Bacterial Taxonomy

INTENDED LEARNING OUTCOMES

Upon completion of this lesson, the MLS student can:
1. Describe the three areas of microbial taxonomy - classification, nomenclature, and
identification.
2. Discuss the significant role of taxonomy in diagnostic microbiology.
3. Accurately apply the rules of the scientific binomial system for bacterial names.
4. Discuss how the phenotypic and genotypic characteristics of bacteria aid in their
identification.

Introduction to Microbial Taxonomy

Taxonomy
– science of biological classification
– consists of three separate but interrelated parts
● classification - arrangement of organisms into groups (taxa; s., taxon)
● nomenclature - assignment of names to taxa
● identification - determination of taxon to which an isolate belongs

I.CLASSIFICATION
It is the organization of microorganisms that have similar morphologic, physiologic, and genetic
traits, into specific groups or taxa.

The following system is hierarchic and consists of the following taxa and designations
1. Domain- Bacteria, Archaea, Eukarya
2. Kingdom- composed of similar phyla;similarities of DNA and RNA
3. Division/Phyla- composed of similar classes
4. Class- composed of similar orders
5. Order-composed of similar families
6. Family-composed of similar genera
7. Genus-composed of various species with common characteristics.

8. Species- is the basic group or the collection of bacterial strains with common physiologic and
genetic features
• Subspecies- are species which are subdivided based on the following differences.
● Biotype- is having similar genetic traits but different biochemical and physiological
characteristics within the same species
● Serotype- is based on serological (surface antigens) differences within the same species.
Il. Nomenclature
It is the naming of microorganisms according to established guidelines provided by the International
Code of Nomenclature of Bacteria or the Bacteriological Code.

In writing the genus name:

1. The first letter should be capitalized and followed by the species epithet(specific name),
which begins with a lowercase letter.
2. Both the genus and species should be italicized in print but underlined when written in
script (e.g., Staphylococcus aureus or
Staphvlococcus aureus)
3. When bacteria are referred to as group, their" in names are neither capitalized nor
underlined (e.g. staphylococci,streptococci,etc)

III. Identification
● It is the process by which the microorganisms' key features are described.
● It is the process of discovering and recording the traits of organisms so that they may
placed in an overall taxonomic scheme.

Genotypic Characteristics
It refers to the organism's genetic makeup
● It involves the detection of a gene or a part thereof, or an RNA product of a specific
organism.
● An example is the base sequencing of
DNA or an RNA product of a specific
organism.

Phenotypic Characteristics
● It is based on the features beyond the genetic level
● Some examples are colony morphology, staining, and biochemical and susceptibility tests.

Classical Characteristics
• It is useful in routine phylogenetic studies of microorganisms such as the understanding of
morphology, physiology and metabolism, ecology, and genetic analysis.

PROKARYOTES , EUKARYOTES, AND ARCHAE

PROKARYOTES
 ● These are organisms that do not contain a true nucleus
● The word "prokaryote"is formed by the words "pro" which means before and the in greek
word "karyon" which means nucleus, nut or kernel

Bacterial cell structures

1. Cell envelope- It is composed of an outer membrane (gram-negative bacteria) cell wall,periplasm,

(gram-negative bacteria) and plasma membrane

2. CELL WALL
● It is also referred to as the peptidoglycan or murein layer.
● It is a rigid structure that maintains the shape of the cell.
● It is composed of disaccharide-pentapeptide subunits and teichoic acid or lipoteichoic acid
● Its synthesis and structure have been the primary target of antimicrobial agents.

Functions
A. It prevents bacterial cells from rupturing when the osmotic pressure inside the cell is greater than
the pressure outside the cell.
B. It serves as apoint of anchorage for flagella.
C. It determines the staining characteristics of a
species.

TYPES OF CELL WALLS

1. GRAM POSITIVE CELL WALL
● It is composed of a very thick protective peptidoglycan (murein) layer.
● It consists of glycan chains of alternating
N-acetyl-D-glucosamine (NAG) and N-acetyl-D muramic (NAM) acid.
● It contains a negatively charged teichoic acid and contributes to the total electric charge of
the cell wall.

2. GRAM NEGATIVE CELL WALL

● It has porins that contribute to the permeability of the cell wall.
● It contains a periplasmic space which is involved in peptidoglycan synthesis.
● It does not contain teichoic acid.

Layers of the Gram-negative Cell Wall

A. Outer membrane/wall
● I It is composed of proteins, phospholipids, and lipopolysaccharide (LPS).
 ● It contributes to the negative charge of the bacterial surface, which stabilizes the membrane
structure.
B. Inner membrane/wall
• It is composed of a thin peptidoglycan layer, which is the reason for its high susceptibility to
mechanical breakage.

3. ACID-FAST CELL WALL

● It has Gram-positive cell wall structure.
● Aside from a peptidoglycan layer, it contains a waxy layer of glycolipids and fatty acids
(mycolic acid)that is bound to the exterior of the cell wall.
● Mycolic acid has a strong hydrophobic structure that affects the permeability of the acid-
fast
● Some examples of bacterial cells that have this kind of cell wall are
Mycobacterium and Nocardia

4. ABSENCE OF CALL WALL

● Prokaryotes that do not have a cell wall contain sterols in their cell membrane.
● Examples: Mycoplasma and
Ureaplasma

PLASMA MEMBRANE
● It is the deepest layer of the cell envelope.
● It consists of a phospholipid bilayer that surrounds the cytoplasm, and the n layer is
embedded with lipoproteins
● It acts as an osmotic barrier.
● It regulates the transport of solutes across the membrane as well as the generation of
chemical energy (ATP).
● It is the site of respiration and photosynthesis.

