I.

History and Scope of

MICROBIOLOGY Microbiology
Reviewer by: Aira Gloria

Microbiology- the study of organisms

and agents that are too small to be seen
by the naked eye (<1mm)

Table of Content A. Diversity of Microorganisms

I. History and Scope of

Microbiology
II. Microbial Diversity,
Structures, and Function
III. Microbial Taxonomy
IV. Microbial Genetics
V. Microbial Metabolism
1. Bacteria
Bacteria are small single-celled
organisms. Bacteria are found almost
everywhere on Earth and are vital to the
planet's ecosystems.
 2. Fungi 4. Algae
is a type of eukaryotic organism are photosynthetic organisms that possess

belonging to the kingdom of Fungi, photosynthetic pigments such as chlorophyll.

alongside plants, animals, protozoa, and

monera. Fungi are incredibly diverse,
with commonly encountered forms
including yeast, molds, truffles, and
mushrooms

5. Viruses
A virus is an infectious agent of small size and
simple composition that can multiply only in
living cells of animals, plants, or bacteria.

3. Protozoa
are single-celled organisms. They come in
many different shapes and sizes ranging
from an Amoeba which can change its
shape to Paramecium with its fixed shape
6. Multicellular Animal Parasites
and complex structure. They live in a wide
Multicellular parasites are eukaryotic
variety of moist habitats including
organisms in the Kingdom Animalia
freshwater, marine environments, and the
soil.
 began the slow process of
oxygenating Earth’s atmosphere.

B. Evolution of Microorganisms
C. Origin of Microbiology
● Microbial cells first appeared
between 3.8 and 4.3 billion years
ago 1. Robert Hooke (1665)
● During the first 2 billion years of ● Coined the word “cell”
Earth, microorganisms are
capable of surviving without ● Formulated Cell Theory
oxygen in the atmosphere. ● Illustrated fruiting structures of
● 1 billion years ago, phototrophic molds “mucor.
microorganisms (that harvest
energy from sunlight) occurred,
○ Purple sulfur bacteria
and Green sulfur
bacteria

2. Antoni van Leeuwenhoek

(1670)
● Constructed a simple microscope
● A billion years later,
(single lens)
oxygen-producing phototrophs
● First to observe bacteria in
called CYANOBACTERIA
pepper-water infusion
evolved and came to life. These
● “Wee animalcules”
3. Louis Pasteur (1822-1895) 5. Joseph Lister (1867)
● Disproved “spontaneous ● Father of antiseptic surgery
generation theory” ● Introduces antiseptic technique
● Studied sterilization and ● Used disinfectant to treat surgical
fermentation wounds
● Developed vaccine for rabies

6. Robert Koch (1843-1910)

● Discovered the causative agent
4. Ignaz Semmelweis (1861) of anthrax- bacillus anthracis
● Introduced handwashing ● Postulates for the germ theory of
● Introduced asepsis in hospitals to disease
prevent childbirth fever
transmission
D. Theories in Microbiology

1. Cell Theory
● All living organisms are
composed of cells
● The cell is the basic unit of
structure for all organisms
4. Koch’s Postulates
● All cells arise from pre-existing
● He generated a set of rigorous
cells
criteria for definitively linking
cause and effect in infectious
2. Biogenesis
disease.
● Living organisms can only arise
from other living organisms

E. Impacts of Microorganisms

1. Agent of disease-
microorganisms are the major
3. Abiogenesis (Spontaneous causative agents of infectious
Generation Theory) agents leading to numerous
● Living organisms could human death
spontaneously arise from 2. Agriculture- microbes in the
nonliving matter rumen of animals convert
cellulose from grass into fatty
acids that can be used by
animals
3. Industry- microbes are used to
produce antibiotics, enzymes,
 insulin, biofuels, and sewage II. Microbial Diversity,
treatment. Structures, and Function
4. Environment- microorganisms
can be also utilized for
A. Two types of Microorganisms
bioremediation as well as
decompose or destroy wastes
1. Cellular
5. Food- beneficial microbes are
● An organism that contains cells.
used for food preservation. Some
● Two types: Unicellular and
microorganisms can cause
Multicellular
foodborne disease and food
1a. UNICELLULAR
spoilage.

