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Topic 1 Classification of Microorganisms

The organization of microorganisms that are similar morphologic, physiologic and genetic traits into specific groups of
taxa.
1. HIERARCHICH TAXA DESIGNATION: NOTE:
a. _________ __________ – most basic taxonomic group; a
b. _________ (composed of similar species) collection of bacterial strains.
c. _________ (composed of similar genera) __________ – are taxonomic subgroup within a
d. _________ (composed of similar families) species.
e. _________ (composed of similar orders) __________, __________, __________ – given to groups
f. _________ (composed of similar classes) below the subspecies levels that share specific, but
g. _________ (composed of similar divisions) relatively minor characteristics.

Topic 2 Nomenclature of Microorganisms

There are rules and guidelines according to the International Code of Nomenclature of Bacteria but changes in naming
is documented by International Journal for Scientific Bacteriology.
RULES:
1. BINOMIAL SYSTEM is used – two-name system of nomenclature, every organism is assigned a GENUS and
SPECIE of LATIN or GREEK derivation.
2. Each organism must have a label in which the genus should always have its first letter capitalized, while the
species designation should always have its first letter in lowercase.
3. The genus and the species should be italicized in print but underlined when written in script.
4. The name may be abbreviated by using the uppercase form of the first letter of the genus designation followed by
a period (.) and the full species name, which is never abbreviated.
5. Informal designation such as staphylococci, streptococci, enterococci should not be capitalized nor italicized.
6. The first two letters or the first syllable are used when two or more genera names begin with the same first
letter.
7. The genus name followed by the word species may be used to refer to the genus as a whole. Species are
abbreviated “sp.” (singular) or “spp.” (plural) when the species is not specified.
8. In cases organisms that were reclassified, the name is written as the new genus designation, followed by the
previous genus designation in parentheses and then by the species name.
9. The family name is capitalized and has an “-aceae” ending.
Table 1-1: This table shows the reclassification of different bacteria published and how to write their nomenclature considering the old classification.

OLD NAME NEW NAME NOMENCLATURE

Clostridium difficile Clostridioides difficile
Haemophilus aphrophilus Aggregatibacter aphrophilus
Haemophilus paraaphrophilus Aggregatibacter aphrophilus
Enterobacter aerogenes Klebsiella aerogenes
Propionibacterium acnes Cutibacterium acnes
Borreliela burgdorferi Borrelia burgdorferi
Enterobacter gergoviae Plulalibacter gergoviae
Xanthomonas maltophilia Stenotrophomonas maltophilia
Burkholderia cepacia Pseudomonas cepacia

Topic 2 Identification of Microorganisms

There are major categories used to establish a microorganism’s identity:
1. GENOTYPIC CHARACTERISTICS – relates to the organism’s genetic makeup. Includes the genes and the
constitution of its nucleic acid. Examples are:
a. _______________________________________ – quantitation of the extent to which the DNA of two
organisms is made up of the four nucleic bases. (i.e., Cytosine-Guanine)
b. _______________________________________ (DNA and/or RNA) – is the extent to which the base
sequence (DNA and RNA strands) is similar (homologous) between two organisms.
2. PHENOTYPIC CHARACTERISTICS – relates to characteristics beyond the genetic level. Includes the readily
observable characteristics and those that may require extensive analytical procedures.
a. ___________________________________ – characteristics of microbial growth patterns on an artificial
media as observed by the naked eye.
b. ___________________________________ – size, shape, intracellular inclusions, cellular appendages
and arrangement of the cells with the help of a microscope.
c. ___________________________________ – ability of organism to reproducibly stain a particular color
with the application of dyes and reagents.

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d. ___________________________________ – ability of organism to grow:

i. at various temperatures
ii. in the presence of oxygen and other gases
iii. at various pH levels, or
iv. in the presence of other ions and salts such as HCl.
e. ___________________________________ – ability to utilize carbon and nitrogen sources as substrates
when grown under certain conditions.
f. ________________________ – ability to resist exposure to:
i. ____________________
ii. ____________________
iii. ____________________
g. ________________________ – profiles of microorganisms by various serologic and immunologic
methods that are useful for determining various microbial groups.
h. ________________________ – molecular components of the cell that are typical of a particular taxon.
Examples are:
i. Cell wall components
ii. Components of cell membrane
iii. Enzymatic content of the microbial cell

Topic 1 A generalization
1. First and smallest organism capable of independent existence.
2. _____________; contains both _______ and _______.
3. _____________:
a. _____ µm to _____ µm (1 to 10 µm in some books)
b. Smallest pathogenic bacteria – ___________________________________________
c. Largest pathogenic bacteria – ___________________________________________
Table 1-2: This table presents the variation in shape of different bacterial cell
SHAPE Description
Coccus
Bacillus
Curved
Coccobacilli
Spirillum
Spirochete
Fusiform
Pleomorphic

Table 1-3: This table presents the variation in arrangement of different bacterial cell
ARRANGEMENT Description
Staphylo
Strepto
Diplo
Tetrads
Sarcinae
Picket fence
Chinese
Palisades

4. Prokaryotic design includes:

a. _____________
b. ______________
c. ______________
d. ______________
5. Chemical nature is similar to eukaryotic cells plus unique components.
6. Design facilitates rapid growth.
7. Bacterial cells reproduce by _________________ – one cell splits in half to become two cells.
8. The length of time it takes for one bacterial cell to split into two cells is referred to as the organism’s generation
time.

