 ‫ﻗﺪ ﺗﺼﻞ إﻟﻰ‬
9
Gram-positive bacteria have a thick layer of peptidoglycan combined with
teichoic acid and lipoteichoic acid molecules
Peptidoglycan ‫ إﺿﺎﻓﺔ ال‬Cell membrane ‫ھﺬول اﻟﻤﻜﻮﻧﯿﻦ ﻣﻮﺟﻮدﯾﻦ‬
Lipoteichoic
acid
Teichoic acid
Peptidoglycan
Cell wall
Cell
membrane

-
1-3 layer
Gram-negative bacteria have a much thinner layer of peptidoglycan, but this
layer is covered with a complex layer of lipid macromolecules, usually referred
to as the outer membrane ‫ و اﻟﺴﺒﺐ ھﻮ وﺟﻮد‬positive ‫ ھﻲ أﻛﺜﺮ ﺗﻌﻘﯿﺪاً ﻣﻦ ال‬Negative ‫ال‬
‫ و ﻋﺪم وﺟﻮدة ﻓﻲ‬Negative ‫ ﻓﻲ ال‬Outer membrane ‫ال‬
. positive‫ال‬
Membrane
proteins
Lipid + charbohydrate
ooh
Lipopolysaccharide
Outer
Phospholipid membrane
Lipoprotein
Cell wall
Peptidoglycan
Periplasm
Inner
membrane
Membrane
proteins

Glycocalyx (Slime Layers and Capsules)
A thick layer of material located outside their cell wall

↳ The outer most layer in the bacteria
Depending on the species, bacterial cells may or may not be

surrounded by glycocalyx.
The two types of glycocalyx are slime layers and capsules.
Bacterial capsules serve an antiphagocytic function

7
‫ و ذﻟﻚ ﻷن‬، ‫ھﺬه اﻟﻮظﯿﻔﺔ ﺗﻤﻜﻦ اﻟﺨﻠﯿﺔ ﻣﻦ اﻟﮭﺮوب ﻣﻦ اﻟﺨﻼﯾﺎ اﻟﻤﻨﺎﻋﯿﺔ‬
Hide receptor on cell wall ‫ ﺗﻌﻤﻞ ﻋﻠﻰ‬Capsule ‫ال‬
that immune cell response to it

Flagella
Motile bacteria usually possess flagella.
Bacteria never possess cilia.

I:X
The number and arrangement of flagella possessed by a

certain species of bacterium are characteristic of that species
. ‫ ﻗﺪ ﺗﺨﺘﻠﻒ ﺑﯿﻦ ﺑﻌﺾ ﻓﻲ اﻟﺸﻜﻞ و اﻟﻌﺪد و اﻟﻘﻮة‬Flagella ‫ال‬
‫ﻣﻦ ﻧﺎﺣﯿﺔ اﻟﻘﻮة ﻓﺈن ﺑﻌﺾ اﻟﺨﻼﯾﺎ ﺗﺘﺤﺮك ﺑﺴﺮﻋﺔ ﻛﺒﯿﺮة و ﺑﻌﻀﮭﺎ ﺑﺒﻄﺊ و ﺑﻌﻀﮭﺎ ﻻ ﯾﺘﺤﺮك ﻟﺬﻟﻚ ﯾﻤﻜﻨﻨﺎ ﺗﺼﻨﯿﻒ‬
.Flagella‫ ﺗﺒﻌﺎ ً ﻟﻨﻮع ال‬Motility and non-motility ‫اﻟﺒﻜﺘﯿﺮﯾﺎ إﻟﻰ‬

One flagella on one pool
Two flagella on two pool
Multiple flagella on whole bacteria surface

Multiple flagella on one pool

Pili (Fimbriae)
Pili or fimbriae are hair-like structures, most often observed

on Gram-negative bacteria composed of a protein called pilin
There are two types of pili:
One type merely enables bacteria to adhere or attach to

surfaces . ‫ و ﯾﻨﺘﺸﺮ ﻋﻠﻰ ﻛﻞ اﻟﺨﻠﯿﺔ‬، very small and numerous like hair ‫ ھﻮ ﻋﺒﺎرة ﻋﻦ‬Fimbriae ‫اﻟﻨﻮع اﻷول ﯾﺴﻤﻰ‬
Infection ‫ و اﻟﺴﺒﺐ ان اﻟﺒﻜﺘﯿﺮﯾﺎ ﻣﺎ ﺑﺘﻘﺪر ﺗﺴﻮي‬attachment to the host cell ‫اﻟﻮظﯿﻔﺔ اﻟﺮﺋﯿﺴﯿﺔ اﻟﮫ ھﻲ ال‬
. ‫ ﻣﻊ اﻟﺨﻠﯿﺔ اﻟﻤﺴﺘﮭﺪﻓﺔ‬attachment ‫ﺑﺪون ﻣﺎ ﺗﻌﻤﻞ‬
The other type (called a sex pilus) facilitates transfer of

genetic material
‫ و ﯾﻠﺘﻘﯿﺎن ﻣﻊ ﺑﻌﺾ‬Sex pilus ‫ و ﺣﺘﻰ ﺗﻨﺘﻘﻞ اﻟﻤﺎدة اﻟﻮراﺛﯿﺔ ﻻزم اﻟﺨﻠﯿﺘﯿﻦ ﯾﺤﺘﻮﯾﺎن ﻋﻠﻰ ال‬، ‫ﺑﺘﻨﺘﻘﻞ اﻟﻤﺎدة اﻟﻮراﺛﯿﺔ ﻣﻦ ﺧﻠﯿﺔ ﺑﻜﺘﯿﺮﯾﺔ ﻷﺧﺮى‬
6‫ ﻋﺪدھﺎ ﻻ ﯾﺘﺠﺎوز ال‬.... wide , long , huge and few ‫ﺗﺘﻤﯿﺰ ب‬

‫)‪Spores (Endospores‬‬
‫‪Sporulation is the process by which the spores are formed‬‬
‫‪Spores are resistant to heat, cold, drying, and most‬‬

‫‪chemicals.‬‬
‫‪Spores have been shown to survive for many years in soil or‬‬
‫‪dust, and some are quite resistant to disinfectants and‬‬
‫‪boiling‬‬
‫ال ‪ Spores‬ﻋﺒﺎرة ﻋﻦ ‪ dormant structure‬ﻣﻘﺎوﻣﺔ ﻟﻠﺤﺮارة و ﻟﺠﻤﯿﻊ اﻟﻈﺮوف ‪ ،‬ﺑﻜﻮن ﻏﯿﺮ ﻧﺸﻂ ‪ ،‬ﺑﺘﺘﻔّﻌﻞ ﻋﻨﺪﻣﺎ ﺗﻘﺘﺮب اﻟﺒﻜﺘﯿﺮﯾﺎ ﻣﻦ اﻟﻤﻮت )ھﻼ ھﯿﮫ ﺑﺲ‬
‫ﺗﻘﺮب ﺗﻤﻮت ﺑﺘﻨﺸﺮ ھﺎي اﻻﺑﻮاغ ﻋﺸﺎن ﺗﺤﺎﻓﻆ ع ﻧﻮﻋﮭﺎ‪ ،‬ﻣﻤﺎ ﯾﺆدي إﻟﻰ إﻋﺎدة ﺗﻜﻮﯾﻨﮭﺎ ﻣﻦ اﻟﺒﺪاﯾﺔ ‪ ،‬و ﻟﯿﺲ ﻟﮭﺎ أي ﻋﻼﻗﺔ ﻓﻲ ﺗﻜﺎﺛﺮ اﻟﺒﻜﺘﯿﺮﯾﺎ ‪.‬‬
‫ﻣﻼﺣﻈﺔ‪ :‬ال ‪ Spores‬اﻟﻤﻮﺟﻮدة ﻓﻲ ال ‪ Fungi‬اﻟﮭﺎ دﺧﻞ ﺑﺘﻜﺎﺛﺮھﺎ ‪.‬‬
‫ھﻨﺎك ﻧﻮﻋﺎن ﻣﻦ اﻟﺒﻜﺘﯿﺮﯾﺎ اﻟﺘﻲ ﺗﻨﺘﺞ ال ‪ , Spores‬اﻷول ھﻮ ‪ Bacillus‬و اﻵﺧﺮ ھﻮ ال ‪. Clostridium‬‬

‫ﻋﻤﻠﯿﺔ اﻟﻨﻤﻮ ‪ :‬ﺑﻤﺠﺮد ﻣﺎ ﺗﻨﺤﻂ ال‪ spores‬ﺑﻈﺮوف ﻣﻌﯿﻨﺔ و ﻣﻼﺋﻤﺔ ﻓﺎﻧﮭﺎ ﺗﺪﺧﻞ ﺑﻤﺮﺣﻠﺔ ﺗﺴﻤﻰ ‪ Vegetative form‬و ھﺬه اﻟﻈﺮوف ھﻲ‬
‫ال ‪. Moisture and heat‬‬

‫ ﺑﺤﯿﺚ إﻧﮫ ﺑﻜﻮن‬spores ‫ ﻟﻠﺒﻜﺘﯿﺮﯾﺎ ﺑﻨﺎًء ﻋﻠﻰ ﻣﻮﻗﻊ ال‬Diagnosis ‫ﺑﻨﻘﺪر ﻧﻌﻤﻞ‬
Central in some cell
and terminal in other
and sub terminal in some

Summary of Structural Differences between
Prokaryotic and Eukaryotic Cells
Eukaryotic cells contain numerous membranes and

membrane-bound structures.
The only membrane possessed by a prokaryotic cell is its cell

membrane.

Prokaryotic Cell Reproduction
Prokaryotic cells reproduce by a process known as binary

fission
Chromosome must be duplicated (a process known as DNA

replication) Then get two identical cells
The length of time it takes for one bacterial cell to split into
two cells is referred to as the organism’s generation time.
2
24 ‫ ﺑﺤﯿﺚ أﻧﮭﺎ ﻟﻮ وﺿﻌﺖ ﺧﻠﯿﺔ واﺣﺪة ﻣﻨﮭﻢ ﻟﻠﺘﻜﺎﺛﺮ ﻟﻮﺻﻠﺖ إﻟﻰ ﻋﺪد أﻛﺒﺮ ﻣﻦ ﺳﻜﺎن اﻷرض ﻓﻲ‬Fast growth ‫ھﻼ ﻓﻲ ﺑﻌﺾ اﻟﺒﻜﺘﯿﺮﯾﺎ ﺗﻌﺘﺒﺮ‬
‫ ) اﻟﺒﻜﺘﯿﺮﯾﺎ اﻟﻤﺴﺒﺒﺔ ﻟﻠﺴﻞ ( ﺗﺤﺘﺎج‬M. Tuberculosis ‫ و ھﺬا ﯾﺤﺘﺎج ﻟﻮﻗﺖ طﻮﯾﻞ ﻟﻺﻧﻘﺴﺎم ﻣﺜﻞ‬Slow growth ‫ و ھﻨﺎك ﻧﻮع آﺧﺮ ﯾﺴﻤﻰ‬، ‫ﺳﺎﻋﺔ‬
. ‫ أﺳﺎﺑﯿﻊ ﻟﻺﻧﻘﺴﺎم‬3 ‫إﻟﻰ‬

Taxonomy
Taxonomy =classification of living organisms
Consists of three separate but interrelated areas:

classification, nomenclature, and identification.
Classification is the arrangement of organisms into

taxonomic groups (known as taxa on the basis of similarities
or relationships
‫ ﻟﻠﺘﺼﻨﯿﻒ‬phenotype and genotype ‫ھﻮن ﺑﻨﻌﺘﻤﺪ ﻋﻠﻰ‬
Physical characteristics Genetic characteristic

‫طﺮﯾﻘﺔ اﻟﺘﺴﻤﯿﺔ ﻟﻠﺒﻜﺘﯿﺮﯾﺎ‬
Nomenclature is the assignment of names to the various taxa

according to international rules.
Identification is the process of determining whether an

isolate belongs to one of the established, named taxa or
represents a previously unidentified species.
Identification ‫ و أﻋﺰل اﻟﺒﻜﺘﯿﺮﯾﺎ وﺣﺪة وﺣﺪة ﻋﺸﺎن أﺣﺪد ال‬Species ‫ ﻻزم أﺻﻞ ﻟﻞ‬Identification ‫ھﻮن ﺣﺘﻰ أﺳﻮي‬

** Classification
An organism’s complete collection of genes is referred to as
the organism’s Genotype or genome.
An organism’s complete collection of physical characteristics

is known as the organism’s phenotype.

Microbial Classification
t.m.DE#g.SiF-wT.rwWoIgWioW
In the binomial system of nomenclature, the first name (e.g.,
Escherichia) is the genus, and the second name (e.g., coli) is
the specific epithet.
diff
When used together, the first and second names (e.g.,

Escherichia coli) are referred to as a species.
Capital ‫ ﺑﻜﻮن‬Genus ‫ﻓﻲ اﻟﻌﺎدة أول ﺣﺮف ﻣﻦ ال‬
Bacterium Small letter ‫ ﺑﻜﻮن‬Species‫ و ال‬letter Disease
Bacillus anthracis Anthrax
Chlamydophila pneumoniae Pneumonia
Chlamydophila psittaci Psittacosis (“parrot fever”)
Chlamydia trachomatis Trachoma
Clostridium botulinum Botulism
Clostridium tetani Tetanus
Corynebacterium Diphtheria
diphtheriae
In 1969, Robert H. Whittaker proposed a Five-Kingdom System of
Classification, in which all organisms are placed into five kingdoms:
• Bacteria and archaea are in the Kingdom Prokaryotae (or Monera)
• Algae and protozoa are in the Kingdom Protista (organisms in this kingdom
are referred to as protists)
• Fungi are in the Kingdom Fungi
• Plants are in the Kingdom Plantae
• Animals are in the Kingdom Animalia

Viruses are not included in the Five-Kingdom System of Classification
because they are not living cells
Archaea comes from archae, meaning “ancient.”
archaea are so different from bacteria
Bacteria have, been referred to as eubacteria, meaning “true” bacteria,

but are now usually referred to simply as bacteria
The Domain Eukarya is divided into four kingdoms:

Kingdom Protista or Protoctista (algae and protozoa); Kingdom Plantae;
Kingdom Fungi; Kingdom Animalia.

Evolution and the Tree of Life
Prokaryotes inhabited Earth from approximately 3 to 4

billion years ago, and eukaryotic cells emerged between 1.6
and 2.7 billion years ago
‫ وذﻟﻚ ﻋﻦ طﺮﯾﻖ‬،‫ﻣﻦ ﺑﺪاﯾﺔ ظﮭﻮر اﻟﺒﻜﺘﯿﺮﯾﺎ وھﻲ ﺗﺘﻄﻮر ﺑﺤﯿﺚ ﺗﻜﺘﺴﺐ ﺻﻔﺎت وﺗﺨﺴﺮ ﺻﻔﺎت‬
. ‫ ﺗﺤﺪث ﻋﻤﻠﯿﺔ اﻟﻜﺴﺐ ﻋﻦ طﺮﯾﻖ إﻟﺘﻘﺎء ﺑﻜﺘﯿﺮﯾﺘﯿﻦ ﻣﻊ ﺑﻌﺾ‬، ‫ﺧﺴﺎرة أو ﻛﺴﺐ اﻟﻨﯿﻮﻛﻠﯿﻮﺗﯿﺪات‬

Determining Relatedness
among Organisms
rRNA sequencing
The most widely used technique for gauging diversity or

relatedness
rRNA can be used not only for taxonomic purposes, but also
in the clinical microbiology laboratory to identify pathogens.
‫ و‬، rRNA or DNA sequencing‫ ﻧﺤﻨﺎ ﺑﻨﻘﺎرن ال‬, Organism‫ ھﻲ أﺣﺴﻦ طﺮﯾﻘﺔ ﻟﺘﺼﻨﯿﻒ ال‬Genetic relatedness‫ال‬
The same species ‫ ھﺬول ﺑﻨﺤﻜﻲ ﻋﻨﮭﻢ‬%77 ‫ ﺑﻨﺸﻮف درﺟﺔ اﻟﺘﺸﺎﺑﮫ و اذا ﻛﺎن ﻓﻲ ﺗﺸﺎﺑﮫ ﺑﺪرﺟﺔ ﺗﻘﺎرب‬Organisms‫ﻟﻨﻘﺎرن ﺑﯿﻦ ال‬

Acellular Microbes
Viruses
isn`t replicating organism ‫سميناها هيك النها‬Acellular
And depend on the host cell for the genetic machinery
 Viruses are extremely small.

