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Microbiology
Toxonomy &Cell Structure
What is Microbiology
Microbiology :
Is The branch of biology that deals
with microorganisms and their effects on other
living organisms. Microorganisms are those
organisms that are too small to see with the
naked eye and include things like bacteria, fungi,
and viruses.
Microbiology is Greek word mikros mean small;
bios mean life
Current classification of all forms of life based on
the genetic relatedness into 3 domains :
Archea
,Bacteria
Eucarya
Archea and Bacteria called Prokaryotes
Eukaryotes (Fugi , protista ,animal, plant and
human)
Prokaryotic Cells
Viruses
are not included in this classification as they •
are unique , metabolically inert organisms and
therefore replicate only within living cells.
Cell component
Nucleus
Extra-chromosomal DNA
Organelles in cytoplasm
Prokaryotes
no membrane, single circular
membrane bound, a number of
chromosome
individual chromosomes.
present in form of plasmid
Present as mitochondrial DNA
Non
Contain enzyme of respiration, sit
Cytoplasmic membrane
Eukaryotes
of phospholipids and DNA
synthesis
Mitochondria and chloroplast in
photosynthetic organisms
Semi-permeable layer not
possessing function
Cell wall
Rigid layer of peptidoglycan
No peptidoglycan
Sterols
Absent
Present
Ribosome
70 S in cytoplasm
80 S in cytoplasmic reticulum
Basis of Classification
• Phenotypic classification
 Morphological
 Anatomical
 Staining
 Cultural characteristics
 Nutrition
 Environmental factors
 Biochemical reactions
 Antigenic structure
• Genotypic classification
 DNA-DNA hybridization
 G+C content
Morphological classification
• Bacteria can be classified into six major groups on morphological basis.
1. TRUE BACTERIA
• Cocci – These are spherical or oval cells. On the basis of arrangement of
individual organisms they can be described as
– Monococci (Cocci in singles) – Monococcus spp.
– Diplococci (Cocci in pairs) – Streptococcus pneumoniae
–
–
–
–
Staphylococci (Cocci in grape-like clusters) – Staphylococcus aureus
Streptococci (Cocci in chains) – Streptococcus pyogenes
Tetrad (Cocci in group of four) - Micrococcus spp.
Sarcina (Cocci in group of eight)
Staphylococcus
tetrad
Streptococcus
Morphological classification
• Bacilli – These are rod-shaped bacteria. On the basis of arrangement of
organisms, they can be described as
– Diplobacilli
– Streptobacilli
– Palisades
– Chinese-letter form
– Coccobacilli
– Comma-shaped
bacilli
bifidobacterium
Coryneform bacteria
vibrio cholerae
Morphological classification
2. ACTINOMYCETES (actin- ray, mykesfungus)
These are rigid organisms like true
bacteria but they resemble fungi in
that they exhibit branching and tend
to form filaments.
They are termed such because of
their resemblance to sun rays when
seen in tissue sections.
Morphological classification
3. Spirochaetes
These are relatively longer, slender, non-branched
microorganisms of spiral shape having several
coils.
Morphological classification
4. Mycoplasmas
These bacteria lack in rigid cell wall (cell wall lacking) and
are highly pleomorphic and of indefinite shape.
They occur in round or oval bodies and in interlacing
filaments.
5. Rickettsiae and Chlamydiae
These are very small, obligate parasites, and at one time
were considered closely related to the viruses. Now,
these are regarded as bacteria.
• Capsule
– Capsulate– Streptococcus pneumoniae
– Non-capsulate – Viridans streptococci
• Flagella
– Flagellate –
• Monotrichous
• Lophotrichous
• Amphitrichous
• Peritrichous
– Aflagellate – Shigella spp.
• Spore
– Spore-forming – Bacillus spp.
– Non-sporing – Escherichia coli
Based on Staining reaction
GRAM’S STAIN •
Gram-positive cocci – Staphylococcus aureus –
Gram-negative cocci – Neisseria gonorrhoeae –
Gram-positive rods – Clostridium spp. –
Gram-negative rods – E. coli –
ACID FAST STAIN •
Acid-fast bacilli –Mycobacterium tuberculosis –
Non-acid-fast bacilli – Staphylococcus aureus –
Based on Cultural characteristics
• Extra growth factors requirements
– Fastidious – Hemophilus influenzae
– Non-fastidious – Escherichia coli
• Hemolysis on Sheep Blood Agar
– Alpha-hemolysis – Streptococcus pneumoniae
– Beta-hemolysis – Streptococcus pyogenes
• Utilization of carbohydrates
– Oxidative - Micrococcus
– Fermentative – Escherichia coli
Based on Cultural characteristics
• Growth rate
– Rapid growers– Vibrio cholerae
– Slow growers – Mycobacterium tuberculosis
• Pigment production
– Pigment producer – Staphylococcus aureus
– Pigment non-producer – Escherichia coli
Based on Nutrition
• Autotrophs
• Heterotrophs
Based on environmental factors
•
•
•
•
•
Temperature
Oxygen dependence
pH
Salt concentration
Atmospheric pressure
Based on environmental factors
1. Temperature
• Psychrophiles (15-200C) – Pseudomonas fluorescens
• Mesophiles (20-400C) – Escherichia coli, Salmonella enterica,
Staphylococcus aureus
• Thermophiles (50-600C)- Bacillus stearothermophilus
• Extremely thermophiles (as high as 2500C) -Archea
Based on environmental factors
2.
