Fundamentals of Microbiology 1st BIMO

Microbiology Dr. Abueva LEC # 1

09/22/2021

● transmit diseases in plants

● obligate intracellular but acellular parasites of plants
OUTLINE
I. Microbiology PRIONS
II. Viroids and Prions
III. Prokaryotes vs Eukaryotes
● Infectious proteinaceous agents
IV. The Major Subdivision of Prokaryotes ● Cellular form of the prion protein (PrPc) is encoded
V. Optical Methods by the host’s chromosomal DNA
VI. Bacteria ● Capable of causing chronic neurologic disease (man
A. Shapes of Bacteria and animals)
B. Bacterial Structures
VII. Different Kinds of Staining Method
VIII. Overview of Medically Important Bacteria
IX. Classification of Bacteria
X. Criteria for Identification of Bacteria

Must Know Book Lecturer

I. MICROBIOLOGY

● Microbiology is the study of microorganisms, a large

and diverse group of microscopic organisms that Table 1. Characteristics of Viruses, Viroids, and Prions
exist as single cells or cell clusters; it also includes
viruses, which are microscopic but not cellular. III. PROKARYOTES vs EUKARYOTES
MAJOR MICROBIAL GROUPS
1. Viruses
○ not considered cells, acellular
○ either DNA or RNA
○ non-motile
○ nature of outer surface are:
■ protein capsid (naked virus)
■ lipoprotein envelope (envelope
virus)
2. Bacteria
○ both DNA and RNA
○ prokaryotic cell
○ rigid wall contain peptidoglycan
○ some are motile
○ replicates through binary fission
3. Fungi
○ both DNA and RNA
○ eukaryotic cell
○ rigid wall contain chitin
○ non-motile Additional info: See appendix TABLE 2. Prokaryotes vs Eukaryotes
○ replicates through budding or mitosis
4. Protozoa and Helminths (Parasites) IV. The Major Subdivisions Within the Prokaryotes
○ both DNA and RNA
○ eukaryotic cell ● Bacteria
○ it has a flexible membrane ● Archaebacteria
○ most are motile o A trait shared by archaebacteria and
○ replicates through mitosis eukaryotes is the presence of introns within
See appendix TABLE 1. CHARACTERISTICS OF genes.
MICROBIAL GROUPS o This common trait has led to the suggestion
that the eukaryotic nucleus may have arisen
II. VIROIDS AND PRIONS from an archaebacterial ancestor.

VIROIDS Protists
● small, single-stranded, covalently closed circular ● The “true nucleus” of eukaryotes is only one of their
RNA molecules existing as highly base-paired rod distinguishing features.
like structures