Cytoplasmic Structures in a Prokaryotic Cell

1. Ribosome (Non-membranous structure)

● It is the site of protein biosynthesis and gives the cytoplasm a granular structure.
It consists of RNA and proteins.
● It is 70S in size and separates into two subunits,
50S and 30S.

2. Genome
 ● It consists of single, circular chromosome.
● It appears as diffused nucleoid or chromatin body that is attached to a mesosome (sac-like
structure)

3. Plasmid
● It is an extrachromosomal, double-stranded element of DNA that is associated with virulence.
● If is located in the cytoplasm and serves n as a site for the genes to encode for antibiotic
resistance and toxin production.

Kinds of Plasmids
a. Large plasmid - is responsible for the production of p-lactamases that provide resistance to B-
lactam antibiotics like penicillin and oxacillin
b. Small plasmid is resistant to tetracyclines and chloramphenicol

4. Inclusion bodies
● They serve as the energy source or food reserve of the bacteria.
● They are composed mainly of polysaccharides, which lessen osmotic pressure.
Examples: Glycogen, cyanophycin granules, poly-B-hydroxybutyrate granules, carboxysomes
(cyanobacteria, nitrifying bacteria, and thiobacilli), gas vacuoles (cyanobacteria, halobacterium, and
Thiothrix), and polyphosphate granules (volutin or metachromatic granules)
Examples: of polyphosphate granules: Babes-Ernst bodies (Corynebacterium diphtheria), bipolar
bodies (Yersinia pests), and Much's granules (Mycobacterium tuberculosis)

5. Endospores/Asexual spores (Resistant structures)

These are small, dormant structures located inside the bacterial cell.
● They aid in the survival of bacteria against external conditions
● They are produced within vegetative cells of some
Gram-positive bacteria.
● They are composed of dipicolinic acid and calcium ions
● (calcium dipicolinate).
● The locations of these structures aid in the microscopic identification of bacteria.
● Examples of endospore-forming bacteria: Bacillus and Clostridum

Types of Spores According to their Location and the Associated Organism.

A. Terminal spore- Clostridium tetan
B. Subterminal spore - Clostridium botulinum
C. Central spore- Bacillus anthracis
CELL APPENDAGES
1. GLYCOCALYX
● It is an outward complex of polysaccharides on the bacterial surface and other cells.
● It helps the bacteria in attaching to the in surface of tissues or solid objects.
● It appears as a capsule or a slime layer.

Types of Glycocalyx
a. Capsule
● It is an organized material that is firmly attached to the cell wall.
● It is mostly made up of polysaccharide polymers.
● It protects the bacteria (virulence factor) from the attacks of human defense system cells
since it resists phagocytosis and desiccation.
b. Slime layer
It is an unorganized material that is loosely attached to the cell wall. in
● It also consists of polysaccharides.
● can either inhibit phagocytosis or aid in the It adherence of the bacteria to the host tissue or
synthetic implants.

2. Flagellum (Organ of Locomotion)

● It is an exterior protein filament (flagellin) that rotates and causes bacteria to be motile.
● It is important in the survivability and the pathogenic ability of bacteria.

Flagellar arrangement
A. Atrichous ~ without flagellum
B. Monotrichous~ single flagellum on one end
C. Amphitrichous ~single flagellum on both ends
d. Lophotrichous-tuff/group of flagella on one end or both ends
e. Peritrichous ~spread over the whole surface

3. Pili (Fimbriae)
● These are hair-like, proteinaceous structures, about 2 um in length, that extend from the cell
membrane to the external environment.

TYPES OF PILI
a. Common/Somatic Pili
They are the organ of attachment - aid in the attachment of bacteria to tissues and surfaces.
● They are considered a virulence factor.
Examples: of bacteria with common pili: Neisseria gonorrhoeae and Pseudomonas
b. Sex Pili
● They are an essential part of the genetic transfer/conjugation process.
● Example of bacteria with sex pili: E. coli (also with somatic pili)

EUKARYOTES
● These are microorganisms that contain a true nucleus (with chromosome bound by a
nuclear membrane).
These are cells of higher plants, animals, fungi, protozoa, and other morphologically complex
and larger organisms than prokaryotes.
● They contain many membrane-bound organelles such as, nucleus, endoplasmic reticulum,
Golgi body,mitochondria, and lysosomes, in which cellular functions are performed.

Archaea (Archaebacteria)
● Archae is from the Greek word "archaics,' which means
ancient.
● The cellular structures of archaea include the cell wall, plasma membrane, ribosomes, and
flagella.
● They do not contain a nucleus and membrane-bound organelles.
● The cell walls of archaebacteria do not contain the typiaa/
peptidoglycan as observed in prokaryotes, instead a protein or glycoprotein wall structure
known as the
"S-layer"is present as a protective coat. These organisms are classified as aerobes,
facultative anaerobes, or obligate anaerobes

● They may be stained either as Gram-positive or

● Gram-negative organisms in various shapes such spherical, rod, and spiral(pleomorphic).
● They grow and survive under extreme environmental conditions
● They reproduce through binary fission, fragmentation, orn budding
● Examples: Methanospirillum, Halobacterium, and Sulfolobus