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Table 1-4: This table shows the key differences in the characteristics of the eukaryotic cells (both plant and animal cells)
and prokaryotic cells.

EUKARYOTIC CELLS
CHARACTERISTICS PROKARYOTIC CELLS
Plant Cell Animal Cell
0.4-2.0 µm in diameter
TYPICAL SIZE 10-100 µm in diameter
0.5-5.0 µm in length
BIOLOGIC
All plants, fungi and algae All animals and protozoa All bacteria
DISTRIBUTION

NUCLEAR MEMBRANE __________________ __________________ __________________

MICROTUBULES __________________ __________________ __________________

Composed of DNA and Composed of DNA and
CHROMOSOMAL DNA Composed of DNA alone
proteins proteins
EXTRACHROMOSOMAL
__________________ __________________ __________________
DNA

ORGANELLES Present in all Present in all Absent (inclusions only)

RIBOSOMES Present in all Present in all Present in all

CYTOPLASMIC
80S 80S 70S
RIBOSOMES (DENSITY)
Sexual and asexual Sexual and asexual Asexual reproduction
REPRODUCTION
reproduction reproduction (Binary fission)
ELECTRON TRANSPORT ________________________
__________________ __________________
FOR ENERGY (if present)
STEROLS IN CELL Absent (except for
Present Present
MEMBRANE _____________________)
When present, of simple
Of complex chemical
chemical constitution;
CELL WALL Absent constitution, containing
usually contains
______________________.
________.
When present, flagella have a
When present, have a When present, have a simple twisted protein
FLAGELLA OR CILIA
complex structure complex structure structure; prokaryotic cells do
not possess cilia.
Present in cyanobacteria and
PHOTOSYNTHESIS Present Absent
some other bacteria

Topic 1 Bacterial Genome

1. All genes that comprise an organism.
2. Composed of a single circular chromosome.

Figure 1-1: Prokaryotic bacterial cell

Source: Prescott, L. M. (2002). Prescott’s Principles of
Microbiology (5th edition). McGraw-Hill Education.

a. NUCLEOID
i. Positive to __________________
ii. Circular chromosome of supercoiled double-stranded DNA
iii. Attached to cell membrane and central structures
iv. Not surrounded by nuclear membrane; no mitotic functions (______________)

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v. “Resting” bacteria: ______________; Rapidly growing: up to ______________.

b. BACTERIAL CHROMOSOME
i. Circular, ________________________
ii. Contains 450-8000 genes
iii. Single copy per cell
iv. Highly folded in cell
c. PLASMIDS
i. Aka. _________________________________
ii. Circular, double stranded DNA but not a part of the chromosome
iii. Not usually attached to cell membrane and sometimes lost during cell division.
iv. Not required for growth and reproduction but may carry genes for selective advantage:
1. _________________________________
2. _________________________________
3. _________________________________
v. Bacterial cell may not contain any plasmids and some may contain up 20 copies per cell.
d. TRANSPOSABLE ELEMENTS
i. Pieces of DNA that move from one genetic element to another, from plasmid to chromosome or
vice versa.
ii. They do not exist as separate entity within the bacterial cell because they must either be
incorporated into a plasmid or the chromosome.
iii. Exist in two types:
1. ______________________
a. Contains genes that simply encode for information require for movement among
plasmids and chromosomes.
2. ______________________
a. Composed of genes for movement, as well as genes that encode for other
features such as drug resistance.
b. Small pieces of DNA that can move the DNA or bacteriophages.
e. BACTERIAL PHAGES
i. Simply, phages, are inter-specie transfer of DNA material from bacteria to viruses and vice
versa.
ii. Transfer of antimicrobial genes and other virulence factors are possible but on rare occurrence that
the two previously mentioned.
f. BACTERIAL RIBOSOMES
i. Site for _______________________
ii. Size: 70S (50S subunit and 30S subunit) – the Svedberg units are not additive.
iii. Consists of RNA and proteins; attached to the cytoplasmic membrane.