TG (6): CORPIN, LAUZON, PREJULA, RUEDA 1 of 16

 ● Microbial eukaryotes—protists—are members of the ○ 3 or 4 lenses with a range of different
4 following major groups: algae, protozoa, fungi, and magnification
slime molds. ○ 4 separate lenses that magnify the image (4X,
10X, 40X and 100X) depending on the objective
Algae in use.
● The term algae has long been used to denote all 2. Nosepiece
organisms that produce O2 as a product of ○ A circular plate with 4 objective lenses that can
photosynthesis. be rotated into position for different
● Contain chlorophyll in the photosynthetic membrane magnifications.
of their subcellular chloroplast. 3. Diaphragm
● A number of algae produce toxins that are poisonous ○ Adjusts the amount of light illuminating the slide
to humans and other animals. ○ Use just enough light to illuminate the object on
○ Example: Dinoflagellates, a unicellular alga, the slide and give good contrast.
cause algal blooms, or red tides, in the 4. Stage
ocean. ○ a platform that holds the slide for observation
5. Slide
Protozoa ○ A thin piece of glass that holds the specimen
6. Lamp
● Are unicellular non photosynthetic protists.
○ provides light to illuminate the specimen,
● The most primitive protozoa appear to be flagellated
sometimes used with a mirror
forms.
7. Eyepiece lens
● From flagellated protozoa appear to have evolved the
○ part of the microscope through which you look
ameboid and the ciliated types; intermediate forms
8. Arm
are known that have flagella at one stage in the life
○ supports and connects the eyepiece lens to the
cycle and pseudopodia (characteristic of the ameba)
base
at another stage.
○ also a handle for carrying
● Sporozoa, a fourth major group of protozoa, are strict
9. Focus wheel
parasites that are usually immobile; most of these
○ used to bring the object in and out of focus
reproduce sexually and asexually in alternate
10. Coarse Adjustment Knob
generations by means of spores.
○ a rapid control which allows for quick focusing
by moving the objective lens or stage up and
Fungi
down.
● Are non photosynthetic protists growing as a mass of ○ It is used for initial focusing.
branching, interlacing filaments (“hyphae”) known as 11. Fine Adjustment Knob
a mycelium. ○ A slow but precise control used to fine focus the
● Mycelial forms are called molds. image when viewing at the higher
● Major subdivisions (phyla) of fungi are: magnifications.
○ Chytridiomycota 12. Base
○ Zygomycota (the zygomycetes) ○ supports the microscope
○ Ascomycota (the ascomycetes)
○ Basidiomycota (the basidiomycetes)
A. LIGHT MICROSCOPE
○ Deuteromycetes (or imperfect fungi)
● Yeast – fungus grows simply as a single cell ● The resolving power of the light microscope under ideal
● Most fungi of medical importance grow dimorphically: conditions is about half the wavelength of the light being
○ exist as a MOLD at ROOM used.
TEMPERATURE but as a YEAST at BODY ● Resolving power is the distance that must separate two
TEMPERATURE point sources of light if they are to be seen as two distinct
images.
Slime Molds
● These organisms are characterized by the presence, TYPES OF LIGHT MICROSCOPES:
as a stage in their life cycle, of an ameboid 1. Bright-Field Microscope
multinucleate mass of cytoplasm called a ● Most commonly used
plasmodium. ● Consists 2 series of lenses
● The plasmodium of a slime mold is analogous to the o Objective
mycelium of a true fungus. o Ocular Lens
● The growth of slime molds depends on nutrients ● Employ a 100-power objective lens with a 10-power
provided by bacterial or, in some cases, plant cells. ocular lens, thus magnifying the specimen 1000
● Reproduction of the slime molds via plasmodia can times
depend on intercellular recognition and fusion of cells ● Differences in contrast between the specimen and
from the same species. the surrounding medium makes them visible.
● Dyes (stains) can be used to stain cells or their
V. OPTICAL METHODS organelles to increase their contrast so that they can
be seen.
Microscope – powerful tool in cell biology and microbiology
2. Phase Contrast Microscope
PARTS & FUNCTION ● Developed to improve contrast differences between
1. Objective Lenses cells and the surrounding medium, making it possible
to see living cells without staining them.