Can`t be seen with the light microscope ,with exceptional
cases such as mimiviruses
 They are observed using electron microscopes
 Viruses are not alive

 To replicate, viruses must invade live host cells.
 Viruses infect humans, animals, plants, fungi, protozoa,
algae, and bacterial cells
 Many human diseases are caused by viruses
 Oncogenic viruses or oncoviruses—cause specific types of

cancer, including human cancers such as lymphomas,
carcinomas, and some types of leukemia.
 Viruses consider as nonliving organism

Viruses have five specific properties
 The vast majority of viruses possess either DNA or RNA
 They are unable to replicate (multiply) on their own

‫ عشان تقدر تتضاعف وتتكاثر‬host cell ‫الزم يكونوا داخل ال‬
 They do not divide by binary fission, mitosis, or meiosis.
 They lack the genes and enzymes necessary for energy

production and they depend on the host cell machinery for metabolism
 They depend on the ribosomes, enzymes, and metabolites

(“building blocks”) of the host cell for protein and nucleic
acid production.

Viruses classification
 type of genetic material (either DNA or RNA)‫نادرا ما يحتوي على االثنين سو‬
 shape of the capsid
capsid: ‫المنطقة الخارجية المحيطة بالفيروس والي بختلف شكلها من فيروس الخر‬
 number of capsomeres capsomeres:is the subunit of the capsid
 size of the capsid
 presence or absence of an envelope
 type of host that it infects
 type of disease it produces
 target cell some viruses are specific for certain type of cells and this
depend on the presence of receptors on these cells
 immunologic or antigenic properties. ‫بعضها عنده قدرة على تحفيز الجهاز‬
‫المناعي أكثر أو ردة فعل الجخاز المناعي بتختلف من فيروس الخر‬
‫‪Origin of viruses‬‬
‫‪1-Coevolution theory : the origin of viruses is the same as bacteria and archaea‬‬
‫لكن مع مرور الوقت فقد جزء من ال ‪ genetic material‬وحافظ على الشكل الموجود حاليا‪.‬‬
‫‪2-retrograde theory:‬‬
‫بتحكي هاي النظرية انه كان في ‪ Prokaryote‬وكان عايش داخلها فيروس ومع الوقت هذا الفيروس طلع منها‬
‫خلية‬
‫وطور من نفسه‪.‬‬
‫‪3-escaped gene theory‬‬

‫بتقول انه الفيروس هو جزء من ال ‪ DNA or RNA‬لل ‪ living cells‬لكن هذا ال ‪ DNA or RNA‬خرج عن‬
‫سيطرة الخلية وخرج منها وتحول الى ‪.infectious particle‬‬
Bacteriophages
 The viruses that infect bacteria are known as bacteriophages
 They are obligate intracellular pathogens, in that they must

enter a cell to replicate
Bacteriophages can be classified according to the events that occur inside the bacterial
cell in two ways:
1)cell lysis
distraction of the bacterial cell ‫ وبأدي الى‬virulent bacteriophage ‫وهذا بنسميه‬
2)temperate phage: integration in the chromosome of the bacterial cell
‫بتصير المادة الوراثية تاعت الفيروس جزء من الكروموسوم تاع البكتيريا وهذا بضيف مواصفات جديدة للخلية‬
virulence factors and antimicrobial resistance ‫البكتيرية منها‬

 Bacteriophages can be categorized by the type of nucleic acid
that they possess
 Bacteriophages can be categorized by the events that occur

after invasion of the bacterial cell
 Some are virulent phages, whereas others are temperate

phages

Virulent bacteriophages
 Once it enters a host cell, a virulent bacteriophage always

initiates the lytic cycle, which results in the destruction of the
cell.
 Bacteriophages can only attach to bacteria that possess

surface molecules (receptors) that can be recognized by
molecules on the phage surface.

Steps of lytic cycle
1. Attachment: most bacteriophages are species and stain specific

attachment ‫ما في اي تأثير للفيروس حتى يعمل‬
2. Penetration: The phage injects its DNA into the bacterial cell
3. Biosynthesis: The phage genes are expressed, resulting in the production

(biosynthesis) of viral pieces
4. Assembly: The viral pieces are assembled to produce complete viral

particle (virions). Viral DNA is packaged into capsids
‫ والي بدورها بتبدأ تتكاثر وتزيد عددها‬virions ‫ الي تصنعت بتبلش تتجمع وبتكون‬particles ‫ال‬
5. Release: The host cell bursts open and all of the new virions escape from
the cell . ‫بتسبب انفجار الخلية وخروج الفيروسات‬
Temperate
phages (lysogenic phages)
 Temperate bacteriophages do not immediately initiate the

lytic cycle. Their DNA can remain integrated into the host
cell’s chromosome for generation after generation.
 Bacteriophages are involved in two of the four major ways in

which bacteria acquire new genetic information.
:‫عملية انتقال المادة الوراثية بتصير بأربع وسائل مختلفة هي‬
Transformation, conjugation, lysogenic conversion and transduction
‫ بنستخدم بس طريقتين‬temperate phage ‫في حالة ال‬
 These processes— called lysogenic conversion and

transduction
Animal Viruses
 Viruses that infect humans and animals
 Animal viruses can only attach to and invade cells bearing

appropriate surface receptors.
 Animal viruses escape from their host cells by either lysis of

the cell or budding.
 Viruses that escape by budding become enveloped viruses.

Step Name of Step What Occurs During This Step
1 Attachment (adsorption) The virus attaches to a protein or

polysaccharide molecule (receptor)
on the surface of a host cell
2 Penetration The entire virus enters the host cell, in

some cases because it was
phagocytized by the cell
3 Uncoating The viral nucleic acid escapes from the

capsid
4 Biosynthesis Viral genes are expressed, resulting in

the production of pieces or parts of
viruses (i.e., viral DNA and viral proteins)
5 Assembly The viral pieces or parts are assembled

to create complete virions
6 Release The complete virions escape from the

host cell by lysis or budding
 Inclusion bodies, are often seen in infected cells and are used
as a diagnostic tool to identify certain viral diseases
 Inclusion bodies may be found in the cytoplasm (cytoplasmic

inclusion bodies) or within the nucleus (intranuclear
inclusion bodies), depending on the particular disease.
 In rabies, the cytoplasmic inclusion bodies in nerve cells are

called Negri bodies
‫مرض داء ال َكلَب هو عبارة عن فيروس بضرب الجهاز العصبي ومن وسائل تشخيصه‬
‫ في سايتوبالزم الخاليا العصبية‬electron microscope ‫ عن طريق ال‬Negri bodies ‫رؤية ال‬
Latent Virus Infections
infection ‫الفيروسات ممكن تعمل نوعين من ال‬
1)active infection ‫بتكون األعراض المرضية واضحة وحادة ومستمرة‬
2)latent infection ‫األعراض ما بتكون مستمرة يعني األعراض بتروح وبتيجي‬
‫ويرتبط ظهوره بحالة الجهاز المناعي والحالة النفسية‬
 In Herpes virus infections although the infected person is

always harboring the virus in nerve cells, the cold sores come
and go
 Latent viral infections are usually limited by the defense

systems of the human body
Antiviral Agents
 Chemicals have been developed to interfere with virus-

specific enzymes and virus production by either disrupting
critical phases in viral cycles or inhibiting the synthesis of
viral DNA, RNA, or proteins
‫ يغني ما بصير‬very specific ‫ تعتبر‬chemicals ‫يجب االنتباه الى ان هذه ال‬
‫ مغ‬antibiotics ‫ أو‬bacterial infection ‫ مع شخص عنده‬antiviral ‫استخدم‬
.‫ مثال‬viral infection ‫شخص عنده‬
 Antibiotics are not effective against viral infections.

Oncogenic Viruses
 Viruses that cause cancer are called oncogenic viruses or

oncoviruses
 Viruses were shown to be the cause of various types of

cancers in rodents, frogs, and cats.
 Epstein–Barr virus = nasopharyngeal carcinoma, Burkitt

lymphoma, and B-cell lymphoma
 Human papillomaviruses (HPV) = cancers of the cervix and

other parts of the genital tract.

Human Immunodeficiency Virus
 HIV is an enveloped, single-stranded RNA virus.
 It is a member of a genus of viruses called lentiviruses, in a

family of viruses called Retroviridae (retroviruses)
 AIDS is caused by HIV.

Mimivirus and Megavirus
 An extremely large double-stranded DNA virus can be

observed using a standard compound light microscope called
Mimivirus, was recovered from amebas.
 The virus was given the name Mimivirus because it “mimics”

bacteria. Its very similar to bacteria because it can be seen
with the light microscope
 Mimivirus may be the cause of some cases of human

pneumonia
 Megavirus chilensis, although it is most often referred to
simply as Megavirus.
 Discovered in 2010 off the coast of Chile
 Its genome is larger than that of some bacteria.
 Megavirus was isolated in a French laboratory by co-

cultivation with amebas.
site of isolation
 Its natural host is not known.

Plant Viruses
 More than 1,000 different viruses cause plant diseases
 Plant viruses are usually transmitted via insects mites;

nematodes (round worms); and contaminated tools .
 These diseases result in huge economic losses, estimated to

be billions of dollars per year worldwide
‫ بتسبب أمراض في هذه النباتات وبتعود على‬viruses specific for ‫كل نوع من انواع النباتات الها‬
‫المزارعين واالقتصاد بخسائر كبيرة‬
Viroids and Prions
 Viroids are infectious RNA molecules that cause a variety of

plant diseases.
‫هاي بتأكد على النظرية الي بتقول انه الفيرسات‬
Escape from the nucleic acid or from the genetic material of the host
cell (escaped gene theory)
 Viroids consist of short, naked fragments of single-stranded

RNA (about 300–400 nucleotides)
Viroids infection in plants

Prions infection in animals and human
 Prions are infectious protein molecules that cause a variety of
animal and human diseases.
 Prions are small infectious proteins cause fatal neurological

diseases in animals, such as scrapie in sheep and goats;
bovine spongiform encephalopathy
 In humans, kuru, Creutzfeldt–Jakob (C–J) disease,

Gerstmann–Strussler–Scheinker (GSS) disease, and fatal
familial insomnia.

 Kuru, C–J, and GSS diseases involve loss of coordination
and dementia.
 Dementia, a general mental deterioration, is characterized by

disorientation and impaired memory, judgment, and intellect.
Alzheimer and Parkinson diseases ‫ بال‬prions ‫كثير من العلماء بربطوا ال‬

 The 1997 Nobel Prize for Physiology or Medicine was
awarded to Stanley B. Prusiner, the scientist who coined the
term prion and studied the role of these proteinaceous
infectious particles in disease
 Possible relationships between prions and Alzheimer disease,

Parkinson disease, Huntington disease, amyotrophic lateral
sclerosis (ALS), some types of cancer, and type II diabetes

Bacteria
‫الميكروب الرئيسي الي بسبب أمراض باألنسان‬
 Bacteria are divided into three phenotypic categories (i.e.,

categories based on their physical characteristics):
cell wall ‫تصنيف البكتيريا بعتمد على ال‬
(a)Gram-negative
Thin cell wall
(b)Gram-positive
Thick cell wall
(c) Cell walless or cell wall deficient bacteria

Cell Morphology
 The size, shape, and morphologic arrangement of various
bacteria are easily observed using compound light
microscope. ‫بتساعدنا بعملية تشخيص البكتيريا‬
 Bacteria vary in size from 0.1 μm in diameter to 10.0-μm-long

spiral-shaped bacteria, to even longer filamentous bacteria.
 A bacterium’s Gram reaction (Gram positive or Gram

negative) or the staining property
‫ كثير مهم بعملية التشخيص‬tetrads octads in pair
 Basic cell shape, and morphological arrangement of the cells

are very important clues to the organism’s identification.
 The three general shapes of bacteria are round (cocci), rod-
shaped (bacilli), and spiral-shaped
 
‫هاي هي األشكال الرئيسية للبكتيريا بس‬

‫في أشكال ثانوية مثل‬
1)Cup-shaped
2)filamentous
 Bacteria reproduce by binary fission.
 Generation time= The time it takes for one bacterial cell to

split into two
Slow grower and ‫ بختلف من بكتيريا الخرى وهو المسؤول عن ظهور ال‬Generation time ‫ال‬
fast grower bacteria
 Cocci may be seen singly or in pairs (diplococci), chains
(streptococci), clusters (staphylococci), packets of four
(tetrads), or packets of eight (octads),
 Cell wall–deficient (CWD) bacteria or L-forms.
 Some CWD bacteria revert to their original shape
 Pleomorphic.



‫مالحظات على الساليد السابق‬
‫• الخلية البكتيرية الي بكون غياب ال ‪ cell wall‬فيها هو ‪ genetically determined‬ما بتقدر‬
‫تصنّع أو تسترج ال ‪.cell wall‬‬
‫• أما الخلية البكتيرية الي غياب ال ‪ cell wall‬فيها هو بسبب خارجي ‪ ( experimentally‬يعني‬
‫احنا أثرنا على الخلية البكتيرية وانتزعنا منها ال ‪ ) cell wall‬بتقدر تسترجع ال ‪ cell wall‬وتعيد‬
‫تصنيعه النها بتحتوي على الجين المسؤول عن تصنيعه‪.‬‬
‫‪• Pleomorphic‬‬
‫يعني البكتيريا بتقدر تظهر بأكثر من شكل والعامل الي بساعدها هو غياب ال ‪ rigidity of the cell wall‬أو‬
‫غياب ال ‪ cell wall‬بشكل كامل‪.‬‬
‫يعني اذا كان ال ‪ cell wall‬مش موجود أو انه هش بتكون الخلية ‪ elastic‬أي عندها مرونة انها تظهر بأكثر من‬
‫شكل‪.‬‬

Staining Procedures
Most bacteria are colorless, transparent, and difficult to see
staining ‫ما بتقدر تشوفها بشكل واضح اال اذا عملتلها‬
Simple stain helps us to see the shape and the arrangement of the bacteria
 Fixation serves three purposes:
1. It kills the organisms.

2. It preserves their morphology.
3. It anchors the smear to the slide.
‫بضمن انه انا بتعامل مع خلية بكتيرية ميتة وبنفس الوقت بحافظ على شكلها وبعمل على تثبيت العينة‬
‫(الخليةالبكتيرية) على الساليد‬
 A simple stain is sufficient to determine bacterial shape and
morphologic arrangement
 The procedures used to observe bacterial capsules, spores,

and flagella are collectively referred to as structural staining
procedures.

 The Gram and acid-fast staining procedures are referred to
as differential staining procedures
primary stain ‫ االول بنسميه‬...stain ‫ بنستخدم فيه نوعين من من ال‬differential staining ‫ال‬
Secondary stain or counter stain ‫والثاني‬
 The Gram stain differentiates between “Gram positive” and
“Gram-negative” bacteria
 Gram-positive
Blue to purple ‫لونها بعد الصبغة بظهر‬
 Gram-negative
pink to red‫لونها بعد الصبغة بظهر‬
 Gram-variable bacteria = M. tuberculosis and M. leprae

‫لونها ما بكون ثابتة يعني مرة بتظهر بلون أحمر ومرة بلون أزرق‬
 The acid-fast stain is of value in the diagnosis of tuberculosis.
 Acid-fast bacteria are red at the end of the acid-fast staining procedure.

Motility
 Motile bacteria = Swim
 Bacterial motility = flagella or axial filaments

‫ وعددها‬flagella ‫سرعة الخلية البكتيرية بتعتمد على قوة ال‬
 Gliding motility = No flagella
 A flagella stain = demonstrate the presence, number, and

location of flagella on bacterial cells.
 Motility = stabbing the bacteria into a tube of semisolid agar

or by using the hanging drop technique
‫في طريقتين انه افحص اذا الخلية البكتيرية قادرة على الحركة وال ال‪:‬‬
‫‪ : hanging drop )1‬بنضع ‪ drop if broth or water‬على ‪ cover slide‬وبنرفع‬
‫الزوايا االربعة للساليد بحيث تكون نقطة الماء أو ال ‪ broth‬معلقة ومن ثم نقوم بفحصها‬
‫من خالل ال‪ microscope‬ورح نشوف اذا البكتيريا رح تتحرك داخل ال ‪.broth‬‬
‫‪ : Semisolid Ager(2‬بنطعن ال ‪ semisolid media‬ببكتيريا عن طريق حقنة وبننتظر ‪ 24‬ساعة‬

‫ورح نحصل على واحد من الشكلين ‪ C‬أو ‪D‬‬
‫• الحظ على األنبوب ‪ C‬حدث نمو بكتيري لكن على طول منطقة الحقن‪...‬يعني ما في حركة‬
‫• أما األنبوب ‪ D‬صار في انتشار للبكتيريا‪...‬يعني البكتيريا قادرة عللى الحركة‬
Colony Morphology
 Bacterial colony.
 Colony morphology includes the size, color, overall shape,

elevation, and the appearance of the edge or margin of the
colony.
 Colony features serve as important “clues” in the

identification of bacteria
Atmospheric Requirements
 Obligate aerobes and microaerophiles require oxygen.
 Obligate aerobes require an atmosphere containing about

20% to 21% oxygen
 Microaerophiles require reduced oxygen concentrations

(usually around 5% oxygen).
anaerobes ‫وفي خاليا بكتيرية ما بتحتاج األكسجين وبنسميهم‬

Relationship to
Oxygen
Obligate Obligate
Anaerobes Aerobes
Microaerophiles
Aerotolerant Faculative
Anaerobes Anaerobes
decrease increase
Percent Oxygen (O2)
 Obligate anaerobes, aerotolerant anaerobes, and facultative
anaerobes can thrive in an atmosphere devoid of oxygen.
 Capnophiles require an atmosphere containing 5% to 10%

carbon dioxide.