Topic 2 Cell Envelope

1. Composed of layers:
a. ________________
b. ________________
c. ________________
2. Some bacteria may or may not have cell wall or capsule.
3. All bacteria have cell membrane
4. CELL MEMBRANE
a. Aka. _________________________
b. Phospholipid–protein bilayer lacking sterols (except for Mycoplasma)
c. Roles in ____________, ____________, ____________, _________________________________ and
_________________________________.
d. Functional equivalent of many eukaryotic organelles.

Figure 1-2: Microscopic view of the Gram-positive

(left) and Gram-negative (right) cell wall.
Legends: M—peptidoglycan or murein layer; OM,
outer membrane; PM, plasma membrane; P,
periplasmic space; W, Gram-positive
peptidoglycan wall.
Source: Prescott, L. M. (2002). Prescott’s Principles of Microbiology (5th
edition). McGraw-Hill Education.

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Figure 1-3: Detailed differences

between each layer of gram-
positive and gram-negative cell
wall.
Source: Tille, P. M. (2017). Bailey & Scott’s Diagnostic
Microbiology [E-book]. Elsevier Gezondheidszorg

5. CELL WALL
a. Outside the cell envelope and inside the capsule.
b. Unique wall structure prevents osmotic lysis, determines ____________.
c. Gram stain distinguishes two major envelope structures.
d. Poorly staining bacteria still have a Gram category.
e. Although most bacteria have cell walls, bacteria in the genus ___________________ and
___________________ do not.
f. Loss of cell wall leads to lysis or production of ___________.
g. __________________________:
i. Major components of Gram-positive walls are peptidoglycan and teichoic acid.
ii. Peptidoglycan
1. Aka. __________
2. Comprises glycan chains cross-linked by peptide chains:
________________________________ and ________________________________
3. Scaffold-like sac surrounds cell
4. Resistance to most mammalian enzymes
iii. ____________________ and ____________________ promote adhesion and anchor wall to
membrane
iv. Other cell wall components related to species:
1. ____________
2. ____________
h. ___________________________________:
i. Gram-negative outer membrane is
1. Phospholipoprotein bilayer. Functions by:
a. Creating the ______________________
b. An outer surface with strong negative charge
c. Providing a barrier against harmful substances
2. Outer leaflet has an embedded lipopolysaccharide _______________.
3. Lipopolysaccharide contains:
a. ________________________ – becomes the toxic moiety of the LPS;
embedded within the cell wall
b. ________________________ – provides stability; attached to the Lipid A
c. ________________________ – antigenic structure of the LPS; extends
outward from the Lipid A
ii. Thin peptidoglycan sac is imbedded in periplasmic space.
iii. Periplasmic proteins functions as:
1. ______________
2. ______________
3. ______________
iv. Impermeability of outer membrane is compensated by ___________.
i. ATYPICAL CELL WALLS
i. Fungi – __________
ii. ___________________ and ___________________ – has no cell wall and thus known as
pleomorphic.
iii. ______________________ – has temporarily lost their cell wall

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iv. ACID-FAST CELL WALLS

1. Pertains to the cell wall of the following organisms:
a. _______________________ – Acid-Fast Bacillus (with long strands of
b. _______________________ mycolic acid)
c. _______________________
Partially Acid-Fast Bacillus (with short strands
d. _______________________
of mycolic acid)
e. _______________________
f. _______________________
g. _______________________
h. _______________________ Partially Acid-Fast Protozoans
i. _______________________
j. _______________________ Acid Fast Fungi that can be treated with
k. _______________________ acid wash. Source: Acid-fastness of fungi in blastomycosis
and histoplasmosis
l. _______________________
m. _______________________ Partially Acid-Fast Helminths
n. _______________________
2. They are characteristically “hard to stain but once stained, they are hard to decolorize”.
3. Gram stain reaction if the mycolic acid is removed: __________________

SIDE NOTE!

Figure 1-4: Cellular color differences in gram-staining

Source: Mahon, C. and Lehman, D., 2015. Textbook of diagnostic microbiology. 5th ed.

DISCUSSION:

SIDE NOTE!

Figure 1-5: Cellular color differences in the acid-fast staining

Source: Mahon, C. and Lehman, D., 2015. Textbook of diagnostic microbiology. 5th ed.
DISCUSSION:

6. GLYCOCALYX
a. _______________ or _______________; contains:
i. Polypeptide and polysaccharide
ii. _____________: Bacillus anthracis – ___________________________
b. Slimy, gelatinous material produced by the cell membrane and secreted outside of the cell wall.
c. Bacterial capsules serve as a virulence factor (primarily, ______________________________)