MICRO Fundamentals of Microbiology 2 of 16

 ● Effect is amplified by a special ring in the objective
lens of a phase contrast microscope, leading to the
formation of a dark image on a light background.
3. Dark-field Microscope
● Lighting system has been modified to reach the
specimen from the sides only
● Creates a “dark field” that contrasts against the
highlighted edge of the specimens.
● Resolution is quite high.
● For Treponema pallidum, a spirochete.
4. Fluorescence microscope
● Used to visualize specimens that fluoresce.
● Widely used in clinical diagnostic microbiology.
o Example: Detection of Mycobacterium
tuberculosis
● Principal use of fluorescence microscopy is a
diagnostic technique called the fluorescent-antibody
(FA) technique or immunofluorescence.
o Example: Detection of Legionella
pneumophila
5. Differential interference contrast (DIC) Microscope
● Employ a polarizer to produce polarized light.
● Intensifies subtle differences in cell structure.
● Spores, vacuoles, and granules appear three-
dimensional.
● Useful for observing unstained cells because of its
ability to generate images that reveal internal cell
structures.
B. ELECTRON MICROSCOPE
● Detailed structures of prokaryotic and eukaryotic cells
can be observed due to its high resolving power.
2 TYPES OF ELECTRON MICROSCOPES:
1. Transmission Electron Microscope (TEM)
● Many features in common with the light microscope
● First to be developed.
● Uses a beam of electrons projected from an electron
gun and directed or focused by an electromagnetic
condenser lens onto a thin specimen.
● Images can be recorded on photographic film.
● Can resolve particles 0.001 µm apart.
● Viruses with diameters of 0.01–0.2 µm can be easily
resolved.
2. Scanning Electron Microscope (SEM)
● Has a lower resolving power than the TEM
● Provides three-dimensional images of the surface of
microscopic objects.
C. CONFOCAL SCANNING LASER MICROSCOPE
● Couples a laser light source to a light microscope.
● Equipped with computer software to assemble digital
images for subsequent image processing.
● Images obtained from different layers can be stored
and then digitally overlaid to reconstruct a three-
dimensional image of the entire specimen.
D. SCANNING PROBE MICROSCOPE
● Measures surface features
● Atoms or molecules on the surface of a specimen can
be viewed
MICRO Fundamentals of Microbiology
o Examples: Scanning tunneling microscope &
Atomic force microscope
VI. BACTERIA
● unicellular. contains both DNA and RNA
● May be free-living, saprophytic, parasitic or
pathogenic.
Nomenclature:
● Binomial system is used for the nomenclature of
bacteria. It is a two-name system composed of the
genus and species. (e.x. Staphylococcus aureus)
● the Genus should always have its first letter
capitalized, while the species should never be
capitalized.
● Abbreviation: Its name can be abbreviated using the
uppercase form of the genus, followed by a period
and the full name of the species. (e.x. S. aureus)
1. Bacterial Structure
● Prokaryotes
● Single cell structure, single circular chromosome
● Transcription (mRNA synthesis) and Translation
(protein synthesis) occur in the cytoplasm.
2. Bacterial Morphology
● Size: 0.2 – 2.0 um
● Distinct shape
● Gram staining
3. Bacterial Ultrastructures
● Single chromosome
● Circular DNA
● Plasmids
o Has something to do with Antibiotic Resistance
or carrier of virulence genes of certain bacteria
4. Cell Division
● Binary fission
● In rod-shaped bacterium (eg. E.coli), cells elongate
to form a partition (septum) which results in the
inward growth of cytoplasmic membrane until the two
daughter cells are pinched off. The chromosomes are
distributed equally
5. Cell groupings
● If the cells remain temporarily attached aſter division,
certain characteristic groupings result.
● Depending on the plane of division and the number
of divisions through which the cells remain attached
● Coccal forms: chains (streptococci), pairs
(diplococci), cubical bundles (sarcinae), grape-like
clusters (staphylococci), or flat plates
● Rods: pairs or chains
Shapes of Bacteria
● Shape is used to identify bacteria. It is determined by
the mechanism of cell wall assembly.
● Bacterial shape usually can be determined with
appropriate staining and a light microscope.
Types:
a. Round (coccus)
b. Rod-like (bacillus)
c. Spiral
● Cocci and bacilli often grow in doublets (diplococci)
or chains (streptococci). Cocci that grow in clusters
are called staphylococci.
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Figure 1. Shapes of Bacteria
BACTERIAL STRUCTURES
1. Bacterial Nucleus - contains the bacterial chromosome;
generally called the nucleoid.
2. Cytoplasmic Structures - can be chromosomal or non
chromosomal.
● Bacteria chromosomes - composed by a set of
genes. Chromosomes contain all genes essential for
the viability, growth and replication of the
microorganism.
● Plasmids - extrachromosomal or non-chromosomal
double stranded DNA. It is capable of self replication
but not essential for bacterial growth. Genes carried