Dr. Waleed
‫‪Thioglycolate broth‬‬
‫بنستخدمها ألنها بتوفر كل ال‪atmospheric conditions‬‬
‫الحظ األنبوب ‪ a‬كل الخاليا متجمعة على السطح (يعني كلها بتبحث عن األكسجين)‬ ‫•‬
‫أما األنبوب ‪ b‬كل الخاليا متجمعة في األسفل (بعيدا عن األكسجين)‬ ‫•‬
‫األنبوب ‪ c‬الخاليا منتشرة على كامل األنبوب (يعني بقدروا يعيشوا مع وجود األكسجين ومع غيابه)‬ ‫•‬
‫األنبوب ‪ d‬بختلف عن ‪ a‬بأنه الخاليا بتكون منخفضة شوي عن السطح (يعني بتبحث عن كمية قليلة من‬ ‫•‬
‫األكسجين)‬
‫األنبوب ‪ e‬شبيه باألنبوب ‪ c‬وبتقدر تعيش مع وجود األكسجين أوعدمه‬ ‫•‬

‫‪The end‬‬ ‫☺‬
Microbial diversity
TASNEEM M DARAWSHEH
&
AISHA OUDAT
Nutritional Requirements
⚫ All bacteria need some form of the elements carbon, hydrogen, oxygen,
sulfur, phosphorus, and nitrogen for growth.
all micro organisms need these elements
⚫ Special elements, such as potassium, calcium, iron, manganese,
magnesium, cobalt, copper, zinc, and uranium, are required by some
bacteria. Some microorganisms need these special elements
⚫ Certain microbes have specific vitamin requirements, and some need

organic substances secreted by other living microorganisms during their
The special thing in microorganisms is that some need organic
growth. compounds such as lipid , ex : mycoplasma need cholesterol
also , clostridium difficil bacteria that live in
⚫ Fastidious organisms = especially demanding nutritional requirements

‫بشكل عام تقسم البكتيريا الى نوعني‬
1 ) fastidious, that is called also needle bacteria
‫ يعني متطلباتها الغذائية كثيرة وغالبا بنخليها بوسط خاص فيها بنسميه‬complex medium
‫فبيكون متوفر فيه كل حاجاتها الغذائية‬
2) bacteria that live in Basal medium
‫يعني بتعيش بوسط يعني فقط على العناصر الضرورية لبقائها‬

Biochemical and Metabolic Activities
‫ رح اوضحلكم الي عارفيته‬، ‫الدكتور ترك هاد الساليد‬
⚫ Bacteria can produce many waste products and secretions enable them to
invade their host and cause disease. infection in host cell ‫بيحكيلك انه كيف البكتيريا سببتلي‬
‫ وتبلش شغلها‬host ‫عن طريق افرازاتها قدرت انها تفوت على ال‬
⚫ The pathogenic strains like staphylococci and streptococci, can be

tentatively identified by the enzymes they secrete.
‫ هو انه انا‬infection ‫من الطرق الي انا بستخدمها لحتى اعرف شو نوع البكتيريا الي سببتلي‬
Te
Text ‫اشوف شو االنزيمات الي افرزتها بخاليا املريض وعن طريق نوع االنزيمات اعرف نوع البكتيري‬
Text ‫ا‬
xt host cell ‫ بال‬infections ‫النه كل بكتيريا بتفرز انواع معينه من االنزيمات ملا تيجي تعمل‬
⚫ Some bacteria are characterized by the production of certain gases, such

as carbon dioxide, hydrogen sulfide, oxygen, or methane

‫‪Pathogenicity‬‬
‫‪⚫ Pathogens = capsules, pili, or endotoxins, exotoxins and exoenzymes‬‬
‫تـقسم الـخاليـا الـبكتيريـة الـى قـسمني ‪ pathogens and non pathogens ،‬هـيك بـشكل عـام لـكن‬
‫بالنظر للتفاصيل في برضو‬
‫شي اسمه ‪ opportunistic bacteria‬الي هي الكائنات االنتهازية‬
‫مواصفات ومعايير لتحديد ال ‪: pathogenicity for bacteria‬‬

‫‪1) capsule : capsulated bacteria is pathogen and non capsulated bacteria is‬‬
‫‪non pathogen‬‬
‫طـيب لـيش! ألنـه هـاي ال ‪ capsule‬بـتتميز بـال ‪ antiphagcyticity‬يـعني قـدرة الـبكتيريـا عـلى الهـرب‬
‫من الجهاز املناعي‬
‫‪2) pilli :‬‬
‫من اهم مواصفات ال الباثوجني النها بتعمل‬
‫‪attachment on the host cell‬‬
‫وبال هاي الخطوة البكتيريا ما بقدر اعمل‬
‫‪infection‬‬
‫)‪3) secretion of toxins ( endotoxins and exotoxins‬‬
‫جـ ـزء مـ ـن تـ ـركـ ـيب الـ ـبكتيريـ ـا بـ ـبلش شـ ـغله وبـ ـيصير نشـ ـط بـ ـعد مـ ـوت وتحـ ـلل الخـ ـلية لـ ـتبدأ ‪Endotoxins‬‬
‫تأثيرها الفيزيائي‬
‫‪ ،‬يتم افرازه من البكتيريا ليؤثر على الخلية بطرق مختلفة سندرسها الحَقا ‪Exotoxins‬‬
‫‪ exoenzymes‬طبَعا هو مشابه جَدا لل‬

Genetic Composition
⚫ Molecular diagnostic procedures = Identification = analyzes the
organism’s DNA or RNA
⚫ The composition of the genetic material (DNA) of an organism is unique

to each species.
⚫ 16S rRNA sequencing can determine the degree of relatedness between

two different bacteria.
Molecular diagnostic procedures :

‫ حـيث انـه لـكل‬DNA sequence ‫تـقنية تسـتخدم لـلتمييز بـني انـواع الـكائـنات الـبكتيريـة حسـب ال‬
‫ فتتم املقارنة بني انواعهم جينيا َا باستخدام هذه التقنية‬DNA ‫نوع بكتيري سلسله معية من ال‬

Unique Bacteria Unusual
⚫ Rickettsias, chlamydias, and mycoplasmas are bacteria, but they do not

possess all the attributes of typical bacterial cells.
⚫ Rickettsias and chlamydias are bacteria with a Gram-negative– type cell

wall.
⚫ They are obligate intracellular pathogens that cause diseases in humans

and other animals host cell ‫مثل الفيروس ما بتعيش اال جوا ال‬

‫‪Mycoplasmas‬‬
‫‪⚫ Mycoplasmas are the smallest of the cellular microbes.‬‬
‫كانوا يصنفوها على انها فيروس عل‬
‫كانوا يصنفوها مع الفيروسات على قد ما هي صغيرة فلما‬
‫قد ما هي صغيرة لكن ملا شافوا انها‬
‫شافو انها ‪ self replicate‬صنفوها ع انها بكتيريا‬
‫‪ self replicate‬عرفوا انها بكتيريا‬
‫‪⚫ Because Mycoplasma spp. do not possess cell walls, they are‬‬
‫‪pleomorphic.‬‬
‫اهم معايير تصنيف البكتيريا هو حجمها‬

‫املايكوبالزما جدا صغيرة ولسا في اصغر الي‬
‫همه ‪nano bacteria‬‬

Especially Large and Especially Small
Bacteria
⚫ Most bacteria are microscopic, requiring the use of a microscope to be
seen
⚫ Coccus (e.g., a Staphylococcus aureus cell) is 1 μm in diameter.
⚫ A typical bacillus (e.g., an E. coli cell) is about 1.0 μm wide × 3.0 μm long
very large ‫في خاليا حجمها بتجاوز هاد الرينج وهي‬
⚫ Some bacilli are long thin filaments—up to about 12 μm in length or even

longer—but still only about 1 μm wide

⚫ The largest of all — Thiomargarita namibiensis, a colorless, marine,
sulfide-oxidizing bacterium.
‫ للسلفر‬oxidation ‫تعيش في البحار وبتعمل‬
⚫ Single spherical cells of T. namibiensis are 100 to 300 μm, but may be as
large as 750 μm (0.75 mm) ‫اضعاف حجم البكتيريا العادية‬
⚫ Epulopiscium fishelsonii, has been isolated from the intestines of the reef
surgeonfish; this bacillus is about 80 μm wide x 600 μm (0.6 mm) long
‫ممكن اشوفهم بالعني املجردة النه حجمهم كبيرا جدا‬

⚫ Nanobacteria. Their sizes are expressed in nanometers because these
bacteria are less than 1 μm in diameter; hence the name, nanobacteria
‫اصغر من املايكوبالزما‬
⚫ Nanobacteria have been found in soil, minerals, ocean water, human and
animal blood, human dental calculus (plaque), arterial plaque, and even
rocks (meteorites) of extraterrestrial origin.
‫بتعيش على االسنان فبتعمل تسوس‬
atherosclerosis ‫وبرضو بتسبب مرض‬
‫ النها‬medical microbiology ‫ما بتشارك كثير بال‬

human diseases ‫مش كثير معروفة ب احداث ال‬

Photosynthetic Bacteria
: ‫تصنف البكتيريا حسب قدرتها على تحويل الطاقة كالتالي‬
⚫ Photosynthetic bacteria include purple bacteria, green bacteria, and

cyanobacteria (blue-green algae)
⚫ Photosynthetic bacteria are bacteria capable of converting light energy

into chemical energy.
⚫ Cyanobacteria are examples of photosynthetic bacteria.
⚫ Cyanobacteria were the first organisms capable of carrying out oxygenic

photosynthesis and, thus, played a major part in the oxygenation of the
atmosphere

⚫ Cyanobacteria in pond or lake water can overgrow, creating a water
bloom—a “pond scum” that resembles a thick layer of bluish green
(turquoise) oil paint. ‫ على‬Cyanobacteria ‫هاي طبقة المعة بتعملها البكتيريا‬
‫سطح البحيرات وبختلف اللون حسب نوع البكتيريا‬
⚫ Convert nitrogen gas (N2) from the air into ammonium ions (NH4) in the
soil or water; this process is known as nitrogen fixation
⚫ Some cyanobacteria produce toxins (called cyanotoxins)= neurotoxin and

hepatotoxin feralization of soil ‫مهمة لل‬
⚫ Global warming will lead to increases in cyanobacterial populations and

concurrent increases in cyanotoxins.

Archaea
⚫ Archae means “ancient,”
⚫ Archaea vary widely in shape = cocci, bacilli, and long filaments
⚫ All archaea possess cell walls, their cell walls contain no peptidoglycan.

⚫ Some live at the bottom of the ocean in and near thermal vents, where, in
addition to heat and salinity, there is extreme pressure.
⚫ Other archaea, called methanogens, produce methane
⚫ Many archaea are extremophiles = live in extreme environments
e.g., environments that are extremely hot, dry, or salty.

Microbial Diversity
Eukaryotic Microbes
Dr. Waleed Al Momani, MLT, PhD

Introduction
 Eukaryotic microbes include some species of algae and fungi,

and all protozoa, lichens, and slime moulds.

Algae
Characteristics and Classification
 Algae are photosynthetic, eukaryotic organisms

Photosynthetic: convert light energy to chemical energy
 Algae and protozoa are referred to as protists because they

are in the kingdom Protista. So they are similar
 Although they are not plants, algae are more plantlike than
protozoa
Algae produce biodiesel ‫فبيستخدموها بالالبات النتاج ما يسمى بالطاقة الخضراء‬

 A few species use organic nutrients, and others survive with
very little sunlight.
 Most algal cell walls contain cellulose
 Depending on pigments they possess algae are classified as

green, golden (or golden brown), brown, or red.
Algae is like plants in its cell wall ,

because its cell wall contain cellulose
Cellulose : protein fiber
‫ يعتمد على الوان الصبغات الي بتفرزها‬algae ‫تصنيف ال‬

Diatoms : ‫لها عندها القدرة على العيش بشكلني‬
 Diatoms algae live in both freshwater and seawater
 Photosynthetic protists = algae
 Nonphotosynthetic protists = protozoa.

Medical Significance
 One genus of algae (Prototheca) is a very rare cause of

human infections (causing a disease known as
protothecosis).
 Prototheca lives in soil and can enter wounds, especially

those located on the feet
surface of water ‫برضو ممكن تعيش على‬
 It produces a small subcutaneous lesion that can progress to
a crusty, warty-looking lesion.
lesion on skin ‫بتدخل على داخل جسم االنسان عن طريق‬

Prototheca cells in several stages of development

‫ لكن اذا‬non pathogen ‫ غير ضارة‬algae ‫هي غالبا ال‬
‫دخلت عن طريق منطقة مفتوحة في جسم االنسان ممكن تكمل‬
infection ‫عالجهاز الليمفاوي وتعمللي‬
 If the organism enters the lymphatic system, it may cause a

debilitating, sometimes fatal infection, especially in
immunosuppressed individuals.
 Algae in several other genera secrete substances

(phycotoxins) that are poisonous to humans, fish, and other
 animals

Protozoa
 Most protozoa are single-celled free-living microorganisms

found in soil and water
 Protozoal cells are more animal-like than plantlike

structure ‫من ناحية ال‬
 All protozoal = eukaryotic
 Structures and organelles = cell membranes, nuclei,

endoplasmic reticulum, mitochondria, Golgi bodies,
lysosomes, centrioles, and food vacuoles
‫ برضو‬Protozoa ‫معظم العضيات الي موجودة بالخلية الحيوانية موجودة بال‬

 Protozoa do not have cell walls, but some, including some
flagellates and some ciliates, possess a pellicle, which serves
the same purpose as a cell wall—protection.
 Some flagellates and some ciliates ingest food through a

primitive mouth or opening, called a cytostome.

 A typical protozoan life cycle consists of two stages:
1. motile trophozoite stage

2. nonmotile cyst stage.
 Many parasitic protozoa are pathogens, causing malaria,

giardiasis, African sleeping sickness, and amebic dysentery
Protozoa can cause parasitic infection ‫وفي بعضها‬
‫طبعا خطير جدا زي املكتوبني‬
Liver ‫ االعراض األولية بسيطة‬amebic dysentery ‫بالنسبة لل‬

abscess liver arches ‫لكن ممكن يصير في مضاعفات وتعمل‬

‫‪Classification and Medical Significance‬‬
‫‪Protozoa are sometimes classified taxonomically by their‬‬

‫‪mode of locomotion.‬‬
‫‪Some move by pseudopodia, others by flagella, others by‬‬

‫‪cilia, and some are nonmotile.‬‬
‫كيييف بنصنف ال ‪ protozoa‬وذلك عن طريق الوسيله اللي بتستخدمها الخليه بالحركه‬

‫‪.....‬االشي المعروف سابقا انه خلية ال‪ protozoa‬بتتحرك عن طريق االقدام الكاذبه‪.....‬‬
‫ولكن هنااااك بعض الخالياااا بعضها بتحرك بال ‪ flagella‬او ‪ cilia‬وبعضهم ما بيتحركواااا‬
‫‪.‬‬ ‫اصال‬
‫مالاحظه صغيره‪:‬هدووول نفس الساليداات اللي بشرح عنهم الدكتور بس انا حذفت االطاار‬
‫االزرق وبس هيك بدي احكي‪ ...........‬كملوااا دراسه‪>>.....‬‬
‫‪Dr. Waleed AlMomani‬‬
Amebae (amebas), such as Acanthamoeba, Entamoeba, and Naegleria spp.
move by means of cytoplasmic extensions called pseudopodia (false feet).
‫اهم االمراض اللي‬ ..‫االميبا زي ما حكينا بتتحرك باالقدام الكاذبه وهااي فيه اصناف منهااا‬
‫بتسببهااا االمبيااااا‬
Medically important ameba =Entamoeba histolytica, amebic dysentery
(amebiasis)
extraintestinal (meaning away from the intestine) amebic abscesses.