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Figure 1-6: (Both) Microscopic picture of

capsular structures using India Ink
preparation.
Source: Mahon, C. and Lehman, D., 2015. Textbook of
diagnostic microbiology. 5th ed.
Source: Tankeshwar, A., 2022. Capsule Stain: Principle,
Procedure, Results • Microbe Online. [online] Microbe Online.
Retrieved from: https://microbeonline.com/capsule-stain-
principle-procedure-results/. Accessed: 13 May 2022

d. _______________:
i. ________________
1. Amorphous;
2. Not highly organized and is not firmly attached to the cell wall;
3. It easily detaches from the cell wall and drifts away.
ii. ________________
1. Highly organized and firmly attached to the cell wall.
2. Usually consist of polysaccharides.
3. __________ – smooth, mucoid and glistening colonies.
4. __________ – dry and rough colonies.
e. Serotyping by Neufeld-Quellung test by detecting the _______________________.
f. Stains:
i. ____________________ (an example of a negative staining)
ii. ____________________
iii. ____________________

Topic 2 Cytoplasmic contents

1. CYTOSOL
a. ____________________________; contains no organelles
b. Contains ribosomes and various types of nutritional storage granules.
2. MESOSOMES
a. Inward invaginations of the cell membranes; important to cell division
b. Cellular respiration takes place in bacteria.
c. Septal mesosomes and non-septal mesosomes.
3. ENDOSPORES
a. Not a reproductive structure but for survival.
b. Two major processes involved (the entire process can be noted in the Figure 2-):
i. ________________ – the process of spore forming where one cell form one spore under adverse
condition (changes to pH gradient and low nutritional content); this is not a process of reproduction
but a mere recurrence of metabolism through the introduction of water.
NOTE: Reproductive/growth state to dormant state
ii. ________________ – the process of forming the vegetative stage; initiated by damage on the
coat of endospores.
NOTE: Dormant state to reproductive/growth state
c. Spores are capable of withstanding extreme conditions such as high pH and temperature for a long period
of time. Due to:
i. Low water content
ii. _____________________ (dipicolinic acid) – seen within the cytoplasm
iii. No metabolic reactions require
d. Location of spores:
i. ______________ – Clostridium tetani
ii. ______________ – Clostridium botulinum
iii. ______________ – Bacillus anthracis
e. Bacterial genera:
i. Anaerobic spores – __________________
ii. Aerobic spores – __________________
iii. Pseudospores (spore-like structures) – _______________ and _______________

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SIDE NOTE!

Figure 1-7: The process of sporulation

Source: Willey J, Sherwood L, Woolverton C. Prescott's Principles of Microbiology. New York:
McGraw-Hill; 2008

DISCUSSION:

Topic 4 Appendages
1. PILI
a.Aka. ______________
b.Pili are tubular hair-like projections
c.a protein called __________ arranged to form a tube
d.Two general classes:
i. COMMON PILI
1. Aka. __________________, __________________ or __________________
2. Cover the surface of the cell
3. Have adherence roles and serves as a virulence factor
ii. SEX PILI
1. Involved in exchange of genetic material between some Gram-negative bacteria.
2. Needs the ______________; Only one per cell
2. FLAGELLA
a. Are rotating helical protein structures responsible for _________________.
b. Have bushing rings in cell envelope.
c. Composed of the protein _______________; antigenic in nature (aka. _______________)
d. Flagellar amino acid sequence is different from strain to strain and used for differentiation most especially
for Enterobacteriaceae.
e. Terminologies associated with Flagella:
i. _________________ – devoid of flagella
ii. _________________ – single flagellum at one pole
iii. _________________ – flagella located at both polar ends
iv. _________________ – single tuft or bundle of flagella is found at a polar end
v. _________________ – flagella are found all around its body
OTHER NOTES:
vi. _________________ and _________________ are most common in pathogens.
vii. _________________ – 18 hours growth can demonstrate motility.
viii. Motility is best seen at __________
ix. Some organisms can be inhibited by __________ SIDE NOTE!

Table 2-4: This table presents the different distinct motility of some bacteria Figure 1-8: Uninoculated SIM medium
Source: https://microbenotes.com/wp-content/ uploads/2019/12/ Sulfur-
Reduction-Test.jpg
MOTILITY BACTERIA DISCUSSION:
_________________/
Vibrio (monotrichous)
_________________
_________________ Campylobacter spp.
_________________ Kingella spp., Bartonella spp.
_________________ Listeria spp.
_________________ Capnocytophaga spp., Mycoplasma pneumoniae
_________________ Spirochetes (axial filaments)
_________________ Leptospira

Staphylococcus, Streptococcus, Neisseria, Moraxella, Klebsiella,

_________________ Shigella, Yersinia, Bacillus anthracis, Clostridium perfringens,
Mycobacteria

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SIDE NOTE!

DISCUSSION:

Figure 2-9: (Left) The “run” and “tumble”

movement of a flagellated bacteria
{Right} Axial filament
Source: Tortora, G., Funke, B., & Case, C. (2018). Microbiology:
An Introduction (10th ed.). Pearson.

