Clinical Microbiology/Bacteriology Lec:
- Species: First name (Jude Anthony)
2 Taxonomy and Prokaryotes
Taxonomy
- comes from Greek word “taxes” means
arrangement and “nomos” means law
- An area of biological science comprising
three distinct, but highly interrelated,
disciplines that include classification,
nomenclature and identification
- Based on the similarities and
differences in genotype (genetic make
up) and phenotype
Carl von Linne
- Carolus Linnaeus developed rules in
taxonomy
DNA sequence – genotype
Colony morphology: Swarming - phenotype
Shape cocci – phenotype
Arrange in chain – phenotype
I. Classification
- Organization of microorganisms that
share similar morpho, physio and gen
traits into specific groups or taxa
Domain – kingdom – division – class –
order – family – genus – species –
subspecies (under it are serotype and
biotype)
- Serotype – based on serological
characteristic (define antigen found on
surface of the cell) ex. RBC
- Biotype – based on biochemical
characteristics
- Epithet – proper word for the name of
species
- Family, Genus, Species, Subspecies
(serotype and biotype) – important in
clinical bacteriology
- Family: synonymous to Clan
- Family: Clan
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- Genus: Family name (Trinidad)
II. Nomenclature
- Naming of microorganism according to
the established rules and guidelines
that developed by the International
Code of Nomenclature of Bacteria or
the Bacteriological code
- Family name: capitalized and has an “-
aceae”
- Genus: capitalized
- Species: lower case
- Example: Staphylococcus aureus
(computerized, italicized) /
Staphylococcus aureus (handwritten)
- Do not abbreviate scientific names in
answering
Take note:
- Sp. (singular), spp. (plural)
- When bacteria are referred to as a
group, neither be capitalized nor
underlined (ex. staphylococci)
III. Identification
- Process by which a microorganism key
features are describe
- Is the process of discovering and
recording the traits of organism so that
they may be placed in an overall
taxonomic scheme
- Phenotypic or genotypic characteristics
- The more specific is genotypic
characteristics determining the DNA
material of the org wherein it is
UNIQUE.
- Phenotypic is not specific because more
species distinguish same characteristics
(1) Genotypic characteristics
- Related to the organism’s genetic
makeup
 - Example: base sequencing of DNA or periplasm (gram negative bacteria only)
RNA to measure the degree of and plasma membrane
relatedness
Gram negative Gram positive
(2) Phenotypic characteristics
outer membrane M-protein
- Includes readily observable
porin Teichoic acid
characteristics and those characteristics
Peptidoglycan (thin) Peptidoglycan (Thick)
that may require extensive analytic
Porins (moves Lack porins,
procedures to be detected antimicrobial product lipopolysaccharide
- Examples: colony morphology, staining, from the bacteria)
nutritional requirements, biochemical Lipopolysaccharide
and susceptibility tests

Major Characteristics Used in Taxonomy:

1. Classical characteristics
- Useful in routine determination and
phylogenetic information –
morphology, physiology and
metabolism, ecology and genetic
analysis
2. Molecular charteristics
- Based on the study of nucleic acid
composition and proteins
- lab medicine deals with this
Prokaryotes, Eukaryotes, Archaeobacteria
Prokaryotes
- these are organisms that do not contain
a true nucleus
- also do not contain membrane-bound
organelles and all functions take place
in the cytoplasm and cytoplasmic
membrane
- Ex. Bacteria
Bacterial Structure
1. Cell envelope
- composed of an outer membrane (gram
negative bacteria only), cell well,
2. Cell wall
- Rigid structure that maintains the shape
of the cell
- Composed of disaccharide-
pentapeptide
- Subunits: also made up of teichoic acid
or lipoteichoic acid
- Chitin: fungi
- Cellulose: for plant cell wall
Functions of cell wall:
- To prevent bacterial cells from
rupturing when the osmotic pressure
inside the cell is greater than outside
the cell
- Serves as a point of anchorage for
flagella
- Determines the staining characteristics
of a species (determine the color of
stain of bac sp. in gram-positive –
violet/purple and gram-negative-pink or

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 red) because of different cell wall b. Gram-negative cell wall
component
Components:
a. Gram-positive cell wall
- Composed of very thick protective 1. Outer membrane
peptidoglycan (murein layer) - Composed of proteins phospholipids
- Consists of glycan chains of alternating and lipopolysaccharide (LPS)
N-acetyl-D-glucosamine (NAG) and N- 2. Inner membrane
acetyl-D-muramic acid (NAM) can be on - Is the reason for high susceptibility to
both gram + and negative** mechanical breakage
- Contains teichoic acid.
Teichoic acid is composed of:
(1) alcohol (glycerol or ribitol)
(2) phosphate - responsible for the
negative charge, because if an
organism has a negative charge, it
can evade the host response
- 2 kinds of TA :
(1) Lipoteichoic acid – bound to the cell
membrane
- (2) Wall teichoic acid – bound to the
peptidoglycan layer Other components of the Gram-negative cell
wall

- Has periplasmic space which involved in

peptidoglycans synthesis
- Has porins which contributes to the
permeability of cell wall
- Does not contain TA