‫ لل‬infection ‫اذااا عملت‬
liver
Naegleria fowleri primary amebic meningoencephalitis)
Acanthamoeba spp eye infections).

algae ‫ بتشارك بشكل فعالل باالمراض باالنسااان مش زي ال‬protozoa ‫يعني ال‬
‫ وهااي‬cilia ‫النوع الثاني للي بتتحرك ببعض المركباات اللي بنسميها ال‬
‫وهااي اكثر اشي بتسبب‬....... ‫ زي االمثله تحت‬ciliates protozoa ‫بنسميهااا‬
‫ وخاصه بدول العالم الثالث‬dysentery ‫امراض بالجهاز الهضمي و بتعمل‬
Ciliates, such as Balantidium, Paramecium, Stentor, and

Vorticella spp., move about by means of large numbers of
hairlike cilia on their surfaces
Balantidium coli dysentery in underdeveloped countries

flagellated protozoa ‫ و هاي بنسميهااا‬flagella ‫النوع الثالث اللي بيتحرك عن طريق ال‬
disease ‫ بتساعدهاا انها تعمل‬flagella ‫و حركة ال‬
Flagellated protozoa (flagellates), such as Trypanosoma, Trichomonas,and

Giardia spp., move by means of whiplike flagella.
‫مرض النوم المعروف بافريقياا‬

Trypanosoma brucei subspecies gambiense African sleeping sickness
Trypanosoma cruzi (Chagas disease); ‫هااد موجود بامريكيا الجنوبيه‬
Trichomonas vaginalis (trichomoniasis) genital tract ‫هو عباره عن‬

female ‫ وخاصة بال‬infections
Giardia lamblia giardiasis ‫المريض المصاب بهاد‬

‫المرض بصير عنده‬
.....severe diarrhea
‫ و هدول بالغالب‬nonmotile protozoa ‫النوع االخيررر هو الغير متحرك يعني‬
. sporozoan protozoa ‫بنسميهم‬
Babesia, Cryptosporidium, Cyclospora, Plasmodium, and Toxoplasma spp.

are examples of sporozoan protozoa that cause human infections.
Sporozoan protozoa are nonmotile.
‫ و كلهم‬plasmodium‫طبعا فيه عنا خمس انواع من ال‬

Plasmodium spp. Malaria ‫بسببوا نفس المرض (المالرياا) لكنه بيختلف االعراض‬
different spices ‫المرضيه بين‬
Cryptosporidium parvum cryptosporidiosis
‫يعني امراض او‬.... amebic dysentery ‫ و ال‬giardiasis‫ زيهاا زي ال‬sever diarrhea ‫بتعمل‬
‫ بتنتقل مثال عن طريق مياه الشرب و بتعمل مشااكل بالجهاز‬parasite ‫اعراض مرضيه سببها هاي ال‬
severe diarrhea ‫الهضمي ومنها بتادي زي ما حكيناا الى‬
Toxoplasma gondii toxoplasmosis

‫ وهااي‬toxoplasmosis ‫ اللي بتعيش بالقطط و بتسبب مرض خطير اللي بنسميه‬parasite ‫هاي ال‬
‫ وغيرها من االعضاء االخرى و تسبب امراض‬genital tract ‫ او ال‬brine ‫ممكن توصل لل‬
.abortion ‫خطيره بعضهااا بتادي الى ال‬
‫ اللي هو الفطرياات‬fungi ‫اخر مايكروب بالشله الكريمه هو ال‬
The study of fungi is called mycology.
Fungi are a diverse group of eukaryotic organisms that

include yeasts, moulds, and mushrooms.
‫ يعني فطرياات صالحه‬edible ‫ هو عباره عن‬mushrooms‫ال‬
‫اللي هوو الفطر اللي بيطلع بس تشتي الدنياا‬..‫لالكل‬
algae ‫ و ال‬plant cell‫ وهي بتختلف شويتين عن ال‬fungi ‫ايش هي مواصفاات ال‬
Fungi differ from plants and algae = not photosynthetic
no chlorophyll or other photosynthetic

pigments.
no cellulose (a polysaccharide) in
fungal cell wall
Fungal cell walls do contain a

polysaccharide called chitin
‫ وال سيليلوز ولكننن فيهااا مركب بتكون من ال‬pigment ‫ماا فيها اي‬
‫وهاد المركب مهم جدا واله استخدااماات مهمه‬chitin ‫ اسمه‬polysaccharide
.very strong fibers‫النه بنستخدمه كخيووط جراحيه النه‬
‫‪Yeasts are unicellular, whereas moulds are multicellular.‬‬
‫ال ‪ yeast‬شبيه جدا بالبكتيرياا وهي وحيدة الخليه بينمااا ال‬
‫‪ moulds‬هي متعدده الخاليااااا‬
‫‪Filaments fungi called hyphae which intertwine to form a‬‬

‫‪mass called a mycelium‬‬
‫ال ‪ yeast‬هي الخليه اللي بتعيش على ‪ room temperature‬وممكن تتقاطع‬

‫مع البكتيريا بانهااا بتنمو على بعض انواع ال ‪ media‬اللي بنستحدمهااا‬
‫للبكتيرياا‪.....‬‬
‫بينما ال ‪ moulds‬هي عباره عن ال ‪ fungus‬اللي بتكون ‪ hyphae‬على سطح‬
‫الخبز مثالاا هاي ممكن يكون فيها ‪ spores‬وهاي السبب الرئيسي من اسبااب‬
‫االمراض لالنسان و خاصه امراض الحساسيه و بعضها ممكن يكون اله تأثير‬
‫سميييي‬
aseptate hyphae=Septate hyphae
Septate or aseptate hyphae is an important “clue” when attempting to

identify a fungus that has been isolated from a clinical specimen
‫ اللي بشكلوا بالنهايه‬hyphae ‫فيه عناااا نوعين من ال‬

‫ نوعععع‬mycelium ‫المكون اللي نسميه‬
walls ‫ فيهاا‬tube ‫ يعني ال‬septate
‫ ما فيه‬aseptate ‫بينمااا ال‬........ ‫مقطعع‬
.‫ لهاد النوووع‬tube ‫فواصل بال‬
Reproduction
Fungi reproduce by spore production.
Sexual and asexual spores.
Sexual spores are produced by the fusion of two gametes

(thus, by the fusion of two nuclei).
Fungi are classified by the sexual spore that they produce or

the type of structure on which the spores are produced
Asexual spores = fusion of gametes
‫ اللي شفنااهم فيهم صفه مشتركه واللي هييي بماانعوا كل اشي‬spores ‫كل انواع ال‬
‫سوااء حموضه وال درجة حراره عاليه و غيره‬
Asexual fungal spores are known as conidia.
Fungal spores are very resistant to heat, cold, acids, bases,

and other chemicals.
Many people are allergic to fungal spores
‫ من اهم االعراض المرضيه اللي بتسببهم هي الحساسيه‬spores ‫قلنا انه ال‬

Yeasts
Yeasts are microscopic, single-celled organisms that usually

reproduce by budding.
‫ يعني بمعنى انه جزء من الخليه بصيرله انغمااد و بنفصل عن الخليه‬budding ‫ عن طريق ال‬production‫يعني عملية ال‬
‫ و بتشوف‬budding ‫وهاااي بنقدرر نشوفهاا تحت الميكرسكوب لماا تعمل‬... ‫ جديده‬yeast ‫االم و الجزء المنفصل بصير خلية‬
.yeast‫ هو ميزه من ميزات ال‬germ tube ‫اشي اسمه‬
Yeasts are found in soil and water and on the skins of many
fruits and vegetables.
Pasteur discovered that naturally occurring yeasts on the

skin of grapes and other fruits and grains were responsible
for these fermentation processes.
fungus ‫ اللي هو المنتج الطبيعي اللي بتنتجه ال‬yeast ‫بنستخدم فيها ال‬.. ‫معظم وساائل التخمير الخبز و الكيك وما الى ذلك كلهااا‬
Saccharomyces cerevisiae (“baker’s yeast”) ferments sugar to
alcohol under anaerobic conditions.
‫ النتاج الخبز همه الفراعنه المصريين‬yeast ‫اول ناس استخدموا ال‬
Yeast breaks down simple sugars to carbon dioxide and water
aerobically, it has long been used as a leavening agent in
bread production
Yeasts are also a good source of nutrients for humans because

they produce many vitamins and proteins
‫عموماااا انجوي وانتوا بتدرسوا‬.........‫ مش تفريغغ‬yeast‫حااسهاا دعايه لل‬

Medically important Yeast
‫ بشكل عام انها مرتبطه‬medical important yeast ‫اهم اشي بال‬.......‫ اللي بتعمل امراض باالنساان‬yeast ‫اهم انواع ال‬
‫لمااا‬...... ‫ مااا بتقدر تسبب مرض‬fungus ‫ او ال‬yeast ‫ ف مدام الجهاز المناعي قوب ال‬....‫بشكل رئيسي بالجهااز المناعي‬
..fungal infection ‫ وقتهاا بصير‬the fungi over come the immune system of the host body
C. albicans and C. neoformans are examples of yeasts that

cause human infections.
‫وخاصه عند االطفال اللي بضل‬mouth thrush ‫ و ال‬vaginitis ‫مثل ال‬
‫الحليب بثمه بعد الرضاعه بالتالي بأدي الى تكوين بيئه مناسبه لنمو‬
. c.albicans ‫ال‬
C. Albicans is the yeast most frequently isolated from human
clinical specimens
In the laboratory, yeasts colonies = quite similar in
appearance to bacterial colonies.
germ tube ‫ وال‬budding ‫لكن لماا نشوفها تحت الميكروسكوب رح نشوف ال‬
A wet mount can distinguish between a yeast colony and a

bacterial colony
Yeasts are usually larger than bacteria, usually oval shaped;

may be observed in the process of budding
Moulds
Moulds are the fungi often seen in water and soil and on food
moulds ‫ زي ما حكينا هي بتعيش على سطح المااء و الزيت وهاد ال‬moulds‫ال‬

‫المهم‬....‫ او ال‬Septate ‫ اللهاا بيختلف انه‬hyphae ‫ و ال‬filaments ‫بالغالب بتكون‬
‫ او ال‬mycelium ‫انه نقدر نميز بينهم تحت الميكرسكوب حتى نقدر نحدد النوع ال‬
.moulds
They grow in the form of cytoplasmic

filaments or hyphae that make up the
mycelium of the mould
‫‪Aerial hyphae = extend above the surface‬‬
‫‪Vegetative hyphae = beneath the surface‬‬
‫هاي انواع ال ‪ hyphae‬اله نوعين‬

‫االول بنسميه ال ‪ aerial‬او برسيل بمزح‪ ....‬زيي مهوو موضح بالصورة‬
‫بكون موجود على سطح ال ‪ media‬والنه ع السطح معناته بكوننن هواائي‬
‫النوع الثاني اسمه ال ‪ vegetative‬اللي بكون تحت سطح ال ‪media‬‬

Many antibiotics are produced by moulds. = Penicillium and
Acremonium
fungus ‫ من المضادات الحيويه المعروفه هي بتم انتاجها من ميكروبات موجوده بالتربه و ال‬60% ‫اذا بتتذكروا حكينا انه‬
‫ بتلعب دور كبير بهالمجااال‬moulds ‫وخاصه ال‬
Some moulds produce = large quantities of enzymes (such as
amylase, which converts starch to glucose), citric acid, and
other organic acids that are used commercially.
‫ يمكن استثماارهم من ناحية تجااريه‬moulds ‫وهدول االنزيمات المنتجه من قبل ال‬
‫النتااج كميات كبيره و اسوقهاا‬
The flavor of cheeses such as bleu cheese and limburger is the
result of moulds that grow in them.
‫ النتج نوع من الجبنه وهي تعتبر من اغلى انواع الجبن بالعالم زي‬moulds ‫بعض المنتجات الغذائيه بستخدمواا فيها ال‬
.limburger ‫ و ال‬bleu cheese ‫ال‬
Fleshy Fungi
Mushrooms, toadstools, puffballs, and bracket fungi

(collectively referred to as fleshy fungi) are examples of fungi
that are not microorganisms.
‫لكن فيه عنا انواع منه بتكووون كثير‬... ‫ حكينا بيعتبر ماده غذائيه‬mushrooms‫ال‬
‫ساااامه‬
Many mushrooms are delicious to eat, but others are
extremely toxic and may cause permanent liver and brain
damage or death
A variety of yeasts and moulds cause human infections
(known as mycoses).
‫ وطبعااا هناك تصنيف‬mycosis ‫االمراض اللي بتسببها الفطريات بنسميهم‬
‫ اذا بالجلد بتعمل‬infection ‫لهاي االمراض حسب المكان اللي بتعمل فيه‬
‫ اللي بتنتشر من‬systemic mycosis ‫ و فيه‬mycoses ‫امراض بنسميهااا‬
.different organs in the human body ‫خالل الجلد وتوصل الى‬
Some moulds and fleshy fungi produce mycotoxins, which

can cause human diseases called microbial intoxications.
Many diseases of crop plants, grains, corn, and potatoes are

caused by moulds.
Fungal Infections of Humans
Fungal infections are known as mycoses
Superficial, cutaneous, subcutaneous, or systemic mycoses.
Superficial mycoses = hair, fingernails, toenails, and the

dead, outermost layers of the skin (the epidermis).
‫كثير من الناس بصير عندهم التهابات فطريه موجوده بفروة الرأس او تحت االظاافر هدول بنعتبرهممم‬
superficial
Cutaneous mycoses = fungal infections of the living layers of

skin (the dermis)
‫ممكن يعيش بالطبقاات الحيه من الجلد‬
Dermatophytes cause = tinea infections, which are often
referred to as “ringworm” infections
‫االمرض الفطريه اللي بتصير بالجلد‬
C. albicans lives harmlessly on the skin and mucous

membranes of the mouth, gastrointestinal tract, and
genitourinary tract.
‫ حتى باالمراض‬...‫ وهاي قلنا انها قريبه من البكتيريا‬.... ‫حكينا عنهااا هااي‬
.fungus ‫اللي بتسببهااا بتكون اقرب للبكتيريا من ال‬
Reduction in the number of indigenous bacteria at these
anatomic locations, C. albicans flourishes, leading to yeast
infections of the mouth (thrush), skin, and vagina (yeast
vaginitis).
This type of local infection may invade the bloodstream to
become a generalized or systemic infection in many internal
areas of the body.
Subcutaneous mycoses are fungal infections of the dermis and
underlying tissues
Madura foot (a type of eukaryotic mycetoma), in which the
patient’s foot becomes covered with large, unsightly, fungus-
containing bumps
‫وهااد عباره عن‬Madura foot ‫ زي‬fugus ‫من االمراض المزعجه الي بتسببهاا ال‬
‫وهاد بنسميه‬.... ‫و شكله موجود بالصوره بالصفحه التاليه‬systemic infection
‫ بمعنى انه االنسان مااا بيستسيغ انه يتطلع ع منظره‬unsity diesaes
Systemic mycoses are fungal infections of internal organs of

the body (e.g., simultaneous infection of the respiratory
system and the bloodstream, or simultaneous infection of the
respiratory tract and the central nervous system).
‫او بالجهاز التنفسي‬.... ‫ بالجهاز العصبيي‬infection ‫ وصل لالجزاء الداخليه لجسم االنسان ممكن يعمل‬fungus‫اذا ال‬
..spores ‫كيف بتوصلله؟؟ممكن عن طريق استنشاق بعض ال‬
Madura foot
Spores of some pathogenic fungi may be inhaled with dust
from contaminated soil or dried bird and bat feces (guano),
or they may enter through wounds of the hands
Inhalation of spores of bread moulds like Rhizopus and

Mucor spp. by an immunosuppressed patient can lead to a
respiratory disease called zygomycosis or mucormycosis.
The mould can then become disseminated throughout the

patient’s body and can lead to death
‫الناس اللي عندهم مشاكل‬immunosuppressed ‫ همه ال‬fungal ‫اكثر ناس معرضه لالصااابه بال‬
‫ اللي سببهمم عباره عن‬mucormycosis ‫ او‬zygomycosis ‫بالجهاز المناعي وهاي االمراض ممكن تكون‬
. spores ‫استنشاق لل‬
In the mycology laboratory, yeasts are identified (speciated)
by determining which substrates they are able to use as
nutrients.
Yeasts are identified (speciated) by inoculating them into a

series of biochemical tests.
budding ‫ و حنشوووف تحت المجهر ال‬biochemical ‫ ممكن تتشخص بطرق بتشبه تشخيص البكتيرياا مثل ال‬yeast‫ال‬
yeast‫وهاي ميزه من ميزات ال‬
Moulds are identified by a combination of macroscopic and

microscopic observations and the speed at which they grow.
hyphae ‫(العين المجرده) بتتطلع و بتشوف ال‬macroscopic ‫ او‬micoscopic ‫ عن طريق‬yeast ‫ و ال‬fungus ‫تشخيص ال‬
‫ هاي انه بتشوفهاا تحت الميكرسكوب اللي هي‬micoscopic ‫و ال‬.....‫او اللون وهااي بتعطيك بعض االشارات لتشخيص المرض‬
‫ اللي سبب هاد المرض‬spices ‫وبنقدر نعرف شو هو ال‬.. ASeptate .‫ او‬Septate ‫ اماا‬hyphae ‫ممكن يكون ال‬
‫اخطر انواع الفطرياات‬ Dimorphic Fungi
Dimorphic fungi can live either as yeasts or as moulds,

depending on growth conditions.
‫ وهاد بيعتمد ع ظروف النمو الموجوده‬moulds ‫ او مثل ال‬yeast ‫ممكن يعيش ك‬
‫بالنسبه الهممم‬
*Dimorphic fungi that cause human diseases include:
Histoplasma capsulatum = histoplasmosis ‫هاااي االمراض تعتبر‬