SIDE
NOTE!

Figure 2-10: The different flagellar rings

Source: Tille, P. M. (2017). Bailey & Scott’s Diagnostic Microbiology [E-book]. Elsevier Gezondheidszorg
DISCUSSION:

Hey, wait for my instructions before you go any further.

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1. The orderly increase in all chemical constituents of the cell.

2. A process that entails the replication of all cellular structures, organelles and protoplasmic components from the
nutrients present in the surrounding environment.
Topic 1 Nutritional Requirements
1. All bacteria have THREE MAJOR NUTRITIONAL NEEDS for growth:
a. CARBON
i. Structural backbone of living matter
ii. It is needed for all the organic compounds that make up a living cell.
iii. 50% the dry weight of a typical bacterial cell is carbon.
iv. Classification according to carbon source:
1. ___________________ – these bacteria require an organic source of carbon, such as
glucose, and obtain energy by ____________ or _____________ organic substances. (for
2. ___________________ – derive their carbon from ___________________ with only water
and inorganic salts required in addition.
v. Classification according to energy source:
1. If they get their carbon photosynthetically, they are known as _______________.
2. If they get their carbon by oxidation of carbon and non-carbon compounds, they are known
_______________.
vi. Classification according to electron source:
1. _______________ – they use reduced inorganic molecules.
2. _______________ – they require organic substances (i.e., carbohydrate, proteins and
lipids) for growth and multiplication
IMPORTANT NOTES:
1. ______________ = ______________; energy is produced via photosynthetically or
oxidatively.
2. ______________ = ______________; energy is produced via oxidation and fermentation
of organic substances.
3. ______________ = ______________; most pathogenic organisms are categorized in
this group.
4. _______________________ – requires other growth factors (refer to item number 3).
Table 3-1: Table presents the major nutritional types of microorganisms.

REPRESENTATIVE
NUTRITIONAL TYPES SOURCES
MICROORGANISM

Energy: ___________________ Algae

Photolithotrophic autotrophy
Electron: ___________________ Purple and green sulfur bacteria
(Aka. PHOTOLITHOAUTOTROPHY) Carbon: ___________________ Cyanobacteria
Energy: ___________________
Photoorganotrophic heterotrophy Purple nonsulfur bacteria
Electron: ___________________
(Aka. PHOTOORGANOHETEROTROPHY) Carbon: ___________________
Green nonsulfur bacteria

Sulfur-oxidizing bacteria
Energy: ___________________
Chemolithotrophic autotrophy Hydrogen bacteria
Electron: ___________________
(Aka. CHEMOLITHOAUTOTROPHY) Carbon: ___________________
Nitrifying bacteria
Iron-oxidizing bacteria

Energy: ___________________ Protozoa

Chemoorganotrophic heterotrophy
Electron: ___________________ Fungi
(Aka. CHEMOORGANOHETEROTROPHY) Carbon: ___________________ Most nonphotosynthetic bacteria
b. NITROGEN
i. Makes up about 14% of the dry weight of a bacterial cell, sulfur and phosphate constitute
about another 4%.
ii. Other bacteria use nitrogen from ammonia (NH4+).
iii. Some important bacteria, including many of the photosynthesizing cyanobacteria, use
gaseous nitrogen (N2) directly from the atmosphere. This process is called nitrogen fixation.
iv. Bacteria use nitrogen to make __________.
c. ___________________________
i. Source of energy
ii. For performing cellular functions.
2. Other nutritional requirements are the following:
a. Sulfur

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i. It is used to synthesize sulfur-containing amino acids and vitamins such as ______________