by the plasmids codes for antibiotic resistance,
virulence factors and toxin production.
3. Cell envelope - these structures protect the organism
from a hostile environment.
4. The Cell Membrane
● Structure: may also be called the cytoplasmic
membrane. It is a typical “unit membrane” composed
of phospholipids and upward of 200 different kinds of
proteins.
● Function:
i. Permeability and transport
ii. Electron transport and oxidative
phosphorylation
iii. Excretion of hydrolytic exoenzymes and
pathogenicity proteins
iv. Biosynthetic functions
v. Chemotactic systems
5. The Cell Wall
● The bacterial cell wall owes its strength to a layer
composed of a substance variously referred to as
murein, mucopeptide, or peptidoglycan. (all are
synonyms).
Most bacteria are classified as gram-positive or gram-
negative. The gram staining procedure was developed by
Hans Christian Gram.
● Gram stain depends on the ability of certain bacteria
(the gram-positive bacteria) to retain a complex of
crystal violet (a purple dye) and iodine after a brief
wash with alcohol or acetone.
● Gram-negative bacteria do not retain the dye–iodine
complex and become translucent, but they can then
be counterstained with safranin (a red dye). Thus,
gram-positive bacteria look purple under the
microscope, and gram-negative bacteria look red.
A. Peptidoglycan Layer
● is unique to prokaryotes. It is found in all bacterial cell
walls except Mycoplasma.
MICRO Fundamentals of Microbiology
● This complex polymer consists of a backbone
composed of alternating N-acetylglucosamine and
N-acetylmuramic acid and a set of identical
tetrapeptide side chains.
● The tetrapeptide side chains are attached to the N-
acetylmuramic acid and are frequently linked to
adjacent tetrapeptides by identical peptide cross-
bridges or by direct peptide bonds.
● The β-1, 4 glycosidic bond between N-acetylmuramic
acid and N-acetylglucosamine is cleaved by the
bacteriolytic enzyme lysozyme (found in mucus,
saliva, and tears).
● It may contain diaminopimelic acid, an amino acid
unique to prokaryotic cell walls.
Note: In Gram-positive bacteria, it comprises up to 50% of the
cell wall. In Gram-negative bacteria it comprises only 2% to
10% of the cell wall. See Appendix
B. Special Components of Gram-Positive Cell Wall
● Most gram-positive cell walls contain considerable
amounts of teichoic and teichuronic acids, which may
account for up to 50% of the dry weight of the wall
and 10% of the dry weight of the total cell.
1. Teichoic and teichuronic acids
● They are water-soluble polymers, containing a
ribitol or glycerol residue linked by
phosphodiester bonds.
● Contain important bacterial surface antigenic
determinants, and lipoteichoic acid helps anchor the
wall to the membrane.
They are found in Gram-positive cell walls or membranes.
a. Teichoic acid is found in cell walls and is chemically
bonded to peptidoglycan.
b. Lipoteichoic acid is found in cell membranes and is
chemically bonded to membrane glycolipid,
particularly in mesosomes.
2. Polysaccharides
● are long chains of monosaccharides linked by
glycosidic bonds.
● subunits of polysaccharides include neutral sugars
such as mannose, arabinose, rhamnose, and
glucosamine, and acidic sugars, such as glucuronic
acid and mannuronic acid.
C. Special Components of Gram-Negative Cell Walls
● Gram-negative cell walls contain three components
that lie outside of the peptidoglycan layer:
lipoprotein, outer membrane, and
lipopolysaccharide
1. Outer membrane
● a bilayered structure; its inner leaflet
resembles in composition that of the
cytoplasmic membrane, and its outer leaflet
contains a distinctive component, a
lipopolysaccharide (LPS)
● ability to exclude hydrophobic molecules
and hydrophilic molecules
● contains a special channel called porins
that permits the passive diffusion of low-
molecular weight hydrophilic compounds
such as sugars, amino acids, and certain
ions.
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 2. Lipopolysaccharide (LPS)
● also known as endotoxins
● large molecules consisting of a lipid and a
polysaccharide composed of O-antigen,
outer core and inner core joined by a
covalent bond
● Lipid A- responsible for toxicity
● O-antigen - a repetitive glycan polymer used
in identification
3. Lipoprotein
● are hydrophilic proteins that are anchored to
a cell membrane by N-terminally linked fatty
acids
4. Periplasmic space
● space between the inner and outer
membrane containing the peptidoglycan
layer and a gel-like solution of proteins.
● 20-40% of cell volume
● include binding proteins, hydrolytic
enzymes, detoxifying enzymes, and a high
conc. of D-glucose.
The Acid-Fast Cell Wall
● Some bacteria, notably the tubercle bacillus (M.
tuberculosis) and its relatives have cell walls that
contain large amounts of waxes, complex branched
hydrocarbons (70–90 carbons long) known as
mycolic acids.
● The cell walls is composed of peptidoglycan and an
external asymmetric lipid bilayer; the inner leaflet
contains mycolic acids linked to an arabinoglycan,