‫من االمراض الخطيره‬
Sporothrix schenckii = sporotrichosis ‫القااااتله وهااي بتسببها‬
dimorphic ‫ال‬
Coccidioides immitis = coccidioidomycosis fungi
Blastomyces dermatitidis = blastomycosis

Lichens
lichen is a combination of two organisms: an algae (or a

‫ هاي عباره عن‬Lichens
cyanobacterium) and a fungus. ‫ و‬algae‫خليط بين ال‬
‫وهاااي‬..... ‫الفطريات‬
‫الميكروب ما بتسبب اي‬
Lichens are classified as protists. ‫و الهااا‬.... ‫مرض لالنسان‬
‫ايجابيه بانه كثير من ال‬
antibacterial
They are not associated with human disease ‫ بينتجوااا من‬compounds
lichens‫ال‬
Some substances produced by lichens have been shown to

have antibacterial properties
Slime Moulds
Slime moulds, which are found in soil and on rotting logs,

have both fungal and protozoal characteristics and very
interesting life cycles
Some taxonomists classify slime moulds as fungi, whereas

others classify them as protists.
They are not known to cause human disease

‫هيك احنااا خلصنااا الميكروبات وبعض االمراض اللي ممكن يسببوها لالنسان و هيك بنكون حطيناا القاعده االولى حتى‬
...... ‫نبدأ نفصل بالمايكرووو لقداام‬
Microbial Physiology & Genetics
TUQA ALMOMANI
&
TALA ABED-ALAZIZ
LEARNING OBJECTIVES
Microbial physiology
The study of vital life processes of microorganisms
‫وبهاد الساليدز رح‬... ‫اخذنا بالساليدات القبل عن المايكروبس وتركيبها وانواعها الخ‬
‫ندرس عن الحياة الحيويه لهاي المايكروبات‬
Microbial nutritional requirements
- Living protoplasm contains 6 major chemicals:
• C, H, O, N, P, S
• Others: Na, K, Cl, Mg, Ca, Fe, I
• Make up of macromolecules
• Essential amino acids, and Essential fatty acid
are not synthesized, but supplied
, ‫• المايكروبات بتحتاج لعناصر كيميائيه بشكل رئيسي واهمها الكربون‬
amino acid ‫كمان الماكروبات بتصنع اجزاء كبيره باستثناء ال‬,‫• وفي منها بحناج عناصر اخرى‬
)‫ (بس بتحتاجهم‬and fatty acid
Categorizing microorganisms according to their energy and
carbon sources
- FOUR major nutritional categories:
1. Photoautotrophs
2. Photoheterotrophs
3.Chemoautotrophs
4. Chemoheterotrophs
‫هسا سموا المايكروبات حسب الطاقه ومصدر الكربون من وين (بدنا نعرف انه لما‬
‫نحكي‬
‫يعني طاقه ضوئيه‬Phototrophs
‫يعني طاقه كيميائيه سواء عضويخه او غير عضويه‬Chemotrophs
co2 ‫يعني مصدر الكربون من‬Auto
‫يعني مصدر الكربون من مواد عضويه‬Hetro
Terms related to an organism’s energy
source
Phototrophs: Light as energy source; Photosynthesis

(means conversion of light to energy)
Chemotrophs: Inorganic or organic chemicals as energy

source:
• Chemolithotrophs (Lithotrophs): Inorganic
• Chemoorganotrophs (Organotrophs): Organic

Terms relating to an organism’s carbon
source
• Autotroph : Use CO2 as the sole source of

carbon, e.g. plants, cyanobacteria
• Heterotroph: Use organic compounds other than
CO2 as a carbon source, e.g. human cells, fungi,
protozoa, most bacteria
Ecology: Is the study of the interaction between organisms

and the world around them, e.g. photoautotrophs
produce food and O2 for Chemoheterotroph
•
Term combined energy&carbon source
Photoautotroph: Light & CO2
e.g. plants, algae, Cyanobacteria
• Photoheterotroph: Light & Organic

e.g. some bacteria
• Chemoautotroph: Chemicals & CO2

e.g. certain bacteria
• Chemoheterotroph: Chemicals & Organic

e.g. All (animal, fungi, protozoa); most bacteria
Metabolic enzymes
• Metabolism: Chemical reactions(metabolic reactions( •
Metabolic enzymes: Control metabolic reactions and
are under gene control
Enzymes (biological catalysts)
- Specific; act on one substrate (Lock-Key)
- Unchanged during the reaction
‫بتعرفو انه االنزيمات بتحفز التفاعل الكيميائي بدون ما تستهلك في التفاعل‬
Endo-enzymes: Within the cell
Exo-enzymes: Produced within a cell & then released, e.g.
Cellulase, Pectinase of saprophytic fungi
‫الرسمه الي تحت ببين كيف شغل االنزيم برتبط بالمتفاعالت وبعطيني النواتج‬
‫وباالنزيم بضل زي ما هو‬
S ‫المتفاعالت‬:
Factors that affect the efficiency of enzymes
- pH
- Temperature
- Concentration of enzyme and substrate
- Metals: Some enhance (Calcium, Magnesium),

some inhibit (Lead, Zinc, Mercury)
- Bind to a similar substrate (mimic the original

one) block/stop reaction, e.g. chemotherapeutics
‫تستخدم هاي الطريقه عند العالج لالدويه بنعطي دوا بشبه االنزيم فبكون هو‬
‫المتفاعالت بحيث اذا البكتيريا ممرضه بوقف عملها‬
Metabolism
1. Catabolism
2. Anabolism
Catabolism/ catabolic reactions
- Breaking bonds of large molecules
- Energy released
Anabolism/ anabolic reactions
- Reassembly of smaller molecules (bonds)
- Energy required (stored energy)
Catabolism vs anabolism
- See Figure and Table; equal or in balance
- ATP transfers energy from glucose
‫شرح الرسمه اللي تحت انه كل عمليه بناء بتقابلها عمليه هدم تمام‬
‫هون بحكيلي عن ال‪ATP‬‬
‫انه بتكون من ‪ 3‬فوسفاتات‬
‫هون بحكي انه اذا اخذنا فوسفاته وحده من ال ‪ATP‬‬
‫بعطيني‪ADP‬‬
‫واذا اخذنا كمان فوسفاته بعطيني‪AMP‬‬

‫هون تلخيص عن عمليه البناء والهدم واهمها انه التنتين بحدثن بالخليه‬
Biochemical reactions
- Starting material
- Intermediate products (intermediary)
- End product
Common metabolic processes
1. Aerobic respiration
2. Fermentation (Anaerobic) reaction
3. Others
‫شرح الرسمه الي تحت انه اي تفاعل بتكون من ماده اولى و اوساط و ماده‬
‫نهائيه هسا‬
‫ماده بدائيه‬A
‫اوساط‬B,C,D
‫ ماده نهائيه‬e ‫و‬
Aerobic respiration of glucose
1. Glycolysis
2. Krebs cycle
3. Electron transport chain
‫اذا في‬O2
‫معناها بدخل‬
‫لحلقه كربس‬
‫اما اذا ما في‬
‫بكمل تخمير‬
Glycolysis (glycolytic pathway; Embden- Meyerof pathway;
Embden- Meyerof-Parnas pathway)
- steps9; each requires a specific enzyme
- Glucose Two 3-carbon pyruvic acid (pyruvate)
- Little energy (2 ATP only) is released.
- Occurs in cytoplasm of Prokaryotes & Eukaryotes
Note: Refer to:

https://online.science.psu.edu/micrb106_wd/node/6153
‫حكا الدكتور ما بدي ادخل بالتفاصيل بهمني فقط انه‬
‫الجلوكوزبتحول‬
‫لحمض ‪pyruvic‬‬
Krebs cycle (Citric Acid Cycle; Tricarboxylic
Cycle)
- 8 steps; each with an enzyme
- Generate energy (only 2 ATP molecules)
- At the mitochondria, but in bacteria at the inner surface

of the cell membrane (mesosomes).
-Starts with Acetyl-CoA combines with Oxaloacetate

to produce citric acid (tricarboxylic acid)
Electron transport chain
- Series of oxidation- reduction
- Energy is released by electrons transfer- End oxygen

(final/terminal electron acceptor)
- Enzymes involved: Cytochrome oxidase (cytochrome c, or

oxidase)- transfer electrons to oxygen, example:
Oxidase positive gram negative bacilli
- Involve 10 NADH (from glycolysis to Krebs cycle) & 2

FADH (from Krebs cycle) to produce 30 ATP plus 4 ATP
respectively = Total 34 ATP cont./…
Cont./… electron transport chain
- In conclusion, as many as 38 ATP molecules are produced
by oxidative-phosphorylation (ADP to ATP) from glucose
catabolism including glycolysis, Krebs cycle and electron
transport chain in prokaryotic cells
vs
Fermentation of glucose (X 18-19 times less)
forms only 2 ATP.
glycolisis ‫هسا بحكيلي انه الطاقه الي بتنتج من عمليه ال‬
‫مره من عمليه‬19 ‫الى‬18 ‫وحلقه كربس وسلسله االلكترونات االنتقاليه اكثر ب‬
‫التخمير‬
Cont./… electron transport chain
- In eukaryotic cells = 36-38 ATP are produced from
catabolism of one glucose molecule
- Oxidation: Loss of electrons
- - Phosphorylation: Conversion of ADP to ATP
- Chemical equation of aerobic respiration

C6H12O6 + 6O2 + 38 ADP + 38 (P)
6H2O + 6 CO2 + 38 ATP
Fermentation of glucose
- Oxygen is NOT involved (anaerobic)
- First step: Glycolysis
- Then pyruvic acid End product; only 2 ATP
- Examples: • Yeast )Saccharomyces) and bacteria
(Zymomonas): Convert pyruvic acid to
ethyl alcohol
• Lactobacilli: to lactic acid (e.g. Yogurt)
• Streptococcus: To lactic acid (damage

enamel of teeth)
Oxidation-Reduction (Redox) Reactions
- Oxidation: Loss of an electron
- Reduction: Gain of an electron; Electrical charge is

reduced
- Dehydrogenation reactions, e.g. Krebs cycle
Video Electron Transport Chain

https://www.youtube.com/watch?v=xbJ0nbzt5Kw
‫هسا الي بفقد الكترونات بتاكسد طب‬
‫معروف‬
‫انه االلكترون شحنته سالبه واللي بختزل‬
‫بكسب الكترون‬
‫بما انه كسب الكترون فبتقل شحنته‬
Anabolism/Anabolic reactions
- Require energy; bonds are formed
- Energy provided by simultaneous catabolic reactions
Example: • 2 Monosaccharides Disaccharide
• Similarly for Proteins & Nucleic Acids
• Organic: Photosynthesis; Chemosynthesis

Photosynthesis
- Light energy Chemical energy (bond)
- Photoautotroph, e.g. Cyanobactia

- Photoheterotroph, e.g. some bacteria
-Trapped light energy chemical bonds in ATP and

glucose forms more ATP by aerobic respiration.
- • Oxygenic photosynthetic bacteria (Produce O2)

• Anoxygenic purple/green sulfur bacteria (obligate
anaerobic photoautotrophs), e.g. Bacteria use S or H
Cont./…. Photosynthesis
Q. Photosynthesis is the reverse of aerobic respiration; Why?
‫ايش يعني السهمين تحت يعني ممكن الجلوكوز مع الماء يتحول ل ثاني اكسيد الكربون وماء‬
)reversible )‫والعكس صحيح‬
CO2+ Water Glucose + Oxygen
- If no light: • Survive Anaerobically by fermentation; or

- If no CO2 (simple C): • Become Photoheterotroph
Chemosynthesis
- Chemoautotrophs: Chemotrophs use CO2
e.g., Primitive bacteria
Archaea (methanogens)
‫االريكا حكينا بتنتج غاز الميثان‬
4H2 + CO2 CH4 + 2H2O
- Chemoheterotrophs: Organics (other than CO2)

e.g., Most bacteria, Fungi,
Protozoa, Animals,
Humans
‫عارفني انه ادلكتور ما بزيد حيك كثري خارج الساليداات ولكن‬
‫حىت اليل ما بده يرجع لفيديو ادلكتور يكون متطمن انه متطلعع‬
‫ادرسواا كويس موفقييني‬....‫عىل لكشييي‬
Microbial Physiology
&
Genetics
(Two Lectures)
Prof. Dr. Zainalabideen A. Al-Abdulla,

MRCPI, DTM&H., Ph.D., FRCPath. (U.K.)
Bacterial Genetics
Genetics: The study of heredity
Genotype (genome): Complete collection of genes
Phenotype: Physical traits, attributes, characteristics;

Dictated by genotype (manifestations)
e.g., Bacterial enzymes, capsule, flagella
‫صفات يسيطر عليها من قبل الجينات‬
Chromosome: A circular strand of linked genes
human chromosome : straight
Bacterial chromosome : circular
Genes: Direct all functions of cell, e.g. mRNA (product)
Any product that bacterial produces that control by mRNA.
Mutation Alter gene product &
Trait(‫ )صفة‬Transmissible to
DNA of gene altered
offspring(‫البكتييا‬
‫ر‬ ‫)احفاد‬
( From bacteria to bacteria)
- Categories:
1. Beneficial, e.g. R to antibiotic.
R : resistance ( ‫يعني انه البكتيريا تحافظ على نفسها من‬
‫)القتل باستخدام المضادات‬
2. Harmful (sometimes Lethal)
e.g. Non-functioning enzyme (Lethal) NOT always.

( when bacteria unable to produce function enzyme ).
3. Silent: Most bacterial mutations

Spontaneous mutations
• Random (‫ )عشوائ‬/Natural ( ‫)طبيع‬
• Some genes: More prone.( ‫دائما جاهزة‬ ً ‫كبي او يعن‬ ‫عندها استعداد ر‬
‫يصيلها‬
‫بإنه ر‬mutation )
• Rate: Per 10,000 (104 ) – 1 Trillion (109 ) DNA
replication rounds (average 1 million)
• This rate increased by : Physical or Chemical agents
(Mutagens : ‫الفييائية او الكيميائية الن تؤدي إىل حدوث طفرة‬
‫)ه المواد ر‬
Mutant (an organism with mutation), e.g.
( ‫ )لقاح شلل االطفال‬is a mutant strain- for
poliomyelitis( virus is mutant use to make vaccine ).
( ‫“ )العالم الذي اكتشف اللقاح‬ ”
Ames Test (1960): Mutagen may also be carcinogen (cause
cancer) .(there is linked between mutagens that cause alteration in
genes and development of cancer .
Bacterial new genetic information
1. Lysogenic conversion
2. Transduction
3. Transformation
4. Conjugation
These are the most important 4 steps that explain How

bacteria can get new genetic info…
Plasmid
• Extra-chromosomal DNA in the cytoplasm
• Genes (many or few) on plasmid
• New genetic information acquired
•Replicate with or without chromosomal DNA