and ______________.
b. Phosphate
i. It is essential for the synthesis of nucleic acids and the _______________ of cell membranes.
c. Electrolytes
i. These are elements that microorganisms require, often as cofactors for enzymes.
ii. _____________, _____________, _____________, _____________and _____________
3. GROWTH FACTORS
b. These are organic compounds needed by a bacterium for growth. These factors are provided in
a culture medium to facilitate proper growth of the bacterial colony.
c. _____________
i. Synthesize their own growth factors.
d. _____________
ii. Require addition of growth factors to culture media for growth.
Examples of growth factors:
i. ____________________
ii. ____________________
iii. ____________________
iv. ____________________
v. ____________________
vi. ____________________
vii. ____________________
4. INORGANIC SALTS
a. In small amounts stimulates the growth of some organisms.
b. _______________________
i. Have adapted so well to high salt concentrations that they actually require them for
growth.
c. ______________
i. Which do not require high salt concentrations but are able to grow at salt concentrations
up to 20%, a concentration that inhibits the growth of many other organisms.
ii. Examples:
1. 6.5% NaCl
a. Used for identification of __________________________
b. Used in __________________________
2. 7.5% NaCl
a. Used for identification of __________________________
b. Used in __________________________
3. 10% NaCl
a. Used for identification of ___________ except for ______________ and
______________.
b. Used in ___________________________________.
d. ______________
i. Organisms can tolerate some level of dissolved solutes but grow best in the absence of
the added solute.
5. ATMOSPHERIC OXYGEN AND CARBON DIOXIDE
a. ______________________ – reduced molecular oxygen that can be seen during normal cellular
metabolism.
b. ______________________ – produced by the addition of hydrogen atoms.
c. ______________________ – produced via the interaction between superoxide anion and the
presence of iron.
d. CLASSIFICATION:
i. AEROBE – use molecular oxygen produce more energy from nutrients
1. _______________________ – organisms that require oxygen to live.
a. Contains ______________________ and __________ for tolerance
b. Requirement: 21% oxygen and 0.03% carbon dioxide
2. _______________________ – has the ability to continue growing in the absence of
oxygen; fundamentally aerobes.
a. Includes most of pathogenic bacteria
3. _______________________ /_______________________ – are aerobic; grow only in
oxygen concentrations lower than those in air.
a. Requirement: 5% oxygen, 10% carbon dioxide, 85% nitrogen
ii. ANAEROBE – do not use or require oxygen for growth; oxygen can be toxic.
1. _______________________ – are bacteria that are unable to use molecular oxygen
for energy-yielding reactions.
a. Has no superoxide dismutase and catalase to tolerate oxygen presence.

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b. Requirement: 0% oxygen, 80-90% nitrogen, 5-10% hydrogen and 5-10%

carbon dioxide.
2. _______________________ – has the ability to continue growing in the presence of
oxygen; fundamentally anaerobes.
3. ___________________________ – do not require or use oxygen for growth, but
they tolerate the presence of atmospheric (free) oxygen.

SIDE
NOTE!

Figure 3-1: Internal structure of an anaerobic chamber jar.

Source: http://www.medical-labs.net/wp-content/uploads/2015/03/GasPak-system-Anaerobic-jar.jpg

DISCUSSION:

SIDE NOTE!

RATIONALIZATION:

iii. ________________
1. Require increased amount of carbon dioxide. Can be achieved using
_____________ or ____________________________.

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Table 3-2: This table shows the different genera of bacteria grouped according to their gram reaction and
oxygen requirement.

AEROBIC ANAEROBIC

Gram POSITIVE Cocci

Gram NEGATIVE Cocci

Gram POSITIVE Bacilli

Gram NEGATIVE Bacilli

6. MOISTURE
a. Indispensable for bacterial growth.
b. Serves as a solvent for food and forms the major portion of the protoplasm.
c. _________________ – organisms that require increased amount of moisture.

Topic 1 Physical Requirements

1. TEMPERATURE
a. ____________________ is the temperature at which the species grows best.
b. ____________________ is the lowest or minimum time required to kill an organism under constant temperature.
c. ____________________ is the lowest temperature required to kill microorganism in a constant time.
d. Diagnostic laboratory usually incubates cultures for bacterial growth at 35°C.
e. There are organisms can grow at 35°C and 42°C.
i. Classification:
1. ____________________
a. Aka. ____________________
b. Grows best at ________
c. Examples: ___________________________ and ___________________________
2. ____________________
a. Grows well at ________
b. Commonly encountered pathogenic bacteria are categorized here.
3. ____________________
a. Grows well at ________
b. Example: ___________________________
4. ____________________
a. Able to live at unusual conditions like absence of oxygen, increased temperature and
below earth’s surface.
b. Example: ___________________________
2. HYDROGEN ION CONCENTRATION
a. Most pathogenic bacteria grow best in a narrow pH range near neutrality, between pH 7.2 and 7.6
b. Classification:
i. _____________ – grows at pH 6.5-7.0 Table 3-3: This table presents the water activity
ii. _____________ – grows at pH 7.5-8.0 of different microorganisms
iii. _____________ – grows at pH 8.4-9.0 BACTERIA Aw
3. OSMOTIC PRESSURE
a. Organisms requiring high osmotic pressures are called Gram negative bacteria 0.95
_____________.
Gram positive bacteria 0.90
b. _________________ (Aw) is the amount of water available
for microbial growth. Most molds 0.80
Halophiles 0.75
Xerophilic yeasts 0.65
Osmophilic yeasts 0.60

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1. Bacterial growth (unicellular) can be interpreted that it depends on the increase of cell mass and ______________.
2. Eukaryotic growth (multicellular) can be interpreted that it depends on the increase of cell mass and
______________.
3. GENERATION TIME
a. Aka. ________________________
b. The time required for one cell to divide into two cells.
4. The growth has 4 (four) different phases:
a. ___________________
b. ___________________
c. ___________________
d. ___________________

Figure 3-2: Bacterial

Growth Curve
Source: Mahon, C. and Lehman,
D., 2015. Textbook of diagnostic
microbiology. 5th ed.