and the outer leaflet contains other extractable lipids.
● a hydrophobic structure renders the bacteria
resistant to many harsh chemicals, including
detergents and strong acids.
Cell Walls of the Archaea
● The Archaea do not have cell walls like the bacteria.
● Some have cell walls composed of a simple S-layer
or a rigid cell wall composed of polysaccharides or a
macromolecule called pseudomurein.
Crystalline Surface Layers
● two-dimensional crystalline, subunit-type layer lattice
of protein or glycoprotein molecules (S-layer) found
in the outermost component of the cell envelope of
G(+), G(-) and Archaebacteria
● resistant to proteolytic enzymes and protein-
denaturing agents
● Functions: protection, cell adhesion and
maintenance of cell shape
Enzymes That Attack Cell Walls
● Lysozyme- hydrolyze the Beta1 to 4 glycan linkage
of the peptidoglycan backbone. it is found in animal
secretions (tears, saliva, nasal secretions) and in egg
white
● Autolysins- hydrolytic enzyme that attack
peptidoglycan (muramidases, glucosaminidases,
endopeptidases, and carboxypeptidases)
Cell Wall Growth
● Rod Shaped Bacteria (eg. E.coli and B. anthracis) -
new peptidoglycan is inserted along a helical path
leading to the elongation of the cell and is inserted in
a closing ring around the future division site.
MICRO Fundamentals of Microbiology
● Coccoid cells (S. aureus) - new peptidoglycan is
inserted only at the division site
● S. pneumoniae - synthesizes cell wall not only at the
septum but also at the so-called equatorial rings.
Protoplasts, Spheroplasts, and L Forms
● Protoplast- cells which have had their cell wall
removed, usually by digestion with enzymes.
● Spheroplast- cell wall deficient bacteria with spherical
form.
● Hydrolysis with lysozyme or blocking of
peptidoglycan synthesis removes the bacterial wall
which liberate protoplasts in G(+), and spheroplasts
in G (-) cells.
● forms -are cell wall deficient bacteria that is difficult to
culture.
● and requires a medium that is solidified with agar and
has the right osmotic strength.
The Mycoplasmas
● The mycoplasmas are cell wall-lacking bacteria
containing no peptidoglycan
● Mycoplasmas lack a target for cell wall-inhibiting
antimicrobial agents (e.g. penicillins and
cephalosporins) and are therefore resistant to these
drugs
● Mycoplasma pneumoniae- is an agent for pneumonia
and it contains sterols in their membranes.
6. Capsule and Glycocalyx
● The terms capsule and slime layer are frequently
used to describe polysaccharide layers; the more
inclusive term glycocalyx is also used.
● Capsule
○ The capsule is a well-defined structure of
polysaccharide surrounding a bacterial cell
and iis external to the cell wall. The one
exception to the polysaccharide structure is
the poly-Dglutamic acid capsule of Bacillus
anthracis.
○ It protects the bacteria from phagocytosis
and plays a role in bacterial adherence.
●
Glycocalyx
○ The glycocalyx refers to a loose network of
polysaccharide fibrils that surrounds some
bacterial cell walls.
○ It is sometimes called a slime layer.
○ It is synthesized by surface enzymes.
○ It is associated with adhesive properties of
the bacterial cell and contains prominent
antigenic sites.
7. Flagella
● are protein appendages for locomotion and contain
prominent antigenic determinants.
● They consist of a basal body, hook, and a long
filament composed of a polymerized protein called
flagellin.
● Motility- flagella are semi rigid helical rotors to which
the cell imparts a spinning movement
○ Rotation is driven by the flow of protons into
the cell down the gradient produced by the
primary proton pump
○ Chemotactic property: presence of a
chemical attractant (eg. sugar or AA)
determines the direction of movement.
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 ○ ● They also may confer antiphagocytic properties, such
as the M protein of S. pyogenes.
TYPES OF ARRANGEMENTS Types:
a. Common pili (adhesins) are involved in bacterial
a. Atrichous- no flagella, non-motile adherence and Gram-positive cell conjugation.
b. Monotrichous- single polar flagellum b. Sex pili are involved in attachment of donor and
c. Lophotrichous- a tuft or multiple polar flagella recipient bacteria in Gram-negative cell conjugation.
d. Amphitrichous- single flagellum found at each of
two opposite poles 9. Endospores
e. Peritrichous- multiple flagella distributed over the ● Endospores metabolically inactive bacterial cells are
entire cell highly resistant to desiccation, heat, and various
f. Amphilophotrichous- tuft of flagella found at each chemicals. They are helpful in identifying some
of two opposite ends species of bacteria (e.g., Bacillus and Clostridium).
● Endospores possess a core that contains many cell
components, a spore wall, a cortex, a coat, and an
exosporium.
● The core contains calcium dipicolinate, which aids
in heat resistance within the core.
● Endospores germinate under favorable nutritional
conditions after an activation process that involves
damage to the spore coat. They are not reproductive
structures.