1b. MULTICELLULAR

2. Acellular
● An organism with no cells
● Infectious agents
Ex: viroid, virus, prions
CELLULAR
PROKARYOTE
MICROORGANISMS A. BARCHAEA
● Unicellular prokaryotes
● A simple cell with a nucleoid
1a. UNICELLULAR
region, surrounded by cytoplasm.
Prokaryotes Eukaryotes But differ in bacteria based on the

No true nucleus True nucleus cell wall structure and chemical

composition
Average size: 10-30 um
0.2-2.0 um ● They lack peptidoglycan in the

DNA is not DNA is found in cell wall

enclosed within a the cell nucleus ● They have the ability to thrive
membrane; one and found in
circular multiple under extreme conditions\
chromosome chromosomes
(linear)
B. BACTERIA
No Has ● Unicellular prokaryotes
membrane-enclos membrane-enclos
ed organelles ed organelles ● A simple cell with a nucleoid
region, surrounded by cytoplasm
Binary fission (cell Mitosis/Meiosis
division) (cell division) and cell wall
● Most have a peptidoglycan cell
wall
● They are divided by binary fission
● May possess flagella
B1. SHAPES
2. Arrangements of Bacilli
1. COCCUS- round shaped, but can
be oval, elongated, or flattened
on one side.

2. BACILLUS- rod-shaped.

3. SPIRAL- contains one or more

twists in shape.
3. Arrangements of Spiral

B2. ARRANGEMENT

1. Arrangements of Cocci
 7. Inclusions- metabolic reserve
particles; include carboxysomes,
gas vacuoles, and
magnetosomes

B3. CELL STRUCTURE (INTERNAL)

8. Endospore- specialized resting

1. Cytoplasmic membrane- stage of cell; forms when

phospholipid bilayer, serves as nutrients are depleted

the permeability barrier of the

cell; gatekeeper for the entrance
and exit of substances.
2. Cytoplasm- a gel-like matrix; it is
where the organelles carry out
the metabolic processes
3. Nucleoid- location of bacterial
(DNA) chromosome
4. Plasmid- extrachromosomal
pieces of circular DNA B4. CELL STRUCTURE (EXTERNAL)
5. Ribosomes- structure responsible APPENDAGES
for protein synthesis
6. Mesosomes- irregular infolding 1. Glycocalyx- sugar coat;
for metabolic activities gelatinous polymer found next to
the cell wall
 a. Capsule- organized and
firmly attached

4. Fimbriae- hair-like bristles which

allow adhesion in surfaces
5. Pili- longer than fimbriae; used for
b. Slime layer- disorganized
DNA transfer to other bacterial
and loosely attached
cells
2. Flagella- long filamentous
appendages that push the cell
forward

3. Axial filaments- endolfagella; B5. EXTERNAL STRUCTURES: CELL

present only in spirochetes ENVELOPE

Cell envelope- comprise of the

glycocalyx cell wall, and plasma
(cytoplasmic) membrane

Cell wall- lends structural strength to a

cell, prevents cell rupture and maintains
shape; composed of a complex polymer ● Many layers of PG; thick and rigid
known as peptidoglycan (murein) structure
● Contains teichoic and lipoteichoic
Major types of bacteria acid
1. Bacteria
- Gram positive (+) Gram-negative (-)
- Gram-negative (-)
2. Archaea ● Very few layers of PG with
- Naturally, they lack a cell wall, additional outer membrane
however, some archaeans ● Outer membrane parts:
contain pseudomurein ○ Lipoproteins
○ Phospholipids
○ Lipopolysaccharides (LPS)
■ O-specific
polysaccharide
■ Core
polysaccharide
■ Lipid A (endotoxin)
● Porins- transmembrane proteins
that permit passage of molecules
● Archaea- most lack a
polysaccharide- containing cell
wall and instead have an
Peptidoglycan (PG)- A disaccharide
S-Layer, which is a rigid protein
consisting of alternating units of
shell that functions to prevent
● N-acetyl-glucosamine (NAG)
osmotic lysis just as does the
● N-acetyl-muramic acid (NAM)
bacterial cell wall
● With B-1,4 glycosidic linkage
● Some archaeans contain
pseudomurein
Gram Positive (+)
○ N-acetylglucosamine
 ○ N-acetyltalosaminuronic package protein into
acid vesicles
○ B-1,3 glycosidic linkage ● Golgi complex- collects, stores.
Modifies vesicles