1. LAG PHASE
(aka.
__________________________ or __________________________)
a. This period has a little or no cell division and it can last for 1 hour or several days.
b. During this time, however, the cells are not dormant.
c. The microbial population is undergoing a period of intense metabolic activity involving, in particular,
synthesis of enzymes and various molecules.
2. LOG PHASE (aka. __________________________ or __________________________)
a. The cells begin to divide and enter a period of growth, or logarithmic increase.
b. Cellular reproduction is most active during this period, and generation time reaches a constant minimum.
Because the generation time is constant, a logarithmic plot of growth during the log phase is a straight line.
c. The log phase is the time when cells are most active metabolically and is preferred for antimicrobial
sensitivity, biochemical reactions and physiological testing.
3. STATIONARY PHASE (aka. __________________________ or __________________________)
a. Eventually, the growth rate slows, the number of microbial deaths balances the number of new cells,
and the population stabilizes.
b. Growth ceases due to:
i. Accumulation of waste products (dead debris)
ii. Exhaustion of nutrients
iii. Change in pH and other factors
4. DEATH PHASE (aka. __________________________)
a. The number of deaths eventually exceeds the number of new cells formed.
b. This phase continues until the population is diminished to a tiny fraction of the number of cells in the
previous phase or until the population dies out entirely.
c. Decline is due to:
i. Depleted growth factors and necessary nutrients
ii. Overwhelming amounts of metabolic waste in the media
iii. In summary, the media cannot support the replication of the organism

1. A culture medium is any material containing the necessary nutritional and environmental requirements for
bacterial growth.
2. _________________ – a nutrient material prepared for the growth of microorganisms.
3. _________________ – microbes that are introduced into a culture medium to initiate growth.
4. _________________ – microbes that grow and multiply in or on a culture medium.
5. CLASSIFICATION OF CULTURE MEDIA:
a. According to Physical State or Consistency
i. Liquid media (aka. __________):

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1. Without any trace of agar or solidifying substances

2. Turbid, or cloudiness, of the broth is due to light deflected by bacteria present in the culture
(more bacterial growth = more turbid)
3. At least _____________________________ are needed for turbidity to be detected with
the unaided eye.
4. Disadvantage:
a. Results to diffuse growth of bacteria showing no to minimal characteristic growth
for initial identification.
b. Difficult to isolate pure colonies.
5. Examples:
a. _____________________________
b. _____________________________
c. _____________________________
d. _____________________________
ii. Solid medium
1. Made by adding solidifying agents to the culture media.
2. Contains ______ of agar
3. Advantage: shows distinct colony morphology (easier identification)
4. Examples:
a. _____________________________
b. _____________________________
c. _____________________________
d. _____________________________
NOTE:
a. ____________________ – most common solidifying agent, melts _______ but
resolidifies _______.
b. Earliest solid media – ______________________ by Robert Koch.
c. ___________ – universally used for preparing solid media, usually obtained from
a seaweed-red alga known as ___________.
d. Contains sulfated polymer of D-galactose, 3,6-anhydro-l-galactose and D-
glucuronic acid.
iii. Semisolid medium
1. Contains __________ agar
a. Example: ________________________________________
b. According to Composition/Constituents/Ingredients
i. Synthetic
1. Aka. ____________
2. Exact composition of the ingredients is known
3. Used for research purposes
4. Example: commercially prepared culture media
ii. Non-synthetic
1. Aka. ____________
2. Precise composition of some or all of the nutritive substances used is not known.
3. Very useful for routine isolation of bacteria.
4. Example:
a. Nutrient broth
b. Trypticase soy broth
iii. Tissue culture media
1. Contains living tissues
2. Used for ____________ or _____________________________ (i.e., Rickettsia,
Chlamydia)
3. Examples:
a. ____________________________________________
b. ____________________________________________
c. McCoy cells
d. Vero cells
e. CA 54
f. HeLa cells
g. Hep-2 cells
d. According to How Medium is Dispensed
i. Plated
1. Distributed in sterile petri dishes

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ii. Tubed
1. Distributed in sterile test tube
2. _____________ (Simmons citrate agar, Urease, Alanine Deaminase medium)
3. _____________ (Sulfide-Indole-motility medium)
4. _____________ (Triple Sugar Iron, Lysine Iron Agar)

Figure 3-3: (A) Simmons citrate agar (B)