VII. DIFFERENT KINDS OF STAINING METHOD

● process where stains combine chemically with the
bacterial protoplasm.

A. Gram-stain Procedure
a. Crystal Violet (Primary stain)
b. Iodine (Mordant)
c. Acetone- Alcohol (Decolorizer),
d. Safranin (Secondary stain/ Counterstain)
● G(+) bacteria will appear purple
● G(-) bacteria will appear reddish-pink

Figure 3. Gram-staining Technique

B. Acid-Fast Stain
Figure 2. Flagellar Arrangement
8. Pili (Fimbriae)
● are rigid surface appendages composed mainly of a
protein called pilin.
● Ordinary pili are the colonization antigens or
virulence factors associated with some bacterial
species such as S. pyogenes and Neisseria
gonorrhoeae.
- for bacteria that retain carbolfuchsin even when
decolorized with hydrochloric acid
- Acid fast organism cannot be decolorized by acid-
alcohol due to presence of mycolic acid
- Ziehl-Neelsen method (hot method)- uses heat as a
mordant
- Kinyoun Method (cold method)- uses phenol or
tergitol as mordant

MICRO Fundamentals of Microbiology 6 of 16

 ● Spirochetes- Borrelia, Treponema, Leptospira
OBLIGATE INTRACELLULAR:
● Rickettsia
● Chlamydia
● Mycoplasma

Figure 4. Acid-Fast Staining Technique

C. Negative Staining
- staining the background with acidic dye, leaving the
cells contrastingly colorless
- uses Black Dye Nigrosin
- for cells or structures that are difficult to stain directly
D. The Flagella Stain
- the cells are treated with unstable colloidal
suspension of tannic acid salts, causing a heavy
precipitate to form on the cell walls and flagella Figure 5. Overview of Medically Important Bacteria
- diameter of the flagella is increased to an extent that
subsequent staining with basic fuchsin makes it IX. CLASSIFICATION OF BACTERIA
visible in light microscopy
Basis of classification:
E. The Capsule Stain
- Modified negative staining • Phenotypic classification
- Welch Method- treatment with hot crystal violet ✓ Morphological
solution then rinsing with copper sulfate solution ✓ Anatomical
- background appear dark blue and the capsule a ✓ Staining
much paler blue ✓ Cultural characteristics
F. Staining of Nucleoids ✓ Nutrition
- Fuelgen stain- specific for DNA ✓ Environmental factors
- DNA- intercalating stains (DAPI) and ethidium ✓ Biochemical reactions
bromide for fluorescence microscopy ✓ Antigenic structure
G. The Spore Stain
• Genotypic classification
- observed as intracellular refractile bodies in
✓ DNA-DNA hybridization
unstained cell suspensions or as colorless areas
✓ G+C content
in cells stained by conventional methods
- requires heating the preparation for dye to
A. Morphology (cocci vs. rod/ “bacilli” vs. coccobacilli)
penetrate spore wall
- malachite green or carbolfuchsin
- ● Cocci- are spherical or oval bacteria having one of
several distinct arrangements based on their planes
VIII. OVERVIEW OF MEDICALLY IMPORTANT BACTERIA
of division.
✓ diplococcus: cocci arranged in pairs
EXTRACELLULAR AND FACULTATIVE:
✓ streptococcus: cocci arranged in chains
● Gram positive ✓ tetrad: cocci arranged in squares of 4
● Cocci- Staphylococci, streptococci, ✓ sarcina: cocci in arranged cubes of 8
enterococci ✓ staphylococcus: cocci arranged in
● Bacilli irregular, often grape-like clusters.
❖ Aerobes- Listeria, Bacillus,
Corynebacteria • Bacilli- are rod-shaped bacteria
❖ Strict Anaeobes- Clostridia, ✓ bacillus: single bacilli
Actinomycetes ✓ streptobacillus: bacilli arranged in chains
✓ coccobacillus: oval and similar to a coccus
● Gram Negative
● Cocci and Coccobacili- Haemophilus, • Spirals- come in one of three forms, a vibrio, a
Bordetella, Francisella, Brucella, spirillum, or a spirochete.
Pastuerella, Neisseria ✓ vibrio: a curved or comma-shaped rod
● Bacilli- Enterobacteriaceae, ✓ spirillum: a thick, rigid spiral
Pseudomonads, Legionella, Vibrio, ✓ spirochete: a thin, flexible spiral
Campylobacter, Helicobacter
● Mycobacteria

MICRO Fundamentals of Microbiology 7 of 16

 Figure 8. Bacterial Growth Factors (Oxygen Availability)

D. Biochemical Reactions (lactose fermenting vs. non-

Figure 6. Basic Shapes of Bacterial Cell fermenting)

