TAXONOMY AND CLASSIFICATION

BACT211 WEEK 2 LEC

Naming, Classifying, and Identifying Micro

organisms

- the science of classifying living things

- is the assignment of scientific names to
the various taxonomic categories and individual
organisms.
- attempts the orderly arrangement of
organisms into a hierarchy of taxa (categories).
- is the process of discovering and
recording the traits or organisms so that they
may be recognized or named and placed in an
overall taxonomic scheme.

CLASSIFICATION
• Carl von Linné (also known as Linnaeus;
1701–1778)
• a Swedish botanist
• laid down the basic rules for classification
and established taxonomic categories, or
taxa
Carl R. Woese
• devised a Three-Domain System of
Classification
• there are two domains of procaryotes
(Archaea and Bacteria) and one domain
(Eucarya or Eukarya), which includes all
eucaryotic organisms.

Robert Whittaker
• Whittaker’s tree
• based on structural similarities and
differences, such as prokaryotic and
eukaryotic cellular organization, and the
way these organisms obtained their
nutrition.

NOMENCLATURE
International Code of Nomenclature of Bacteria
(ICNB) or the Bacteriological Code (BC)
• provides the accepted labels by which
organisms are universally recognized.

Binomial system of nomenclature

• every organism is assigned a genus and a
species of Latin or Greek derivation.
• Each organism has a scientific “label”
consisting of two parts:
• GENUS - the first letter is always capitalized

ARAGONCILLO, SYDNY P.
 • SPECIES -first letter is always lower case.
• Printed in italics or underlined in script.

Guidelines:
The first letter of the family name (similar to a
human “clan”) is capitalized and has a suffix –
aceae

The first letter of the genus is capitalized followed

by the species in lowercase; both the genus and
species should be italicized in print or should be
underlined when written in script.

Commonly, the genus is abbreviated with the

first letter (capitalized) of the genus followed by
a period and the species. To avoid confusion,
the first two letters of the first syllable are used
when two or more genera begin with the same
first letter.

The genus followed by the word species may be

used to denote the entire genus as a whole. The
species are abbreviated as “sp.” (singular) or
“spp.” (plural) when the species is not specified.

Lastly, when bacteria are referred to as a group,

their names are neither capitalized nor
underlined

IDENTIFICATION
Genotypic characteristics
• relate to an organism’s genetic makeup,
including the nature of the organism’s
genes and constituent nucleic acids

Phenotypic characteristics
• are based on features beyond the
genetic level and include both readily
observable characteristics and
characteristics that may require extensive
analytic procedures to be detected.
BACTERIAL CELL COMPONENTS
Cell Wall
• also referred to as the ______________
• This structure gives the bacterial cell
shape and strength to withstand changes
in environmental osmotic pressures that
would otherwise result in cell lysis.
• protects against mechanical disruption of
the cell
• offers some barrier to the passage of
larger substances.

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 GRAM VARIABILITY
a characteristic exhibited by gram positive
bacteria
◦ Natural gram variability: ________
◦ Acquired gram variability (for gram
positive bacteria)
◦ Contributing factors
◦ Use of old culture
◦ pH of staining reagents
◦ bacterial autolysis
◦ Staining reaction time
Gram Positive Cell Wall
GUIDING RULES IN THE GRAM STAIN REACTION OF
• Has a very thick protective peptidoglycan
MEDICALLY IMPORTANT BACTERIA
(murein) layer
• All COCCI are Gram POSITIVE except
• Teichoic acid and lipoteichoic acid
_______________________________________
• All BACILLI are Gram NEGATIVE except
Gram Negative Cell Wall Mycobaterium, Bacillus, Clostridium,
• Thin peptidoglycan layer Corynebacterium, Lactobacillus, Listeria,
• _______________ Erysipelothrix, Aerobic Actinomyces,
• Outer membrane: proteins, phospholipids, Rothia, Kurthia (MBCCLLEARK)
and lipopolysaccharide (LPS). • & usually have a gram
• Functions of the Outer Membrane negative reaction NOT because it has a
o It acts as a barrier to hydrophobic gram negative cell wall but because they
compounds and harmful DO NOT HAVE a CELL WALL.
substances. • are very difficult to stain
o It acts as a sieve, allowing water- using gram staining however stainable
soluble molecules to enter through spirals are usually gram negative
protein-lined channels called • have a gram positive cell wall
porins. structure however because 60% of the cell
o It provides attachment sites that wall is made of hydrophobic lipids mainly
enhance attachment to host cells. mycolic acid, it affects its permeability this
makes it difficult to gram stain.