A. FUNGI
EUKARYOTES ● unicellular/multicellular
eukaryotes
● Yeasts (unicellular eukaryotes)
● Molds and mushrooms
(multicellular eukaryotes)
● Most of the fungal cell wall is
composed of chitin, a polymer of
N-acetylglucosamine
● Mitochondrion- the powerhouse
● Nutrient modes;
of the cell’ produces ATP for
○ Saprophytic
cellular energy by aerobic
(decomposers)
respiration
○ Symbionts (mutualistic)
● Nucleus- the control center of
○ Parasitic
the cell
● Nuclear membrane- encloses
the nucleus
● Endoplasmic Reticulum (ER)
○ Rough ER- Studded with
ribosomes; produces
proteins for export via
smooth ER and Golgi
complex; helps sort
proteins
○ Smooth ER- lacks
ribosomes, produces lipids
MULTICELLULAR ● It lacks collagen and chitinous
cell walls’ most of the cell walls
A. ALGAE
are made of cellulose
● Unicellular/multicellular
● Contains a nucleus and complex
eukaryotes
organelles
● Live in water, damp soil, and
● Contains a nucleus and complex
rocks
organelles
● Obtain nourishment through
● Obtain nutrients through
photosynthesis
absorption or ingestion
● Red and green algae, are a large
● Traditionally divided based on
and diverse group of eukaryotic
locomotion
organisms that contain
○ Flagellates
chlorophylls
○ Ciliates
● Some are endolithic
○ Amoeboids
phototrophs-green algae can
○ Sporozoans
grow inside rocks

B. PROTOZOA

● Unicellular eukaryotes
 1a. STRUCTURE
ACELLULAR

1. VIRUS
● Non-cellular entities that
consist of a nucleic acid core
(DNA or RNA), surrounded by a
protein coat (capsid)
○ Lack cytoplasmic
membrane, cytoplasm, ● Nucleocapsid- it is the inner
and ribosomes structure of nucleic acid + capsid
● Obligatory intracellular protein in enveloped viruses
parasites ○ Capsid- protein shell
● Unable to conserve energy and (capsule) that surrounds
carry metabolic processes the genome of the virion
● Viruses are often classified based (animal virus)
on structure, genome ● Envelope- layer composed of a
composition, and host specificity phospholipid bilayer taken from
● Depending on the specific virus, the host cell
the host may be a plant (viroids), ● RNA- the genetic material of the
animal (virions), or bacterial cell virus
(bacteriophage) ● Spike glycoprotein- allow the
virus to penetrate host cells and
cause infection
● Small envelope protein- important
component in assembly, release
and virulence phases of the viral
life cycle.
● Nucleocapsid protein-
RNA-binding protein critical for
viral genome packaging
 (changing further its chemical

2. VIROID bonds)
● Collectively, animal prion
● An infectious agent with a small
diseases are known as
circular RNA molecule and lacks
transmissible spongiform
a protein coat
encephalopathies
● No evidence was found that
naked viroid RNA can encode
any proteins, thus, it utilizes the
cell proteins of the host for
biochemical activities
● Most plant viruses are naked, ●
with no further layers

3. PRIONS
● Proteinaceous infectious particle
● Misfolded proteins; lacks both
DNA and RNA
● Unable to replicate on their own
but could cause infection by
interacting with normal protein
and altering its structure
 III. Microbial Taxonomy B. COMPONENTS OF TAXONOMY
B1. Description- assignment or listing
of characteristics to a taxon
Taxonomy- the science of
B2. Identification- a process of
biological classification. It is
determining that a particular organism
concerned with the description,
belongs to a recognized taxon
identification, classification, and
B3. Classification- arrangement of
nomenclature of organisms.
organisms into groups or taxa.
B4. Nomenclature- assignment of
Taxis- arrangement or order
names to a taxonomic group in
Nomos- law
agreement with published rules.