B. Gram Stain (positive vs. negative vs. variable)

Figure 9. Examples of Lactose & Non-Lactose Fermenting

Bacteria

E. Serotype (group A vs. B vs. D streptococcus)

Figure 7. Gram Stain (Gram Positive & Gram Negative
Bacteria) • Serotype or serovar is a distinct variation within
species of bacteria or virus or among immune cells of
C. Growth Requirements (aerobic vs. anaerobic) different individuals. There are classified together
based on their cell surface antigens, allowing the
• Obligate/Strict Aerobes- REQUIRE oxygen for epidemiologic classification of organisms to
growth. subspecies level.
• Obligate/Strict Anaerobes- CANNOTt grow in the
presence of oxygen.
• Facultative Anaerobe- can grow EITHER WITH or
WITHOUT presence of oxygen.
• Aerotolerant Anaerobe- can survive in the presence
of oxygen but DO NOT use oxygen in metabolism.
• Microaerophilic- require REDUCED level of oxygen
to grow.

Table 2. Classification of Streptococcus

MICRO Fundamentals of Microbiology 8 of 16

F. Antibiotic Resistance Patterns (MSSA vs. MRSA)
• Methicillin-susceptible Staphylococcus aureus
✓ Susceptible to penicillin antibiotics
• Methicillin-resistant Staphylococcus aureus
✓ Resistant to penicillin drugs and thus
requires use of alternative antibiotics.
G. rRNA Sequence Analysis
• Ribosomal RNA sequences have been used
extensively in the classification and identification
of Bacteria and Archaea.
X. CRITERIA FOR IDENTIFICATION OF BACTERIA
A. Growth on media
• The general cultivation of most bacteria requires
media rich in metabolic nutrients.
• These media generally include agar, a carbon
source, and an acid hydrolysate or enzymatically
degraded source of biologic material (ex. casein).
• These types of media may be supplemented by
vitamins and even intact red blood cells in the case
of blood agar media.
• Because of their undefined composition, these types
of media are referred to as complex media.
• Media can be nonselective or selective.
1. Nonselective Media
• Different bacterial species growing on these types of
agar often give rise to colonies with distinctive
morphologies—for example, large or small, yellow
versus white, serrated or smooth.
• Colonial growth patterns on different types of media
can be useful in the identification of a particular
bacterial species.
• Examples: Blood agar and chocolate agar
2. Selective Media (addition of inhibitory agents)
• Upon culture, some bacteria produce characteristic
pigments, and others can be differentiated based on their
complement of extracellular enzymes; the activity of these
enzymes often can be detected as zones of clearing
surrounding colonies grown in the presence of insoluble
substrates (ex. hemolysis around colonies on agar
medium containing intact animal red blood cells).
• Example: pathogenic Salmonellae and Shigellae that
do not ferment lactose on a MacConkey plate form
white colony, while lactose fermenting members of the
Enterobacteriaceae (ex. E. coli) form red or pink colonies.
B. Microscopy
• Gram-stain, together with visualization by light
microscopy, has been among the most
informative methods for classifying the
eubacteria.
• This staining technique broadly divides bacteria
based on their fundamental differences in the
structure of their cell walls.
• This typically represents the first step in
identifying individual microbial specimens (eg,
are they Gram-negative or Gram-positive) grown
in culture or even directly from patient
specimens.
C. Biochemical Tests
• Oxidase test - uses an artificial electron acceptor,
can be used to distinguish organisms by detecting the
presence or absence of a respiratory enzyme,
cytochrome C, the lack of which differentiates the
Enterobacteriaceae from other Gram-negative rods.
• Catalase activity - can be used to differentiate
between the Gram-positive cocci; the species
staphylococci are catalase positive, whereas the
species streptococci are catalase negative. If the
organism is demonstrated to be catalase positive
(Staphylococcus spp.), the species can be
subdivided by a Coagulase test into Staphylococcus
aureus (coagulase positive) or Staphylococcus
epidermidis (coagulase negative).

• Used to eliminate (or reduce) the large numbers of

irrelevant bacteria in these specimens.
• The basis for selective media is the incorporation of
an inhibitory agent that specifically selects against
the growth of irrelevant bacteria.
• Examples of such agents are:
✓ Sodium azide selects for Gram-positive bacteria
over Gram-negative bacteria.
✓ Bile salts (sodium deoxycholate) select for Gram-
negative enteric bacteria and inhibit Gram-negative
mucosal and most Gram-positive bacteria.
✓ Colistin and nalidixic acid inhibit the growth of
many Gram-negative bacteria. • Examples of selective
media:
✓ MacConkey agar (containing bile) that selects for
the Gram-negative rods and CAN blood agar (containing Figure 10. Algorithm for differentiating the Gram-positive
colistin and nalidixic acid) that selects for Gram-positive cocci
cocci.