(episome- autonomous or integrated plasmid)
. ‫ او مستقل عنه‬DNA ‫البالزمايد إما يكون مرتبط مع‬
Lysogenic Conversion
Phages
1. Virulent (lytic): cause lysis .
*Bacteriophages:
Virus that infect bacteria.
Not cause lysis
2. Temperate :(Not lytic; Lysogenic)

ogenic)
3. Lysogeny: DNA injected into bacteria but no lysis
• Prophage: Remaining phage DNA in bacteria.
( ‫)ما سيتبق من المادة الوراثية‬
• Lysogenic bacteria (Cell): Bacteria with prophage; Phage
DNA replicate within bacteria daughter cells.
( ‫البكتييا‬
‫ر‬ ‫رفيوس يحتوي عىل المادة الوراثية بحيث يتم إدخالها إىل‬
cont./… Lysogenic conversion
Phage conversion: A lysogenic bacterium is capable of
producing one or more new gene products and exhibit new
properties (i.e. converted).
Bacteria with
DNA of virus
Examples of m.o with prophage become pathogenic:
• Corynebacterium diphtheriae(‫)الخناق‬: Diphtheria; tox

gene .( ‫غي مرضية بمجرد انتقاله لها‬
‫ه ر‬
‫الفيوس ي‬
‫البكتييا بدون اإلصابة بهذا ر‬
‫ر‬
‫)تصبح مرضية‬.
• Streptococcus pyogenes: Scarlet fever.(‫)الحىم القرمزية‬
• Clostridium botulinum: Botulism.( ‫)التسمم الغذائ‬
• Vibrio cholerae: Cholera.
Transduction (“to carry across”): doesn’t cause lysis.
- Involves temperate bacteriophages
- Prophage activated (stimulants) new viruses +

attached bacterial genes carried to other cells
Bacteriophage : (carrier) ‫تلعب دور الناقل‬
- Two types: General (see the Figure) & Specialized
‫يلعب دور الناقل‬
‫ويحتوي على‬
‫صفات البكتيريا وال‬
Bacteiophages
(integrated
together)
New host .
New genetic
Infect with information.
new
microphage
Transformation: ‫التغيي ف الصفات‬
‫ر‬
-DNA (“naked DNA”) of disintegrated bacteria (cell) uptake
or absorption by competent bacteria (cell).
-) ‫ ممكن البكتيريا توخذه من المحيط وتدخله لجوا‬، ‫ خارج البكتيريا‬DNA ‫( مثالً لو عندي‬
- Examples:
• S. pneumoniae: DNA extract of Capsulated +
non-capsulated broth Capsulated m.o
•Latent virus gene (in human) + Bacteria

(indigenous microbiota) Parkinson
disease (?)
• ‫البكتييا تأخذ جينات من‬
‫ر‬ ‫بعض‬
PARKINSON‫الفيوسات وتسبب‬ ‫ر‬
Absorbed by
bacteria
Conjugation (see Figures) Linked between 2 bacteria by sex pilus
Sex pilus (F pilus = conjugation bridge)
- Donor( ‫( )مانح او معط‬F+) attaches Recipient (‫()مستلم‬F-)

bacteria by F pilus
-Pilus retracts Relaxase splits plasmid dsDNA
- ‫ رح تسحب البكتيريا االخرى‬pilus ‫هذه ال‬
- Is not reproduction (Bacterial mating/ male & female)
# m.o: most offiety
Examples: Enteric bacilli, Pseudomonas \powerfull factor
# transfer F factor very
function of conjugtion: efficently and frequency
- Transfer antibiotic resistance (R Factor= multiple drug
resistance = “superbug”) & Fertility “F” factor (delivered by
F+ & high frequency of recombination “Hfr+” m.o.)
Recipient
-
Donor
+
Genetic engineering (vs. Recombinant DNA Technology)
‫ تستخدم يف التصنيع او العالج وممكن استخدمها لما يكون يف نقص بجينات معينة‬:G.E
Human genes Plasmid (Vector = Vehicle)
can carry these genes (rDNA Technology)
‫الجي المنقول لها‬
‫البكتييا سوف تكتسب صفة ر‬
‫ر‬ ‫جي من اإلنسان إىل‬
‫لو تم نقل ر‬
Examples: E. coli, Yeast, human macrophages and
fibroblasts (manufactures) are used to produce/create
new products (Genetic Engineering):
• Growth hormone (GH) • Somatostatin (Inhibitor)
• Insulin • Interferon
• Resistant plants in “agriculture”
• Marine bacterium to break oil down( engulf)for
clearance. ( ‫البكتييا الها قابلية امتصاص أو أخذ‬
‫ر‬ ‫لما يتلوث البحر بالنفط هاي‬
‫الزيت و النفط والتخلص منه وتنظيف البحر‬
‫نقل الجين إلى البكتيريا‬
‫‪Ex:‬‬
‫‪Target gene‬‬
‫‪that‬‬
‫‪responsible‬‬
‫‪un produced‬‬
‫هون اخذنا‬ ‫‪of insuline‬‬
‫‪Target DNA from‬‬
‫‪source of DNA‬‬ ‫‪when we‬‬
‫ومن ثم نأخذ المادة‬ ‫‪transfer‬‬
‫الوراثية ويتم إدخال‬ ‫‪them to new‬‬
‫الجين المحدد عليها‬ ‫’’’’’’‘ ‪host cell‬‬
‫عن طريق ناقل وبعد‬ ‫‪The host cell‬‬
‫ذلك يتم إدخالها إلى‬ ‫‪can produce‬‬
‫خلية أخرى‬ ‫‪insuline‬‬
‫يعني الخلية‬
‫البكتيرية الجديدة‬
‫اكتسبت صفات‬
‫جديدة‬
Gene Therapy
Insertion of normal human gene into cells:
• Viral delivery (e.g. adenoviruses, retroviruses)
• Bacterial (Bacto-infection, e.g., Salmonella)
• Synthetic vector(‫ ?( )تصنيع الناقل‬For the
future)
- Prescribe genes (considered as drugs) to treat:

• Autoimmune diseases
• Sickle cell anaemia
• Immunodeficiency disorders
• Cancers
• Many other conditions
STERILIZATION & DISINFECTION
#7
Ala'a AL-SHORMAN
HADEEL TAWALBEH
Sterilization
Destruction or elimination of all microbes including cells, sp
ores, and viruses
- Sterile = Devoid of microbial life
Spores&viruses ‫يشمل قتل كل الجراثيم بضمنها ال‬
- Physical or chemical methods in healthcare
• Dry heat‫ بالحرارة‬..‫الحرق‬
• Autoclaving (steam under pressure ‫)بخار تحت الضغط‬
• Ethylene oxide gas
• Formaldehyde
• Radiation (UV, gamma rays)
Disinfection nonliving ..‫(( طاولة مطهر عليها مثال‬
The elimination of most or all pathogens (except bacterial s
pores) from nonliving objects; using:
1. Liquid chemicals (disinfectants)‫األسواق المتواجدة المعقمات مث اًل‬
‫ب‬ 2. Wet pasteurization ‫مثالً بسترة الحليب‬
Antiseptics: Disinfectants used on living tissues as the skin

‫ مثالً تطهير طاولة‬Non living ‫يستخدم لل‬Disinfectant
antisepticً‫بصيرًاسمه‬livingً‫لماًنستخدمهًلل‬
Sanitization: Reduction of the microbial population to safe l
evels, e.g. in resturants‫المطاعم في التنظيف مثالً بحيث ما يسبب أمراض‬
Microbicidal agents
- Suffix: cide or cidal = “killing”
Examples:
• Bactericidal = Kill bacteria
• Sporicidal = Kill bacterial spores
• Viricidal = Kill viruses
• Fungicidal = Kill fungi
• Pseudomonicidal= Kill Pseudomonas
• Tuberculocidal = Kill M. tuberculosis
Pasteurization
- A method to disinfect liquids (e.g. milk) ‫بسترة الحليب‬
- Is not sterilization
- Not all microbes are killed ( just kill those who are the harmful(
- 63o C 30 minutes
72o C 15 seconds
140o C 4 seconds This is can be use fo perparation of long life milk
Microbiostatic agents
-Drugs or chemicals that inhibit reproduction and metabolis
m of microorganisms (NOT necessarily kill them)
-So biocidal or bacteriocidal it means (killing)
-Static it means inhibition only
- Freeze drying & rapid freezing: Bacteriostatic
- Freeze drying = Lyophilization: To preserve
powder‫ إلى‬liquid ‫هو التحويل من‬Freeze drying :

‫مثالً اما أحول الحليب من سائل إلى باودر‬
freeze‫ بعمللها‬liquid be ‫ لما تكون البكتيريا عندي‬bacteriology ‫وبرضو بال‬
drying "lyphophilization
‫ إذا بتضل بالسائل حتنعدم فبحولها ل باودر‬..‫منشان مثالً بدي أحتفظ فيها فترة طويلة‬
This will keep the microorganisms for long time
Sepsis: Presence of pathogens in blood or tissues
‫الجراثيمًيليًبتدخلًاألنسجةًوالدم‬
Asepsis: Absence of pathogens no micropes
- Medical or Surgical aseptic techniques, e.g., hand hygiene,
sterile gloves, masks, and gowns
Antisepsis: Prevention of infection
Antiseptic technique: Use of antiseptics

For example : material like iodin
Physical Methods
Heat Inanimate ‫ غير حيّة‬:
- The most common type of sterilization for inanimate obje

cts which are able to withstand high temperatures.
‫الزم المادة تكون قادرة على تحمل الحرارة مثالً عندي‬
‫قطعة حديد وبدي أعقمها البالستيك ما بتحمل الحرارة‬
- Effect depends on: ‫فهيك أنا ما بقدر أعقمها بالحرارة‬
1. Temperature
2. Time
- Pathogenic > susceptible than nonpathogenic
organisms.‫قاعدة عامة‬
Thermal Death Point (TDP)
Lowest temp. that kill all organism in a standardized
pure culture within specified period.
(‫)الحرارة األقل في وقت معين‬
Thermal Death Time (TDT)

The length of time to sterilize a pure culture at a sp
ecified temperature.
‫بينما هون الوقت في حرارة معينة‬
Dry heat
- 160 – 165o C 2 hours or ‫كل ما زادت الحرارة كان الوقت أقل‬
o ً ‫طبعا‬
- 170 – 180 C 1 hour
- In oven
- Items: Metals, glassware, oils, waxes
Incineration: Burning; contaminated disposable materials;

must NOT be overloaded with protein and moist materials a
s feces, vomitus or pus
Flaming: Bunsen burner flame or electrical heat device for f

orceps, wires, or loops, e.g culturing
bunse‫ ب‬loop ‫هون بعقم ال‬ electrica‫وهون عقمتو ب‬
n burner l heating device
Moist heat
1. Boiling for 30 minutes, e.g. metal (needles), or glass. No
t effective against spores, viruses and Mycobacterium.
2. Autoclave (Moist heat + Pressure):

- 15 psi + 121.5o C for 20 minutes*
- Kills spores, viruses, and vegetative form
- Rubber can be autoclaved
- Indicators for completion: • Autoclave tape
or • Solutions of bacterial spores
- Keep cans open, bottles covered loosely
Without the lines it means it failed
You have the pink c
olor solution
You put it with the
outoclave
After the outoclave
You put it in inqupa
tor in 37°C
If it’s become yello
w It meanes there i
s falier
Because it meanes
the spores has not
been killed ..transf
orm to avegedetive
form and changed t
he color of this sol
ution to yellow . Bu
t if the color was pu
rple it is success
Cold
Kill or inhibit microorganismً‫كيفًبنستخدمهاًل‬
-Refrigeration: Slows metabolism & growth rate
- Slow freezing: Forms crystals & rupture cells (not good in b

acteriology)
- Rapid freezing (liquid nitrogen): Keep/Preserve
• Freeze- Thawing of food: Unsafe

(spores vegetative forms)
Spores change to vegetative ‫كالهما يتحول لآلخر يعني ال‬
Vegetative change to spores ‫وال‬
Desiccation
- Dried clinical specimens and dust may contain
viable microorganisms. Dose not kill microbes it can live in
dust
Radiation
- UV: • Sterilize vaccines, antisera, toxins
• May cause skin cancer, eye damage ‫معلومة عامة‬
- X-ray, gamma and beta ray:
• Gamma ray sterilizes food as meat
from Salmonella & Campylobacter
Ultrasonic (US) Waves
- For cleaning delicate equipment
- Tank of water + short US waves then sterilize
- In dental or medical clinics, e.g. glassware

Filtration
- Different pore sizes; separate organisms
(bacteria, viruses, others) from liquid or gases
- Using micro-pore filters .felter bacteria&virus
- High-Efficiency Particulate Air (HEPA) used

in operating rooms, patient room to filter
air (e.g. positive pressure isolation room for
bone marrow transplantation, and negative pressure isolation room for contag
ious diseases ‫)أمراض معدية‬
Gaseous Atmosphere
- Aerobs/ Microaerophiles: Remove O2 from
environment to kill them.
- Anaerobic: Provide O2 to kill them:

• Expose wounds to atmosphere
or adding oxygen
• Hyperbaric Oxygen Chamber
(increased pressure) to kill the
microorganisms, e.g. gas gangrene
caused by Clostridium perfringens
Disinfectants (Chemical Agents)
- Temporal or permanent
- Factors affecting disinfectants:

• Prior cleaning/proteinaceous materials
• Organic matter load
• Bio-burden (microbial) number of microbes
• Concentration
• Time
• Physical nature
• Temperature • pH
cont./… Disinfectants
- Susceptible: Vegetative state, fungi, protozoa,
most viruses
- Resistant: Mycobacteria, bacterial endospore,

Pseudomonas ‫ جرثومة‬spp., fungal spores,
hepatitis viruses
- Degree of resistance (see Table)

cont./… Disinfectants
- Never use disinfectant if physical sterilization ‫ألنها آمنة وأفضل‬
is possible ‫قاعدة عامة‬
- Can not destroy all bacteria & bacterial spores

- Spore/ Mycobacteria/Viruses destruction:
• Formaldehyde / fumigation ‫تبخير‬
• Ethylene oxide
# Also, for example electronics, optical
equipment, paper, rubber and plastics
(which can not tolerate other methods)
Disinfectant characteristics
• Broad
• Fast-acting
• Not affected by organic materials
• Non-Toxic; Evaporation-Concentration level
• Leave residual anti-microbial film
• Soluble in water
• Inexpensive ‫رخيص‬
• Stable
• Odorless ‫عديم الرائحة‬
Antiseptics
- Chemicals used safely on human tissues
such as skin, e.g., alcohol, iodine, H2O2
- Reduce numbers of organisms on surfaces

- Used at surgical incisions ‫مكان العملية‬, at pores of folds
of the skin.
- Antiseptic soup + Brushing is effective, e.g.

hand washing of surgeons prior(before) operations
THE END
Antimicrobial Agents
TASNEEM DARAWSHEH
 Chemotherapeutic agents
Any drug used to treat any condition or disease
 Antimicrobial agents
Chemotherapeutic agents used to treat infectious diseases:
- Anti-Bacterial - Anti-Viral - Anti-Fungal - Anti-Protozoal
o Antibiotic (AB)
- A substance produced by a microorganism that is effective in killing or inhibiting the growth of other organisms
.‫ اخر‬organism ‫و تقتل او تثبط‬.....‫ زي البكتيريا او الفطريات وغيرهااا‬organism ‫اي ماده ُتنتج من قبل‬
Examples according to its sources:
- Mould-produced: Penicillin , Cephalosporin (mould means fungal)
- Bacteria-produced: Erythromycin, Chloramphenicol (mainly soil bacteria)
 Types of Antibiotics/Antimicrobials
1. Natural AB 2. Semisynthetic AB, ‫بنغير في تركيبهاا شوي‬ 3. Synthetic Antimicrobials
e.g. Peniciilin G e.g. Modified AB (Ampicillin, Carbenicillin) e.g. Monobactam (Aztreonam)
 The first person who descoverd pancliin was Alexander Fleming :
penicileum ‫ اللي اسمهاا‬fungus droop ‫ و ال‬...A ‫ للبكتيرياا زي بالشكل‬culture ‫عمل‬
‫) الحظ انه هاي البكتيريا اللي زرعهاا صارللها‬C ‫اللي بتنتنج البنسلييين(الموضحه بالشكل‬
AB ‫وهو كان اول واحد يالحظ هاالشيي و بدأ اكتشافات ال‬... ‫ بواسطة البنسليين‬inhibtion
Characteristics of an ideal antimicrobial agent: ‫رح نحكي عن كل اليه لحال مع ذكر امثله لقداامم‬
....
(Selective toxicity)
‫يعني بيبقى بالجسم مو يروح خالل دقائق‬

 Antibacterial Agents based on mode of action:
1) Bacteriostatic: Inhibit growth of bacteria
- Should NOT be used in immuno-compromised or leukopenic patients
2) Bactericidal: Kill bacteria
Selective toxicity: The drug affects microorganisms but NOT human cells.
Antibacterial Agents based on their spectrum of action:

1) Narrow-spectrum antibiotic: Destroy (affect) either gram positive or gram negative bacteria
- Examples: Vancomycin: G+ Colistin : G-
2) Broad spectrum antibiotic: Destroy (affect) both gram positive and gram negative bacteria
- Examples: Ampicillin (semisynthetic) Chloramphenicol Tetracycline
3) Extended spectrum Antibiotics
- Broad spectrum antibiotics with extended activity against certain microbes such as cetain gram negative bacteria,
Pseudomonas, or others.(G+,G-,some bacterial resistence)
4) Competitive inhibitors
- Example: Sulfonamide
- Inhibition of Nucleic Acid synthesis
para aminobenzoic acid ‫ فيه ماده اسمهاا‬..‫هساا نوخد عن االنزيمات‬
‫ وبساااعدها على ذلك انزيم اسمه‬folic acid ‫بتستخدمها البكتيريا لصناعة ال‬
para ‫ شبيه بال‬drug ‫لو جبنااا ماده او‬....... dihydropteroate synthetase
‫هااد االنززيم رح‬....... sulfonamide ‫ اللي اسمهااا‬aminobenzoic acid
‫ ف البكتيريااا بتمووت او بتتثبط‬folic acid ‫يشتغل عليهاا فمااا رح ينتج عناا‬
: AB ‫ اللي بيشتغل فيها ال‬mechansim‫هسااا رح نفصلهم لقروباات حسب ال‬

i :Inhibtion of cell wall synthesis
1) Penicillins
- Beta-lactam drugs, inhibit cell wall synthesis.
- Act on actively dividing bacteria(if it was bacteria inhibited it cant act on them because cell wall is nonactive)
- Are bactericidal
- Natural penicillin:
• Penicillin-G (use in hospitels, when it ingected is very bainful) , Penicillin-V (weak antibiotics)
• Against: G+: Strep., anaerobes, spirochetes ‫اللولبياات‬ ‫وبيشتغل على‬... G+ ‫ البنسلين بيشتغل اكثر على‬:‫نووت‬
G-: N. meningitidis, H. influenzae G- ‫بعض ال‬
- Aminopenicillin and Extended penicillin:

• Against G- and G+ bacteria, e.g. Ampicillin, Amoxicillin(absorbed more rabidly than Ampicillin in intestine)
 Stracture of penicillin: it has a ring called beta-lactem and sometimes penicilinase , we have enzyme called
betalactmaes it will degreded beta lactam ring ,,,,,,,look the figur below:
2) Cephalosporins (inhibit cell wall synthesis)
1. First generation: G+, e.g., cephalexin
2. Second generation: Increased activity against G-
(besides G+), e.g., cefuroxime ....‫ معهممم‬AB ‫مشكلة ال‬
3. Third generation: Greater G- & Pseudomonas Very resistance ‫النهممم‬
bacteria
(besides G+, but less), e.g., cefotaxime.
4. Fourth generation: Greater G-/Pseudo & G+,
e.g., cefepime
5. Fifth generation: G+ as methicillin-resistant Staph. & weaker on G-, e.g., Ceftaroline
3) Monobactams
- Beta-lactam drug, inhibits cell wall synthesis - Active against gram negative rods only
- Not against gram positive bacteria - Not against anaerobes
Example: Aztreonam (synthetic antibacterial)
4) Carbapenems
- Beta lactam drug, inhibit cell wall synthesis.
- Active against most G+, G-, and anaerobes
- Examples
a) Imipenem: Inactivated by dihydropeptidase(DHP) which secreated from renal tubules ; so protected by Cilastatin.
b) Meropenem: Not inactivated by DHP enzyme
c) Ertapenem: Not P. aeruginosa, is long acting
II. Damage to cell membrane:
III. Inhibition of Protein synthesis:

‫ وعناا مجموعه كبيره جدا من االدويه ((وفيه جدول فقط لالطالاع)) عشاان‬ribosome protein synthesis ‫وهاد بيحصل بالسيتوبالزم وتحديداا بال‬
<<<< ‫سووو خليناا نبلش فيهم‬....‫هيك ما حطيته بالتفرييغ ولكنن رح نوخذ بعض االمثله المهمه واللي نشرحت بالساليداات نفسهاا‬
1)Tetracyclines
- Broad-spectrum (e.g. Tetracycline, Doxycycline)
- Action on ribosome (inhibit protein synthesis) action on ribosome
- Bacteriostatic
- Effective against:
•G+ and G- bacteria • Chlamydia • Mycoplasma • Rickettsias • Vibrio cholerae
• Spirochete (Borrelia, Treponema pallidum which caused seohlix disease )
2) Aminoglycosides
- Broad-spectrum (against many G-, some G+,NOT anaerobes (it naturally resistant to aminoglycosides)) :
- Effective against: • Enterobacteriaceae • V. cholera • P. aeruginosa
- Bactericidal
- Inhibit protein synthesis
- Ototoxic, Nephrotoxic
‫وخاااصه باالستخدام‬....‫ يعني على الكليه تأثيرهاا‬nephrotoxic‫بينماا ال‬.....ototoxic ‫ بالعصب الثامن و بسببوا‬damage ‫مشكلتهمم انهممم بعملوا‬
......‫الطويل‬
- Example: Gentamicin, Amikacin
3) Macrolides
- Inhibit protein synthesis
- • Bacteriostatic (low doses) • Bactericidal (Higher doses)
- Effective against:
1) Many G+, some G- bacteria 2) Chlamydia 3)Mycoplasma 4)T. pallidum 5) Legionella
- examples: Erythromycin, Clarithromycin
IV. Inhibition of Nucleic Acid Synthesis
Fluoroquinolones ((fluro means flour)) Now it Becomes resistant to ciprofloxacin

- Bactericidal - Inhibit DNA synthesis - Example: Ciprofloxacin - effective against: Enterobacteriaceae P.aeruginosa
V. Inibition of enzyme activity
Trimethoprim/sulfamethoxazole (TMP 1/SMX 5; e.g. 40/200 or 80/400), is also known as:

Co-trimoxazole ‫ اكثر بخمس مرراتت من‬SMX ‫لو دمجنااهم مع بعض بدوا واحد رح يكوون تركيز ال‬
(Jordanian: Balkatrin) ‫ وهاد‬balkatrin‫فيه عنااا دواء اردنييي اسمه‬....‫ زي مهو موضح بالجمله فوق‬TMP ‫ال‬
.co-trimoxazole
Multidrug therapy
- To kill all bacteria, and to prevent resistance

‫ مع بعض‬antimicrobial agent ‫يعني نستعمل اكثر من‬
- Example:
Mycobacterium tuberculosis: )‫)السل الرئوي‬
(isoniazid + rifampin(act on inhibition nucleic acid synthesis) + pyrazinamide + ethambutol)
*Synergism * Antagonism
Degree of killing that is far greater than that achieved
Degree of killing that is less than that achieved by either
by either drug alone or the sum of both drug alone
Example: Co-trimoxazole (Trimethoprim + Example: Penicillin (cidal) + Tetracycline (static)
sulfamethoxazole) ‫ في ان واحد لييش؟؟؟ النه‬static ‫ مع ال‬cidal ‫ال يجوز استخدام ال‬
‫ و التيترااسايكليين‬active bacterial cell wall ‫البنسليين يشتغل على‬
‫ مع بعض‬two antibiotics ‫يعني لما نستخدم‬ inhibition cell ‫ بالتالي حيصير‬inhibition for bacteria ‫بعمللل‬
1+1>2 ‫يعني‬...‫ويعطوناا فعاليه اكثر من استخدام كل واحد لحال‬ .‫ ومااا رح يشتغل البننسليين اصالا‬wall synthesis
‫ فانه حاولوا لخصواا‬..‫و بماا انه ضل شوي من الصفحه فاضي‬........... ‫ الدكتور بهااي المحاضره ماا حكاا غير اكمن جمله خاارج الساليداتتت‬:‫نووت صغيره‬
...........‫عليهااا المحاضره بمخطط ذهني يسااعدكم ع الحفظ او خربشوا عليهااااااا احسننلكم‬
‫موفقيين يااا رب‬
om 4a5a
9
9
Saja Abo Ali

Antifungal Agents
- Can be toxic to patients (why ?)
Antifungal and antiprotozoaldrugs
tend to be more toxic to the patient because, like
the infected human,they are eukaryotic
organisms
Mechanism of action:
1. Binding cell membrane sterol
e.g. Nystatin, Amphotericin-B
2. Interfere with sterol synthesis
e.g. miconazole
3. Blocking mitosis, or nucleic acid synthesis
e.g. Griseofulvin - old anti fugi and very useful
Antiprotozoal Agents
- Toxic to human cells (selective toxicity ?)
- Mechanism of action
1. Interfere with DNA and RNA synthesis
e.g. Chloroquine (antimalarial drug)
2. Interfere with protozoal metabolism and

DNA destruction:
e.g. Metronidazole (Flagyl) affective against ameba
Antiviral Agents
- Relatively few agents are available
- WHY?- see your textbook
Antiviral agent difficult to develop because viruses are

produced within host cell
-
Examples:
• Anti-HIV: Zidovudine (AZT); 1989
Drug resistance
- Drug resistant bacteria (Superbugs)
BUG mean microbs
- Superbugs USUALLY Multidrug Resistant
- Viruses/HIV, Fungi, Protozoa, Helminthes

(Also, Multidrug Resistant)
- See the Table

Important Resistant Bacteria
• MRSA, MRSE
• VISA, VRSA; ‫ﻫﺎد ﺗﻠﺨﻴﺺ ل اﻷﺷﻴﺎء‬
‫اﻟﻤﻄﻠﻮﺑﺔ ﻣﻦ اﻟﺠﺪول‬
• VRE (UTI)
• P. aeruginosa
• Clostridium difficile
• Acinetobacter baumanni
• Klebsiella pneumonia
• M. tuberculosis (MDR-TB) = Resistant to
rifampin and isoniazid.
Streptococcus pyogens and S.pneumoniae
in lung
Mechanisms of bacterial resistance
- Intrinsic resistance: Natural
- Acquired resistance: Acquired
- FOUR mechanisms (See the Table)

‫اﻟﺪﻛﺘﻮر‬
‫ﺷﺮح‬
‫اﻟﺠﺪول‬
‫ﻛﺎﻣﻞ وﻛﻠﻪ‬
‫ﺣﻔﻆ‬
Beta-Lactamases
- Beta-lactam antibiotics with Beta-lactam ring
are affected with these enzymes.
- Two types:
1. Penicillinases destroy pinicillin
2. Cephalosporinases destroy cephalosporin
- Some bacteria produce one or both enzymes

Prevention of Beta-lactamase action
Combine antibiotics with Inhibitors:
Examples:
Clavulanic acid + Amoxicillin = Augmentin
Clavulanic Acid + Ticarcillin = Timentin
Sulbactam + Ampicillin = Unasyn
Tazobactam + Piperacillin = Zosyn

Strategies against drug resistance
- Education, Prudent use ‫اﺳﺘﺨﺪام رﺷﻴﺪ‬
- Proper prescription (most unnecessary)
- First: Narrow spectrum & inexpensive
- Complete the full coarse as prescribed
- No need for prophylactic unless by clinician

- Good infection control and prevention
‫اﻟﺪﻛﺘﻮر ﺣﻜﺎه‬
‫ﻛﺎﻣﻞ‬
Empiric therapy
To “ guess”; “educated guess”:
• Pocket chart/Antibiogram (Clinical Microbiology Lab)
‫ﻧﺸﺮة ﺑﺎﻟﻤﻀﺎدات اﻟﺤﻴﻮﻳﺔ ﺗﻜﻮن ﻣﻊ اﻟﻄﺒﻴﺐ‬
• Allergy history of the patient
• Age for example Tetracyclin
‫ ﺳﻨﻮات‬7 ‫ﻻ ﻳﻌﻄﻰ ﻟﻌﻤﺮ أﻗﻞ ﻣﻦ‬
• Pregnancy
• Inpatients ‫اﻟﻤﺮﻳﺾ اﻟﻠﻲ داﺧﻞ اﻟﻤﺴﺘﺸﻔﻰ ﺑﺨﺘﻠﻒ ﻋﻦ اﻟﻠﻲ ﺑﺎﻟﺨﺎرج‬
• Site of infection, e.g. Brain, bladder, etc.? ‫ﻛﻞ دواء ﻳﺘﻢ اﺧﺘﻴﺎره‬
‫ﻟﻤﻜﺎن ﻣﻌﻴﻦ وﻫﺪف ﻣﻌﻴﻦ‬
• Drug cross-reaction
• Toxic side effects
• Immune status
Undesirable effects of antimicrobial agents
• Selecting for drug-resistant organisms
• Allergy
• Toxic, e.g. Chloramphenicol Aplastic Anemia
Streptomycin Deafness
• Superinfection “population explosion”, Fig.
- By opportunistic or secondary invaders
- Example: C. difficile antibiotic-associated/

pseudomembranous colitis, e.g. Lincomycin
- Candida albicans Vaginitis; e.g. Tetracycline
Some drug like Lincomycin kill colon flura and keep resistant bactria like C. difficile
that cause pseudomembranous colitis that are killer disease
‫ ﻋﻨﺪي ﻋﺪد ﻣﻦ‬flora
bactria that are
sensitive to
antibiotic
‫ﻋﻨﺪ أﺧﺬ ال‬

antibiotic : flora
bacteria will die
and resistant will
stay
Resistant
bacteria will
make population
explosion
WAR
NORMAL flora
#10
We’am Aljbaly
Neda’a Ashour
Normal Flora
HUM A N M ICRO BIO M E IN HEA LTH
A ND DISEA SE
Dr. Waleed Al Momani, MLT, PhD

We will talk about new topics in microbiology, especially how
microorganism stimulate an infection
Microbial ecology is the study of the numerous
interrelationships between microbes and the world around
them. As we said, the relationship between humans and
microbes is not always hostile, and most of it is beneficial
Microbes interact with humans in many ways and at many

levels.
The most intimate association that we have with

microbes(normal flora that building immunity, the first
mechanism in human body against pathogen) is their
presence both on and within our bodies

Symbiotic Relationships (‫)التعايش‬Involving
Microorganisms
Symbiosis is defined as the living together or close

association of two dissimilar organisms (usually two
different species).
The human body contains thousands of microbes

We have different types of symbiosis:
Neutralism There are neither gain nor loss, they just live
together (None of them affect the other)
Commensalism One of them benefits and the other is not

affected
Mutualism: Both benefit from the other, the microbes take

the nutrient, and the human takes the important minerals
and vitamins which use in our metabolism
Parasitism: One of them lives at the expense of the other, we

have a gain and a loss
This type has a direct relationship in medical biology (infection)
as the microbes that cause pathogen
Indigenous Microbiota of Humans
Microbiota= Normal flora ,Microbiome , Bioneme
A person’s indigenous microbiota (sometimes referred

to as the human microbiome or human bioneme)
includes all of the microbes (bacteria, fungi,
protozoa, and viruses) that reside on and within that
person

If we start from the first stages of human existence
During pregnancy, the human fetus lives in a

remarkably protected and for the most part sterile
environment
‫الجنين بكون محمي مش معرض وال ألي نوع من المايكروبات‬
Over the next few years, communities of organisms

(microbiota or normal flora form on the surfaces of
the skin, nares, oral cavity, intestines, and
genitourinary tract.
(The most important stage; a building good normal flora
occurs ),

The period in which the normal flora begins to build is
the first 3 years of a child's life,
This normal flora can be lost and can also be
compensated for through the use of biological
therapy
The first stage that a newborn is exposed to the

microbes normal flora is during the birth process
in the birth canal
‫تعتبر عملية بناء النورمل فلورا تراكمية فكل ما تعرض الطفل لبيئات‬
‫مختلفة كل ما زاد عنده نشاط النورمل فلورا‬
The picture expresses that the first encounter between
the normal flora and the human being was when he
was born in birth canal
‫الصور هون بتوضح انو‬
‫األهل همه الي بيتحكموا‬
‫بالطفل انو اي بيئة يتفاعل‬
‫معها و يعيش فيها فبناء‬
‫على نوع البيئة حيختلف‬
‫نوع النورمل فلورا الي‬
‫حيكتسبها مثال حسب نوع‬
‫الغذاء الي بيتناوله المكان‬
‫الي بيلعب فيه و‬
‫هكذا‪......‬‬

‫وجدوا انو األطفال الي بتتعرض‬
‫لبيئات مختلفة عندها أقوى نورمل‬
‫فلورا من األشخاص الي حذرين‬
‫زيادة عن اللزوم‬
‫و وجدوا انه أفضل مكان بيتواجد‬
‫فيه النورمل فلورا هو التربة لذلك‬
‫في بعض الناس بتشتري تربة‬
‫ألطفالها ليلعبوا فيها و يكتسبوا‬
‫نورمل فلورا اقوى‬
‫‪-‬األشخاص الي عندهم نورمل‬
‫فلورا قليلة او ضعيفة همه أكثر‬
‫عرضة لل‬
‫‪Sevier disease + Less‬‬
‫‪immunity to microbes‬‬
‫و هاد أقرب واقع للبيئة الي بعيشوا فيها األطفال في مجتمعنا‬
‫)مثل ما حكى الدكتور(‬
How did they study the normal flora ?
By The Human Microbiome international Project
‫طريقة اجراء هاي الدراسة من خالل جمع عينات من أعضاء مختلفة من‬
‫االنسان و بلشوا يصنفوا النورمل فلورا بناء على المكونات الموجودة فيها‬
: ‫و نتيجة لهاي الدراسة صنفوا هاي الماكروبيوم الى‬
1-Core Microbiome
2-Secondary Microbiome
5-year multinational study to analyze the genetic

composition (microbiome) of the microbial
populations that live in and on healthy adults.
It is estimated that bacterial cells outnumber

human cells in the host by 10 : 1
‫ مايكروب اي عشر أضعاف الخاليا عندنا‬10 ‫مقابل كل خلية بجسمنا عندنا‬