Oxygen dependence
• Aerobe (grow in ambient temperature, which contains 21% O2
and a small amount of CO2, 0.03%)
• Obligate aerobes – Strictly require O2 for their growth
(Pseudomonas aeruginosa)
• Microaerophilic (grow under reduced O2, 5-10% and
increased CO2, 8-10%)- Campylobacter jejuni, Helicobacter
pylori
Based on environmental factors
2. Oxygen dependence
• Facultative anaerobe (capable of growing either in presence or
absence of O2)- E. coli
• Obligate anaerobe – Clostridium spp.
• Capnophilic (require increased concentration of CO2, i.e., 510%) –
H. influenzae,
N. gonorrhoeae
• Aerotolerant
Based on environmental factors
3.
pH
• Acidophiles (Lactobacillus acidophilus)
• Alkaliphiles (Vibrio)
• Neutralophiles (pH 6-8)
Majority of the medically important bacteria grow best at neutral or
slightly alkaline reaction (pH 7.2-7.6)
Based on environmental factors
4. Salt concentration
• Halophiles
• Non-halophiles
Other ways of classification
•
•
•
•
•
Motile/Non-motile
Pathogenic/Non-pathogenic
Sensitive/Resistant (to particular antibiotic/ chemicals)
Lactose fermenter/Lactose non-fermenter
Bergey’s Manual of Determinative Bacteriology
–
–
–
–
Gram-negative eubacteria that have cell walls
Gram-positive eubacteria that have cell walls
Cell wall-less eubacteria: Mycoplasma
Archaeobacteria
Structure
• Structures external to the cell wall
1. Flagella
Flagella are whip-like filaments that act as
propellers and guide the bacteria towards
nutritional and other sources. Composed of
single protein called Flagellin.
Type of Flagellum
•
•
•
•
•
Flagella may be
located at one end Monotrichous
a single flagellum Lophotrichous
All over the outer surface Peritrichous
Located at the polar ends Amphitrichous
Fimbriae and pili
1-are fine, hair-like filaments, shorter than flagella,
that extend from the cell surface.
2- Pili found mainly on Gram-negative organisms
3- Composed of subunits protein, pilin.
4- mediate the adhesion of bacteria to receptors on
the human cell surface – a necessary first step in the
initiation of infection.
.
A specialized type of pilus,
the sex pilus, forms the attachment between
the male (donor) and the female (recipient)
bacteria during conjugation, when genes are
transferred from one bacterium to another.
THE STRUCTURES EXTERNAL TO THE
CELL WALL
AXIAL FILAMENTS
Anchored at one end of the spirochete.
Have a structure similar to flagella.
Filament rotation produces a movement of the
outer sheath. Propels the bacteria in a spiral
motion (corkscrew motion).
E.g. Treponema pallidum – syphilis
Borrelia burgdorferi – Lyme disease
Glycocalyx (slime layer)
1- is a polysaccharide
2-coating that covers the outer surfaces of many
bacteria
3-allows the bacteria to adhere frmly to various
structures, e.g. oral mucosa, teeth,heart valves and
catheters.
4-contribute to the formation of bioflms.
This is especially true in the case of Streptococcus
mutans
Capsule
1-An amorphous, gelatinous layer (usually more
substantial than the glycocalyx) surrounds the
entire bacterium.
2- it is composed of
polysaccharide, and sometimes
protein (e.g.anthrax bacillus).
The capsule is important
• It mediates the adhesion of bacteria to human
tissues or prosthesis such as dentures or
implants prerequisite
colonization and infection.
It hinders or inhibits phagocytosis; hence, the
presence of a capsule correlates with virulence.
The capsule is important
• It helps in laboratory identifcation of organisms
(inthe presence of antiserum against the capsular
polysaccharide the capsule will swell greatly – a
phenomenon called the quelling reaction).
• Its polysaccharides are used as antigens in certain
vaccines because they elicit protective antibodies
(e.g. polysaccharide vaccine of S. pneumoniae
THE CELL WALL
• Cell wall – a complex, semirigid structure
• Protects cell from adverse changes in the
outside environment.
• Almost all prokaryotes have cell walls.
• Major function is to prevent bacterial cells
from rupturing.
• Maintain the shape of the bacterium.
• Serve as point of anchorage for flagella.
THE CELL WALL
• Contributes to Pathogenecity
• Site of action of some antibiotics.
• Cell wall composition used to differentiate
major types of bacteria.
Cell Wall In Gram positive bacteria
• Peptidoglycan layer forms 50% of cell wall material.
• Peptidoglycan is responsible for cell wall rigidity.