3. Differential Media (LF vs. NLF)

MICRO Fundamentals of Microbiology 9 of 16

 D. Immunologic Tests

Figure 11. Direct Agglutination

REFERENCES

● Doc Abueva’s Ppt Lecture

● Jawetz Medical Microbiology 27th Edition (Chap 1-3)
● BRS Microbiology and Immunology
● Ixtlilton’s Microbiology Transes 1A - 1C
● https://www.yc.edu/v6/academics/pathway/biodocs/
Microscope181.pdf
● Lecture Video
✓ MICRO (1.1) Fundamentals of Microbiology
https://youtu.be/XDdViYu_NNE
✓ MICRO (1.2) Fundamentals of Microbiology
https://youtu.be/V9n48vmo1nI

FREEDOM WALL

MICRO Fundamentals of Microbiology 10 of 16

 VI. APPENDIX

Characteristic Viruses Bacteria Fungi Protozoa and

Helminths

Cells No Yes Yes Yes

Approximate diameter 0.02-0.2 1-5 3-10 (yeasts) 15-25 (trophozoites)

(𝒖𝒎)𝟑

Nucleic acid Either DNA or RNA Both DNA and RNA Both DNA and RNA Both DNA and RNA

Type of nucleus None Prokaryotic Eukaryotic Eukaryotic

Ribosomes Absent 70S 80S 80S

Mitochondria Absent Absent Present Present

Nature of outer Protein capsid and Rigid wall containing Rigid wall containing Flexible membrane
surface lipoprotein envelope peptidoglycan chitin

Motility None Some None Most

Method of Replication Not binary fission Binary fission Budding or mitosis Mitosis

TABLE 1. CHARACTERISTICS OF MICROBIAL GROUPS

FIGURE 2A. THE MICROSCOPE FIGURE 2B. THE MICROSCOPE: Parts and Its Function

MICRO Fundamentals of Microbiology 11 of 16

 Character Prokaryotes Eukaryotes

Term Origin “primitive nucleus” “true nucleus”

Definition Organisms made up of cell/s that lack Organisms made up of cells that possess
nucleus or any membrane-encased a membrane- bound
organelles nucleus as well as membrane-bound
organelles

Major Groups Bacteria, Archae, and Bluegreen algae Algae, Fungi, Protozoa, Plants, Animals

Cell Type Unicellular (some cyanobacteria may be Multicellular

multicellular)

Complexity Simple Complex organization

Nucleus Absent Present

Nucleus Location Free in the cytoplasm, attached to Contained in membrane bound structure
mesosomes

Nuclear Membrane Absent Present

Nucleolus Absent Present

Chromosome Number One More than one

Chromosome Shape Circular Linear

Genes Expressed in groups Expressed individually

Genome DNA haploid genome DNA diploid genome

Genome Nature Efficient and compact with little repetitive With large amounts of non-coding
DNA repetitive DNA

Membrane- bound organelles Absent Present

Ribosomes 70S (50S+30S) 80S (60S+40S)

(sedimentation coefficient) Smaller Larger

Ribosome’s Location Free in cytoplasm or bound to cell Attached to rough endoplasmic reticulum
membrane

Mitochondria Absent Present

Golgi Bodies Absent Present

Endoplasmic Reticulum Absent Present

Mesosomes Present (performs function of golgi bodies Absent

and mitochondria, and also separates
chromosomes)

Lysosomes Absent Present

Peroxisomes Absent Present

Chloroplasts Absent Present (plants)

Fimbriae May have pili and fimbriae (appendage Absent

that can be found on many gram-negative
and some gram-positive bacteria)

Microtubules Absent or rare Present

MICRO Fundamentals of Microbiology 12 of 16

 Centrosome Absent Present

Cytoskeleton Absent Present

Glycocalyx Present Only in some

Cytoplasmic Membrane Does not contain sterols (except Contains sterols

Mycoplasma)

Cell Wall Complex structure containing protein, Present for plant cells and fungi; otherwise
lipids, and proteoglycans absent
Table 2. Prokaryotes vs Eukaryotes

MICRO Fundamentals of Microbiology 13 of 16

 Figure 3. Gram Positive and Gram Negative Cell Envelope

MICRO Fundamentals of Microbiology 14 of 16

 Table 3. Gram Positive vs Gram Negative

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