3 regions of LPS

1. Lipid A – major constituent; endotoxin

2. Core polysaccharide
3. Antigenic O-specific polysaccharide
Function of Outer membrane:
Importance of LPS
- The strong negative charge of the outer - LPS is vital in evading the host defenses;
membrane is an important factor in
it contributes to the negative charge of
evading phagocytosis (monocyte,
the bacterial surface (stabilize
neutrophil: phagocytosis. basophil is
membrane structure
not) because of a phosphate charge of
the TA.
- Allows the hydrophilic compounds to
enter the cell through porins
- Acts as the barrier to toxic substances
from moving inside the cell

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 Properties Gram- Gram-
positive Cell negative Cell
Cell wall

Shape

TA
Periplasmic
space 3. Plasma (inner) membrane
Endospore - Deepest layer of the cell envelope;
Flagellar internal matrix of the cell
Surface - Made up of phospholipid bilayer with
Resistance to embedded proteins (lipoproteins) that
physical surrounds the cytoplasm
disruption
Resistance to
lysozyme
disruption
Sensitivity to
penicillin
Reproduction

c. Acid-fast cell wall

- Contains a waxy layer of glycolipids and
fatty acids (hydroxymethoxy acid or Functions of plasma membrane:
mycolic acid) bound to the exterior of
• Acts as mitochondria, golgi complexes
the cell wall – a strong hydrophobic
and lysosomes of eukaryotic cells
structure that affects the permeability
• Regulates transport of solutes across
of the cell wall
the membrane
- Hard to stain because of a waxy layer of
• Site for generation of chemical energy
glycolipids
(ATP)
- Once they are stain, they are difficult to
remove
- Ex: Mycobacterium tuberculosis Cytoplasmic Structures:
d. Absence of cell wall
- Contain sterols (substitute to the cell a. Ribosomes (nonmembrane structures)
wall) - Consists of RNA and proteins
- Ex. Mycoplasma and Ureaplasma - Site for protein biosynthesis: give the
- Pleomorphic: many shape because no cytoplasm a granular structure
rigid structure of cell wall b. Genome
- Consist of single, circular chromosome

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 - Appear as diffused nucleoid or
chromatin body is attached to a
mesosome (sac-like structure)
c. Plasmids
- Are extrachromosomal, double-
stranded elements of DNA that are
associated with virulence
- Located in the cytoplasm
- Serve as the site for the genes that code
for antibiotic resistance and toxin
production
- Can transform bacteria to become
pathogenic mostly gram-negative
bacteria
- Not essential for bacterial growth, so
bacteria cell may or may not contain
plasmid
Identify the bacteria:
d. Inclusion bodies
- Energy source or food-source of
bacteria
- Mainly polysaccharide, thus lessen the
osmotic pressure
- Examples of polyphosphate granules
are Babes-Ernst bodies
(Corynebacterium diphtheriae, bipolar
bodies (Yersinia pestis), Much’s
granules (Mycobacterium tuberculosis)
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e. Endospores/Asexual Spored (resistant
structures)
- Are small, dormant structures that
develop inside the bacterial cell as
means of survival against harsh
environmental condition
- Composed of dipicolinic acid and
calcium ions (calcium dipicolate)
- Produce within the vegetative stage of
some Gram-positive bacteria
- Types of spores according to their
location are:
(1) Terminal spore – Clostridium tetani
(2) Subterminal spore – Clostridium
botulinum
(3) Central spore – Bacillus anthracis
4. Cell Appendages
a. Glycocalyx
- Is an outward complex of
polysaccharide from the bacterial
surface and other cells
- Helps on the attachment of the bacteria
to surfaces of solid objects or tissue
- Composed of the capsule and slime
layer
- Function: Evade host response and
bacteria uses this as a appoint of
attachment
 - Majority of is made up of - Aid in attachment of bacteria to
polysaccharide surfaces
- D-glutamic acid: an amino acid made
Two Types of Pili:
up of proteins
Example: Bacillus anthracis is an (1) Sex pili
example of bacteria that is made up of - genetic material transport/coagulation
D-glutamic acid in its capsule; causative process (specifically the plasmid, an
agent of anthrax; has central spores extra DNA incorporated to another
• Capsule layer bacteria)
- organized material attached firmly to - NOT ASSOCIATED WITH THE
cell wall REPRODUCTION
- made up of polysaccharide polymers (2) Common/somatic pili
• Slime layer - attachment bacteria to surfaces
- Unorganized material loosely attached - virulence factor/organ of attachment
to cell wall Eukaryotes
- Inhibits phagocytosis or aid in the
adherence to host issue Archeobacteria
- found to be more closely related to
BOTH ARE STICKY
eukaryotic cells than to prokaryotic
b. Flagellum (organ of locomotion) - cell wall never contain peptidoglycan
- Exterior protein filament (flagellin) that - they do not have nucleus and
rotates and cause bacteria to be motile membrane bound organlles, but do
- Important in the survival (organism can contain gas vesicles
evade the response of the host) and the
Identify flagellum arrangement:
ability of bacteria to cause disease
(flagellum can go to the different parts
of the body)
- Gliding motility exhibited by the
cyanobacteria, myxobacteria,
cytophages
a. Monotrichous – SINGLE flagellum on
ONE end
b. Lopotrichous – TUFF/GROUP of
flagellum on ONE end of BOTH end
c. Amphitrichous – SINGLE flagellum on
BOTH ends
d. Peritrichous – SPREAD all over the
whole surface. Example: e. coli
e. Atrichous – WITHOUT flagellum
c. Pili (fimbriae)
- Hairlike, proteinaceous structures that
extend from cell membrane into the
external environment (2 um in length)

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