A. TAXONOMY VS SYSTEMATICS
C. TAXONOMIC
CHARACTERISTICS

1. Cultural- nutrients and physical

conditions of an environment
required for growth
2. Morphological- external and
internal characteristics of an
Taxonomy- the science of biological organism (e.g., size, shape,
classification structures, embryology,
karyology)
3. Metabolic- biochemical or
physiological characteristics (e.g.,
enzyme activities, body
secretions)
4. Antigenic- distinctive antigenic
Systematics- the study of the diversity (immunological reactive)
of organisms and their evolutionary properties
relationship
 5. Genetic- genetic material (DNA) ● Based on the expressed
composition and homology characteristics or the phenotype
analysis of an organism
● Only a few characters are
D. TAXONOMY: IDENTIFICATION considered
● Non-generic or non-evolutionary
● A process of determining that a ● More stable classification
particular organism belongs to a
recognized taxon 2. Natural/ Phylogenetic
● During this process, the key ● Based on the inferred evolution of
features of a microorganism are an organism
delineated ● It shares a common ancestor
● Two identification methods: ● Almost all existing characters are
GENOTYPIC and PHENOTYPIC considered
characteristics ● Genetic or evolutionary (related
○ GENOTYPIC- the genetic phylogenetically)
makeup of an organism ● May change with advancement in
including the nature of the knowledge
organism’s genes and
constituent nucleic acids F. TAXONOMY: CLASSIFICATION
(DNA/RNA) (METHODS)
○ PHENOTYPIC- the
morphological and 1. Phenotypic Classification
observable features of an System
organism or the features ● Also known as the Phenetic
beyond the genetic level Classification System
● Based on overall similarity
E. TAXONOMY: CLASSIFICATION ● Groups do not necessarily reflect
(TYPES) genetic similarity or evolutionary
relatedness
1. Artificial ● Examples:
 ○ Morphology H. TAXONOMY: CLASSIFICATION
○ Antibiotic sensitivity (SPECIES)
○ Cell chemistry
○ Biochemical 1. Subspecies- taxonomic
subgroups within a species
2. Genotypic Classification Subspecies types:
System ● Biotype- a group of organisms
● It can be associated with the with or nearly the same genotype
Cladistic Classification system ● Serotype- a group of organisms
○ Based on the genome that contains the same type and
characteristics with an number of surface antigens
application of phylogenetic
classification 2. Strain- originated from a pure
● Examples: culture of the same species but
○ 16s rRna not identical in all ways
○ DNA-RNA Hybridization
○ DNA fingerprinting Strain types:
○ REP-PCR ● Serovar- strains vary in their
antigenic properties
G. TAXONOMY: CLASSIFICATION ● Biovar- strains are differentiated
(RANK) by means of biochemical
activities
● Morphovar- strains that differ
morphologically

I. TAXONOMY: NOMENCLATURE
- Nomenclature is an assignment
of a name using a formal system
- Introduced by Carolus Linnaeus >
Binomial Nomenclature
 - Binomial Nomenclature: EXAMPLE:
contains rules governing
microbial nomenclature by
limiting the name to two taxa

J. TAXONOMY: NOMENCLATURE
(PRINCIPLES)

1. Reference
● Every organism is assigned a
genus and species of Latin or
greek derivation by the addition
of the appropriate suffixes
● International Code of
Nomenclature of Bacteria (ICNB)
or Bacteriological Code (BC)-
denotes rules for the naming of
microorganisms
● The taxonomic classification
scheme for prokaryotes is found
in Bergey’s Manual of Systematic
Bacteriology.

2. Principles