• Peptidoglycan is formed of N-acetyl glucosamine and
N-acetyl muramic acid.
• Attached to each muramic acid molecule is a
tetrapeptide.
• Then the tetrapeptide chains are cross-linked
together by transpeptidase enzyme.
In addition to peptidoglycan, there is
teichoic acid which:
is highly immunogenic adheres the bacteria to
mucosal surfaces.
Lipoteichoic acid links peptidoglycan layer to
the cell membrane.
Gram-negative organisms
• Inner peptidoglycan layer forms only 5-10% of the cell
wall material.
• Outer membrane layer formed of
lipopolysaccharides:
• The lipid portion (lipid A) is called endotoxin. It is
released when the bacterial cells are lysed. It is highly
toxic.
• The polysaccharide portion is called somatic or O
antigen. It is highly immunogenic.
• The space between the inner and outer layers is
called periplasmic space which contains beta
lactamase enzyme that degrades beta lactam
antibiotics.
Lipoprotein molecules cross-link the peptidoglycan
layer and the outer membrane
Gram Positive Cell
Grame Negative Cell
2 Layers
1-Inner cytoplasmic
membrane
2-Outer thick peptidoglycan
layer (60-100%)
3 Layers
1-Inner cytoplasmic membrane
2- Thin peptidoglycan layer (5-10%)
3-Outer membrane with
Lipopolysaccharide(LPS)
Low lipid content
High lipid content
No endotoxine (except Listeria
monocytogenes)
Endotoxine(LPS). Lipid A
No periplasmic space
periplasmic space
No porin channel
porin channel
Virulence to Lysozyme and
penicillin attack
Resistto Lysozyme and penicillin
attack
In acid fast bacteria
These bacteria contain high concentration of
mycolic acid and wax in their cell wall.
These bacteria are not stained by Gram stain but
stained by Ziehl-Neelsen stain.
Example: Mycobacterium tuberculosis.
Bacteria with defective cell walls
Mycoplasma spp
Lacks cell wall.
Pleomorphic in shape.
Not affected by penicillin.
Not stained by Gram stain.
The only bacteria that contains sterol in its cell
membrane.
Protoplast , Spheroplast, L-Form
• When bacterial cell wall is lost under the
effect of certain conditions like penicillin:
• Gram positive bacteria form protoplasts.
• Gram negative bacteria form spheroplasts.
• If protoplasts and spheroplasts grow and
divide, they are called L-forms.
• Unlike mycoplasma, L-forms can revert to the
parental form on removal of the cell wall
inhibitor.
Cytoplasmic membrane
The cytoplasmic membrane lies just inside the
peptidoglycan layer of the cell wall and is a ‘unit
membrane’ composed of a phospholipid bilayer
similar in appearance to that of eukaryotic cells.
However, eukaryotic membranes contain sterols,
whereas prokaryotes generally do not (the only
exception being mycoplasmas.
The membrane has the following
major functions
active transport and selective diffusion of molecules
and solutes in and out of the cell
.• electron transport and oxidativephosphorylation
in aerobic specie.
• synthesis of cell wall precursors
• secretion of enzymes and toxins
• supporting the receptors and other proteins of
The chemotactic and sensory transduction systems
Mesosome
This is a convoluted
invagination of the
cytoplasmic membrane
that functions as the origin
of the transverse septum
that divides the cell in half
during cell division.
It is also the binding site of
the DNA that will become
the genetic material of
each daughter cel
Cytoplasm
The cytoplasm comprises an inner, nucleoid region
(composed of DNA), which is surrounded by an
amorphous matrix that contains ribosomes,
nutrient granules, metabolites and various ions.
Nuclear material or nucleoid
Bacterial DNA comprises a single, supercoiled,
circular chromosome that contains about 2000
genes(It is analogous to a single, haploid
chromosome.)
During cell division, it undergoes semiconservative
replication bidirectionally from a fixed point.
Electron micrograph of a thin section of
Neisseria gonorrhoeae showing the
organizational features of prokaryotic cells.
Note the electron-transparent nuclear region
(n) packed with DNA fibrils, the dense
distribution of ribosomal particles in the
cytoplasm, and the absence of intracellular
membranous organelles
Ribosomes
Ribosomes are the sites of protein synthesis.
Bacterial ribosomes differ from those of eukaryotic
cells in both size and chemical composition.
They are organized in units of 70S, compared with
eukaryotic ribosomes of 80S. These differences are
the basis of the selective action of some antibiotics
that inhibit bacterial, but not human.
Cytoplasmic inclusion granules
The cytoplasm contains different types of
inclusions, which serve as sources of stored
energy; examples include polymetaphosphate,
polysaccharide and β-hydroxybutyrate.
Bacterial spore
Spores are formed in response
to adverse conditions by the
medically important bacteria
that belong to the genus
Bacillus (which includes the
agent of B.anthrax) and
Clostridium (which includes the
agents of
Cl. tetanus and CL.botulism).
These bacteria sporulate (form
spores) when nutrients, such as
sources of carbon and nitrogen,
are scarce