Acid-Fast Cell Wall

• contain a waxy layer of glycolipids and
fatty acids ( )

Acid- Fast Staining

• specifically designed for a subset of
bacteria whose cell walls contain long-
chain fatty (mycolic) acids.
• Mycolic acids render the cells resistant to
decolorization, even with acid alcohol
decolorizers.
• Mycobacteria
o are the most commonly
encountered acid-fast bacteria,
typified by Mycobacterium
tuberculosis, the etiologic agent of
tuberculosis.
• Partially Acid Fast Organism
o Nocardia
o Rhodococcus
o Legionella micdadei
• Distinctly Acid Fast

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 o Cryptosporidium
o Isospora
• 2 methods:
o _______
o _______
Acid Fast (Ziehl- Neelsen or Hot Method)
Kinyoun acid- fast method
• does not require the use of heat or boiling
water, minimizing safety concerns during
the procedure.
• Because of a higher concentration of
phenol in the primary stain solution, heat is
not required for the intracellular
penetration of carbol fuchsin.
• referred to as the “__________ ” functionally similar to the membranes of
method.
PARTS INTERNAL TO THE CELL WALL
CYTOPLASMIC/PLASMA MEMBRANE
a phospholipid bilayer embedded with
proteins that envelops the cytoplasm but does
not contain sterols (except
Mycoplasma/Ureaplasma)
FUNCTIONS
◦ Separates the intracellular components of
the bacterial cell from the extracellular
environment
◦ Acts as an osmotic barrier between the
inside and outside of the bacterial cell by
allowing selective permeability of the
membrane to macromolecules
◦ Site of electron chain transport necessary
for energy production, hence maintaining
the viability of the bacterial cell
◦ Houses enzymes involved in outer
membrane and cell wall synthesis, and
the assembly and secretion of
extracytoplasmic and extracellular
substances
• present in both gram-positive and gram
negative bacteria and is the deepest layer of
the cell envelope.
• Serves as an additional osmotic barrier and is
several of eukaryotic cellular organelles.
MESOSOMES
• folds or invagination along the length of
the cytoplasmic/plasma membrane
which serves as a point of attachment for
chromosomes
FREE RIBOSOMES
• sites of protein synthesis in bacterial cells
which has a size of 70S comprised of two
subunits being 50S and 30S.
INCLUSION BODIES
◦ serves as depot or storage deposits under
certain circumstances such as limited or
excess of a particular nutrient.
◦ These may accumulate, precipitate out,
and form an inclusion body which is not
bounded by a membrane freely floating
in the cytoplasm of the bacterial cell.
◦ Inclusion bodies may be in the form of
glycogen (carbohydrate reserves,
polyphosphates (ATP reserves), and poly-
β-hydroxybutyric acid (lipid reserves)
◦ ________ GRANULES – contains lipids
(Mycobacterium tuberculosis)
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 ◦ _______ /BABES-ERNST ◦ Associated with H Antigen ( )
BODIES/METACHROMATIC GRANULES – which is very useful is serologically typing
contains polyphosphates or inorganic and identifying species of____ .
phosphates (Corynebacterium
diphtheriae)
◦ ______ BODIES – prominent staining
of each end of the bacilli Yersinia pestis
using Methylene Blue or WAYSON stain
giving it a “safety pin appearance”

BACTERIAL SPORES/ENDOSPORES
◦ complex multilayered highly refractile
structure that can be found within the
cytoplasm of the vegetative cell of the
bacteria or in the environment when the
bacterial cell has been disintegrated.
◦ serves as a resting or hibernating stage for
GLYCOCALYX
bacteria when they are exposed to
◦ exterior high molecular weight
unfavorable conditions.
appendage or structure usually made up
◦ It is highly resistant to desiccation, heat,
of polysaccharide polymers or sometime
chemical agents.
polypeptides which are produced be
◦ MAIN COMPOSITION: _____ or Calcium-
certain bacteria depending on
Dipicolinic Acid Complex
environmental and growth conditions
surrounding the bacterial cell.
PARTS EXTERNAL TO THE CELL WALL
There are two (2) forms:
PILI (plural) or PILUS (singular)
◦ 1._____________– uniform and condensed
• protein projections that are thinner and
organized material that is firmly attached
shorter than flagella and are most usually
to the cell wall of the bacteria.
found in gram negative bacteria.
◦ It is associated with K Antigen (________)
• The terms FIMBRIAE (Latin, fringe) and PILI
and a slight change in the capsular
(Latin, hairs) are commonly used
synonymously (Brinton, 1965; Duguid &
MEDICALLY IMPORTANT CAPSULATED BACTERIA
Anderson, 1967).
◦ Neisseria meningitidis
• COMPOSITION: made up of protein
◦ Haemophilus influenzae serotype b
material known as PILIN ◦ Streptococcus pneumoniae
• ___________– usually shorter, numerous, ◦ Klebsiella pneumoniae
sticky hair-like appendages that are ◦ Bacillus anthracis
primarily used for adherence to one
another, host cells, and environment SLIME LAYER
surfaces.
• _______ – usually longer and singular, ◦ loose or diffused, thick, viscous
long and hollow protein tubes that is unorganized material that appears to be
primarily used for bacterial conjugation. detached from the bacterial or not firmly
attached to the cell wall of the bacteria.
◦ FUNCTIONS: primarily it also serves as a
FLAGELLA (plural) or FLAGELLUM (singular) form of protection from phagocytosis, or
◦ exterior protein filaments or whip-like in some instances, it helps the bacteria to
projections which is embedded in the cell adhere to host tissues or synthetic implants
envelope with a motor attached in a such as prosthetic heart valves.
basal body responsible for its propeller-like
rotation of the flagella which makes
bacteria move.
◦ Hence, flagellated bacteria are said to be
moving of motile.
◦ COMPOSITION: made up of protein
material known as ______________

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