The Human Microbiome Project was launched in
2007 with the collection of samples from the nose,
mouth, skin, gut, and vagina from healthy adult
volunteers

Bacteria colonizing the gut are different from those in
the mouth, skin, and other body sites.
The greatest taxonomic and genetic diversity was the

intestine (The most common places where bacteria live are
50% of the substance in it is bacteria), , and the vagina was
the least complex.
Microenvironments such as different regions of the

mouth, gut, skin surface, and vagina also had their
own unique microbiome

Core Microbiome
Most individuals share a core microbiome, arbitrarily defined

as the species that are present at a specific site in 95% or
more of individuals. Staphylococcus usually found on skin as
normal flora, .
The greatest numbers of shared species are present in the

mouth, followed by the nose, intestine, and skin, and the
fewest shared species are found in the vagina
Secondary microbiome (as Propiol Bacterium is present in

40% on the skin) consists of small numbers of many
species that may not be widely shared by individuals

Every part of
the human
body has a
different type
of bacteria

The reason for the different types of bacteria compared to the
organs, ear, skin, vagina, intestine.
Microbiota of the Skin
Skin; The largest organ of the human body, and it is considered the
first line of defense for the body if it is not affected by wounds
The resident microbiota of the skin consists primarily
of bacteria and fungi—as many as 300 different
species, depending on the anatomical location
‫انو بعض األجزاء بجسمنا بتكون مكشوفة فبيختلف انواع الباكتيريا فيها مقارنة بالعضو او‬
....‫الجزء الغير مكشوف‬
The most common bacteria on the skin are species of
Staphylococcus (especially S. epidermidis and other
coagulase-negative staphylococcia), Corynebacterium,
and Propionibacterium )The most common thing on the skin is
bacteria and fungi( Dr. Waleed Al Momani
The number and variety of microorganisms present on the skin
depend on many factors, such as:
Anatomical location
Amount of moisture present=>( some Bacteria prefer moisture)
pH=>(Some of them prefer the basic medium, some are acidic, and some are
neutral)
Temperature=>(Some like hot, some cold, and some moderate)
Salinity=>;(Some of them like salty mediums such as staphylococcus and
some prefer very high salinity and may reach 6.5 and above)
Presence of chemical wastes such as urea and fatty acids
Presence of other microbes, which may be producing
 toxic substances=>
‫في بعض الباكتيريا بتعيش على نفس المكان لكن وحدة منهم حتفرز مادة سامة تقتل الباكتيريا االخرى و‬
‫حتمنعها من العيش بهالمكان مثال‬
gram (-ve) Kill gram(+ve) or the opposite
Microbiota of the Ears and Eyes
The middle ear and inner ear are usually sterile,

whereas the outer ear and the auditory canal contain
the same types of microbes as are found on the skin.
(of the individual ; because each Individual has a different normal

flora from the other).
Sterile; No Microbes

Microbiota of the Respiratory Tract
The respiratory tract can be divided into the upper

Respiratory tract and the lower respiratory tract.
The Upper respiratory tract consists of the nasal

passages and the throat (pharynx). The most
common normal flora here
The lower respiratory tract consists of the larynx

(voice box), trachea, bronchi, bronchioles, and lungs.
Microbiota of the Oral Cavity (Mouth) The most
complicated place because they grow a large number of microbes because
they provide the right conditions to live aerobic and aerobic
The anatomy of the oral cavity (mouth) affords shelter for

numerous anaerobic and aerobic bacteria.
The list of microbes that have been isolated from

healthy human mouths includes:
The types of bacteria that are found in oral cavity Gram Gram-
positive and Gram negative bacteria (both cocci and bacilli),
spirochetes, and sometimes yeasts, mouldlike organisms,
protozoa, and viruses. The bacteria include species of
Actinomyces, Bacteroides, Borrelia, Corynebacterium,
Fusobacterium,

Microbiota of the GI Tract
(microbiota of esophagi, stomach, small & large
intestine and the accessory gland )
The GI tract (or digestive tract) consists of a long tube

with many expanded areas designed for digestion of food,
absorption of nutrients, and elimination of undigested
materials.
Excluding the oral cavity and pharynx, which have already

been discussed, the GI tract includes the esophagus, stomach,
{small intestine, large intestine (colon), and anus.}=>full of
microbe
Accessory glands and organs of the GI system include the

salivary glands, pancreas, liver, and gallbladder.
There is one bacterium—a Gram-negative bacillus
named Helicobacter pylori—that lives in some
people’s stomachs and is a common cause of ulcers.
• {Usually there is few type of bacteria can live in the stomach

because of its environment (very acidity less than 3 ph) and it isn’t
favorable for bacteria except the acid bacteria like(Helicobacter
bacteria which cause the stomach ulcer, even this one cant hold
out the acidity but it has ability to produce urease enzyme which
increase the ph around the bacteria (to 5.5 ph by cleaves the
ammonia) which is suitable for helicobacter to live )}.

• A few microbes, enveloped by food particles,
manage to pass through the stomach during
periods of low acid concentration.
• Also, when the amount of acid is reduced in

the course of diseases such as stomach
cancer, certain bacteria may be found in
the stomach.
The colon (contain the largest genetic diversity of
microbiome because it consider optimal environment for
bacteria to growth it contain nutrition and atmospheric
condition ) contains as many as 500 to 600 different
species— primarily bacteria.
Bacteria found in the GI tract include:

Actinomyces, Bacteroides, Clostridium, Enterobacter,
Enterococcus, Escherichia, Klebsiella, Lactobacillus, Proteus,
Pseudomonas, Staphylococcus, and Streptococcus.
Also, many fungi, protozoa, and viruses can live in the colon

Microbiota of the GU Tract
The GU tract (or urogenital tract) consists of the urinary

tract (kidneys, ureters, urinary bladder, and urethra)
and the various parts of the male and female reproductive
systems.
The healthy kidney, ureters, and urinary bladder are

sterile (organism free). So any growth of any
microbe inside them be as indication of a disease
(urinary tract infection).
However, the distal urethra (the part of the urethra farthest
from the urinary bladder) and the external opening of the
urethra harbor many microbes, including bacteria, yeasts, and
viruses.

The reproductive systems of both men and women are
usually sterile, with the exception of the vagina
(having microbiome in the vagina is essential and
healthy, the absent of them can diagnoses as infections
especially the absent of Lactobacillus)
The microbiota varies with the stage of sexual development.

(the existence of normal flora in the vagina is depend on
sexual development {hormonal change} on puberty and pre-
puberty and menopause)
‫"تضم كل مرحلة بكتيريا مختلفه باالعتماد على التغيرات الهرمونيه التي تؤثر علي‬
‫الطبيعه الحمضية التي تعتبر عامل مهم جدا في تحديد نوع البكتيريا المتواجده في المكان‬
."‫\البيئة‬
Bacteria found in the vagina include species of Actinomyces,
Bacteroides, Corynebacterium, Klebsiella, Lactobacillus,
Mycoplasma, Proteus, Pseudomonas, Staphylococcus, and
Streptococcus Dr. Waleed Al Momani
Beneficial and Harmful Roles of Indigenous Microbiota(31:08-33:12)
Certain of our intestinal bacteria are beneficial to us in that

they produce useful vitamins and other nutrients
Microorganisms of the normal flora may aid the host (by

competing for microenvironments more effectively than such
pathogens as Salmonella spp or by producing nutrients the
host can use)
May harm the host (by causing dental caries, skin abscesses, or
other infectious diseases)
May exist as commensals (inhabiting the host for long

periods without causing detectable harm or benefit).
Microbial Antagonism
The term microbial antagonism means “microbes

versus microbes” or “microbes against microbes

Microbial Antagonism part of defense mechanism
1. Competition for nutrition

‫ تستطيع التغلب على االنواع االخرى في‬normal flora ‫ غالبا‬, ‫التنافس للحصول على الغذاء‬
‫ لسبب بسيط انها مقيمة في المكان بالتالي‬microenvironment ‫الحصول على الغذاء من ال‬
.‫) من التكاثر‬pathogens( ‫\ الغزاة‬invaders ‫تمنع‬
2. Competition for space

attachment ‫ الدخول الى الجسم يلزمه ارتباطه مع السطح‬pathogens ‫حتى يستطيع اي‬
.‫ محتلة المكان بالتالي ال يستطيع االرتباط وال يستطيع التكاثر‬normal flora ‫بما انه‬
3. Production of antibiotics and bacteriocins.

Normal flora can produce antibacterial substance which kill the
invaders.

Opportunistic Pathogens
Many members of the indigenous microbiota

waiting for the opportunity to cause infections
If the normal microbiome characterizes health,

alterations in the microbiome can signify disease, a
relationship we are only beginning to understand.

Microbiome research has introduced a new
concept— disease caused by a community of
organisms rather than a single species of bacteria
We are now at the forefront of a new era of defining
infectious diseases.
• As we know previously
• One species of bacteria=> can cause one type of disease
• BUT now it consider that
• More species of bacteria =>can cause one type of disease which is called
the super infection or the polymicrobial infections

Biotherapeutic Agents
Indigenous microbiota is upset by:
Antibiotics, other types of chemotherapy, or changes in pH,

many complications may result.
Bacteria and yeasts that are ingested to reestablish and

stabilize the microbial balance within our bodies are called
biotherapeutic agents or probiotics.

‫• في بعض االحيان نتيجة االستخدام الخاطئ للمضادات الحيوية قد تختفي ‪normal‬‬
‫‪ flora‬بالتالي تصبح المساحه خالية امام البكتيريا الضارة للتكاثر‪ ,‬يمكن تعويض ذلك‬
‫من خالل اعطاء كبسوالت تحوي بكتيريا نافعه معروف عدم تسببها باحداث‬
‫مرض(‪ )biotherabeutic=> probiotics‬او مواد غذائية ُمدعمة بالبكتيريا‬
‫النافعه مثل ‪ lactopacillus‬حيث انها تفيد في تجديد ورفع مستوى البكتيريا النافعه‪.‬‬
‫‪ <= Preprobiotics‬تزويد المريض بمواد غذائية تستخدمها ‪ normal flora‬مثل االلياف‬ ‫•‬
‫‪fibers‬‬
‫‪• In the cases of big loss of normal flora we can use fecal‬‬
‫?‪transplant, HOW‬‬
‫‪By treatment the faeces from all pathogens and then reinjection in‬‬
‫‪the intestines‬‬
Disruption of the normal microflora (commonly
referred to as dysbiosis) can lead to disease by the
elimination of needed organisms or allowing the
growth of inappropriate bacteria
Shifts in the skin microbiome wound infections

and dermatitis.
Alteration in the vaginal microbiome vaginitis.

‫‪Pathogen‬‬
‫‪Microbiota‬‬
‫‪AMPs‬‬
‫‪IgA‬‬
‫‪Mucin‬‬
‫‪B‬‬ ‫‪A‬‬
‫يمثل الجانب ‪ B‬الوضع الطبيعي حيث تشكل ‪ Normal flora‬طبقه تمنع ‪pathogen‬‬
‫من االرتباط على سطح الخاليا وتشكيل مرض‪ ،‬بينما الجانب ‪ A‬يمثل انخفاض عدد‬
‫‪ normal flora‬بحيث تمكن ‪ pathogen‬من االرتباط وتسبيب مرض‪.‬‬
Microbial Communities (Biofilms)
‫تجمع بكتيري لعدد كبير من البكتيريا(نوع او اكثر) التي تصبح قادرة على مقاومة المضادات‬
infections ‫) بالتالي تصبح لديهم القدرة على عمل‬drug resistance( ‫الحيوية‬
Can increase the possibility of infections .
In nature, microbes are often organized into

complex and persistent communities of assorted
organisms called biofilms.
Biofilms=>endocarditis, cystic fibrosis, middle

ear infections, kidney stones, periodontal disease,
and prostate infections.

Synergism (Synergistic Infections)
‫تعاون بين نوعين من البكتيريا او اكثر الحداث عدوى معينة‬
Sometimes, two (or more) microorganisms may

“team up” to produce a disease that neither could
cause by itself. This is referred to as synergism or a
synergistic relationship.
The diseases are referred to as synergistic infections,

polymicrobial infections, or mixed infections.

Soil Microbes
A variety of human pathogens live in soil, including:
Various Clostridium spp.=> spore former anaerobic

bacteria cause tetanus disease.
The spores of Bacillus anthracis => spore former

cause antherix disease .
Various yeasts

The types and amounts of microorganisms living in soil
depend on many factors, including:
The amount of decaying organic material,
Available nutrients,
Moisture content=> bacteria spore former can beat it e.g.

clostridium & bacillus antrades
Amount of oxygen available,
pH, temperature,
The presence of waste products of other microbes.

Infectious Diseases of Farm Animals
zoonotic ‫ من االمراض المعدية تنتقل الى االنسان من الحيوان و تُسمى‬%70
.) ‫ (من الحيوان الى االنسان والعكس غير صحيح‬disease
‫ اي دراسة يتم‬:)one health( ‫ بمصطلح‬infectious disease ‫يتم التعامل مع‬
‫ مثالً عند دراسة المضادات‬،‫اجرائها على الحيوانات تُستكمل بنفس الدراسة على االنسان‬
‫الحيوية على الحيوان النها بطبيعة الحال تنعكس على االنسان كونه مستهلك للحيوان‬
‫غاية في االهمية للتغلب على‬one health ‫بالتالي من الممكن انتقالها اليه لذلك مفهوم ال‬
‫هذا النوع من االمراض‬
Farmers, ranchers, and agricultural microbiologists are

concerned about the many infectious diseases of farm
animals— diseases that may be caused by a wide variety of
pathogens (e.g., viruses, bacteria, protozoa, fungi, and
helminths)
Microbes cause many diseases of farm animals, wild animals,

zoo animals, and domestic pets.

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INTRODUCTION

Weam Aljbaly & Nedaá Ashour

DR. WALEED AL MOMANI, MLT, PHD

only with the use of various types of microscopes with only

“microbiology considers to be one of the biological science, we can define it as simple

Dr. Waleed Al Momani

The general feature of microorganisms:

 Indigenous microbiota. (the body has many organisms in or on

Dr. Waleed Al Momani

Human pathogens have existed for thousands of

** How we can determine if the resulting effect happen by bacteria

The father of microbiology

Dr. Waleed Al Momani

 life can arise spontaneously from nonliving

Dr. Waleed Al Momani

 Francesco Redi debunk the spontaneous

Dr. Waleed Al Momani

2. The microorganism must be isolated from a

3. The isolated microorganism must cause the

4. The microorganism can be reisolated from the

Dr. Waleed Al Momani

 Golden Age of microbiology 1875-1918 )The most

Dr. Waleed Al Momani

 The importance of medical microbiology as an active field

DR. WALEED AL MOMANI, MLT,

Dr. Waleed Al Momani

Two major categories of microbes:

Acellular microbes (infectious particles)

Dr. Waleed Al Momani

Dr. Waleed Al Momani

1. To learn about the structure of microorganisms

2. Discuss the ways in which microbes and their cells reproduce

Dr. Waleed Al Momani

Metabolism refers to all of the chemical reactions that occur

Note: metabolism is divided to anabolism and catabolism

Dr. Waleed Al Momani

EU section mean true nucleus

Eukaryotic cells possess a true nucleus, whereas prokaryotic

Bacteria and Archaea, are called prokaryotes or prokaryotic

Dr. Waleed Al Momani

Viruses are composed of only a few genes protected by a

Viruses depend on the energy and metabolic machinery of a

Because viruses are acellular (not composed of cells), they are

Dr. Waleed Al Momani

These factors must be known before one can determine or

Dr. Waleed Al Momani

Dr. Waleed Al Momani A typical eukaryotic animal cell

↳ ‫ ﺑﻌﺾ أﻧﻮاع اﻟﺒﻜﺘﯿﺮﯾﺎ ﻻ ﺗﺤﺘﻮي ﻋﻠﻰ‬Cell wall

Dr. Waleed Al Momani

Prokaryotic cells are about 10 times smaller than eukaryotic

Reproduction of prokaryotic cells is by binary fission

Embedded within the cytoplasm of prokaryotic cells are a

Dr. Waleed Al Momani

Dr. Waleed Al Momani

Chemically, the cell membrane consists of proteins and

Many enzymes are attached to the cell membrane, and

Mesosomes—are foldings of the cell membranes—where

Dr. Waleed Al Momani

The prokaryotic c h r omo s ome usually consists of a single,

The chromosome is suspended or embedded in the

The DNA-occupied space within a bacterial cell is sometimes

Dr. Waleed Al Momani