SIM agar (C) Triple Sugar Iron. Examples of
tubed media
Source (A): https://cbsalife.com/wp-
content/uploads/2022/01/Citrate-2-scaled.jpg
Source (B):
https://slideplayer.com/16760771/97/images/slide_9.jpg
Source (C): https://microbiologyinfo.com/wp-
content/uploads/2019/04/featured-The-Triple-Sugar-Iron-TSI-
test.jpg

e. According to Use or purpose

i. _____________ or _____________
1. Contain nutrients that support growth of most non-fastidious organisms without giving
any particular organism a growth advantage.
2. For routine cultivation of microorganisms.
3. Example: Nutrient agar, Brain Heart Infusion agar
ii. _____________
1. Specific nutrients required for the growth of particular bacterial pathogens that may be
present alone or with other bacterial species in a patient specimen.
2. Enhance growth of particular bacteria
3. Inhibits the growth of microbial flora.
4. Liquid type media
5. Example:
a. GN broth
b. Alkaline Peptone Water
c. LIM broth
iii. _____________
1. For fastidious organisms
2. Substances like blood, serum, egg, vitamins and yeast extract are added to the basal
medium.
3. Used to grow bacteria that are exacting in their nutritional needs.
4. Solid type media
a. Example: BAP
i. _____________
ii. _____________
iii. _____________
iv. _____________ – not for routine use
b. CAP
iv. _____________
1. contain one or more agents inhibitory to all organisms except those being sought.
2. Inhibitory agents include chemicals, dyes and antibiotics
3. Inhibitor for Gram positive organisms:
a. _____________ (Crystal violet, Gentian violet)
b. _____________
c. _____________
Inhibitor for Gram negative organisms:
a. _____________
b. _____________
Inhibitor for swarming of Proteus:
a. _____________
b. _____________
c. _____________

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EXAMPLES of SELECTIVE CULTURE MEDIA

Selective for Mycobacterium tuberculosis Lowenstein-Jensen Agar

Selective for Corynebacterium diphtheriae Mueller Tellurite

Selective for Campylobacter spp. Campy-blood agar

Selective for Gram positive cocci Columbia Nalidixic agar

Selective for Staphylococci Mannitol salt agar

Selective for Vibrio spp. Thiosulfate Citrate Bile salt Sucrose agar

Selective for Shigella and Salmonella Tetrathionate broth

Selective for S. pyogenes and S. agalactiae Streptococcal selective agar

Selective for Gram positive cocci and anaerobic

Phenyl Ethyl Alcohol
gram-negative bacilli

Selective for Neisseria gonorrhoae CAP with Antibiotics

THAYER MARTIN MARTIN LEWIS
1. ____________ 1. ____________
2. ____________ 2. ____________
3. ____________ 3. ____________
4. ____________

MODIFIED THAYER MARTIN NEW YORK CITY

1. ____________ 1. ____________
2. ____________ 2. ____________
3. ____________ 3. ____________
4. ____________ 4. ____________

Note:
1. ___________________ – it is a Thayer Martin medium with ____ agar, __________, _______________
and _____.
2. ____________________ – same as NYC medium with the addition of ___________.

v. DIFFERENTIAL
1. Allows bacterial colonies of one bacterial species or type to exhibit certain metabolic or
cultural characteristics that can be used to distinguish them from other bacteria.
2. Examples:
a. Blood agar plate (differential for hemolytic patterns)
vi. SELECTIVE-DIFFERENTIAL
1. Most selective are also differential media. Thus, they are known as Selective-Differential
media.
2. Used in the primary isolation of Enterobacteriaceae
a. Rapid Lactose Fermenters
i. ________________
ii. ________________
iii. ________________
b. Late Lactose Fermenters
i. ________________
ii. ________________
iii. ________________
iv. ________________
v. ________________
vi. ________________
c. Non-Lactose Fermenters
i. All Salmonella spp. except for ____________________________
ii. All Shigella spp. except for ____________________________
iii. ________________
iv. ________________
v. ________________

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vi. ________________
vii. ________________
vii. SPECIAL AGAR – specially prepared to support the growth of specific microorganisms.
Examples:
1. ________________________ – Mycobacterium tuberculosis
2. ________________________ – Leptospira spp.
3. ________________________ – Brucella spp.
4. ________________________ – Bordetella pertussis
5. ________________________ – Neisseria
6. ________________________ – Listeria monocytogenes
7. ________________________ – Vibrio cholerae
viii. TRANSPORT MEDIUM
1. ________________________ – for stool pathogens
2. ________________________ – used as Viral Transport Medium (VTM)
3. ________________________ – respiratory specimens
4. ________________________ – Neisseria
5. ________________________ – El tor vibrios, Vibrio parahaemolyticus

Hey, wag excited. Wait lang.

No. Answer rationalization

---------------------------- End of Session 1 ----------------------------

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