MICROBIOLOGY

Preliminary
1st Semester S.Y. 2019-2020
 WHAT IS MICROBIOLOGY?

■ It is essentially an advanced biology course.

■ It is the study of microbes
Microbes – nonliving entities and living organisms
Micro means very small. They are said to be ubiquitous, meaning they
are virtually everywhere.
 WHAT IS MICROBIOLOGY?

Various categories:
■ Viruses
■ Bacteria
■ Archaea
■ Protozoa
■ Certain types of algae and fungi
Viruses Bacteria
Archaea Protozoa
Algae Fungi
■ VIRUS - Viruses are microscopic organisms that exist almost everywhere on earth. They can
infect animals, plants, fungi, and even bacteria. Sometimes a virus can cause a disease so
deadly that it is fatal. Other viral infections trigger no noticeable reaction.

■ A virus may also have one effect on one type of organism, but a different effect on another.
This explains how a virus that affects a cat may not affect a dog.

■ Viruses vary in complexity. They consist of genetic material, RNA or DNA, surrounded by a coat
of protein, lipid (fat), or glycoprotein. Viruses cannot replicate without a host, so they are
classified as parasitic.

■ They are considered the most abundant biological entity on the planet. There is no cure for a
virus, but vaccination can prevent them from spreading.
■ Bacteria are microscopic, single-celled organisms that exist in their
millions, in every environment, both inside and outside other
organisms. Some bacteria are harmful, but most serve a useful
purpose. They support many forms of life, both plant and animal, and
they are used in industrial and medicinal processes.
■ Bacteria are thought to have been the first organisms to appear on
earth, about 4 billion years ago. The oldest known fossils are of
bacteria-like organisms.
■ Bacteria can use most organic and some inorganic compounds as
food, and some can survive extreme conditions.
■ Archaea are unicellular organisms that make up the third domain of
organisms on earth. Due to their ability to survive extreme conditions,
they can be found in a variety of environments ranging from lakes and
soil to the Dead Sea and the deepest parts of the ocean (ocean floor).
■ Protozoa are one-celled animals found worldwide in most habitats.
Most species are free living, but all higher animals are infected with
one or more species of protozoa. Infections range from asymptomatic
to life threatening, depending on the species and strain of the
parasite and the resistance of the host. Many protozoan infections
that are inapparent or mild in normal individuals can be life-
threatening in immunosuppressed patients, particularly patients with
acquired immune deficiency syndrome (AIDS).
■  Algae is the name given to a large and diverse group of oxygenic, phototrophic,
eukaryotic microorganisms. Algae are eukaryotic, which means they have a
nucleus. This differentiates them from bacteria and photosynthetic Cyanobacteria.
They are oxygenic phototrophs, meaning they use light as their energy source for
growth and produce oxygen as a byproduct, like plants.
■ Fungi, singular, fungus, is a group of eukaryotic, non-phototrophic organisms
with rigid cell walls, that includes mushrooms, molds and yeasts. Eukaryotic simply
means that fungal cells have a nucleus, like plant and animal cells, which
distinguishes them from the Bacteria and Archaea. Non-phototrophic means that
they can't use light for energy because they lack chlorophyll, distinguishing them
from plants. The cell walls of fungi are unique in that they contain large amounts
of chitin, a structural component only found in the cell walls of fungi. The chitin
makes the cells walls rigid.
 Microbes

Acellular Infectious Cellular

Agents Microorganisms
Prions
Prokaryotes Eukaryote
Viruses
Archaea s
Bacteria Algae
Fungi
Protozoa
 WHY STUDY MICROBIOLOGY?

■ Pathogens – disease-causing microorganisms

■ Non-pathogens – those that do not cause disease
■ Indigenous microbiota – microbes that live on and in the human
body
■ Opportunistic pathogens(opportunists) – do not cause disease
under ordinary conditions, but have the potential to cause disease
should the opportunity present itself.
■ An example of this is the Escherichia coli (E.coli) lives in our intestinal
tracts. It can cause disease if it gains access to our urinary bladder,
bloodstream or a wound.
 WHY STUDY MICROBIOLOGY?

■ Many microbes are involved in the decomposition of dead organisms

and the waste products of living organisms. These microbes are called
decomposers or saprophytes.
■ Saprophytes aid in fertilization by returning inorganic nutrients to the
soil. They break down dead and or decaying organic matter. They
break down dead and dying organic materials into nitrates,
phosphates and other chemicals necessary for the growth of plants.
Microbes cause two categories of
diseases:
1. Infectious disease – it results when a pathogen colonizes the body
and subsequently causes disease. Examples: MRSA infection, Gas
gangrene
2. Microbial intoxication – it results when a person ingests a toxin that
has been produced by a microbe. Examples: staphylococcal food
poisoning, foodborne botulism
 INFECTIOUS DISEASES

Methicillin-resistant
Staphylococcus
aureus (MRSA Gas gangrene
Microbial Intoxication

■ Foodborne botulism is a food poisoning caused by a toxin produced

by the bacterium, Clostridium botulinum. The disease most often
develops after consuming improperly processed home-canned foods
or home-preserved meats.
■ Staphylococcal food poisoning results from
eating food contaminated with toxins produced by certain types
of staphylococci, resulting in diarrhea and vomit
Pioneers in the Science of
Microbiology
1. Anton van Leeuwenhoek (1632-1723)
He is the first person to see live bacteria and protozoa, he is sometimes
referred to as the “Father of Microbiology”, the “Father of Bacteriology”
and the “Father of Protozoology”.
He observed various tiny living creatures, which he called “animalcules”.
■ Abiogenesis – life can arise spontaneously from nonliving material.
Other term is the theory of spontaneous generation
■ Biogenesis – life can only arise from preexisting life
 Pioneers in the Science of
Microbiology
2. Louis Pasteur – a French chemist, made numerous contributions to the
newly emerging field of microbiology and his contributions are considered
by many people to be the foundation of a science of microbiology and a
cornerstone of modern medicine.
■ Pasteurization – can be used to kill pathogens in many types of liquids.
■ He also made significant contributions to the germ theory of disease.
Examples: Bacillus anthracis - anthrax; Mycobacterium tuberculosis –
tuberculosis
■ He developed vaccines to prevent chicken cholera, anthrax, and swine
erysipelas(skin disease).
 Pioneers in the Science of
Microbiology

3. Robert Koch (1843-1910)

■ A German physician, proved that the anthrax bacillus was truly the
causative agent of anthrax. He accomplished this using a series of
scientific series that later became known as Koch’s postulates.
■ He developed methods of fixing, staining & photographic bacteria.
■ One of Koch’s colleagues, R.J Petri, invented a flat glass dish (now
known as Petri Dish) in which to culture bacteria on solid media.
■ He discovered the M. tuberculosis that causes tuberculosis and the
Vibrio cholera that causes cholera.
CAREERS IN MICROBIOLOGY

■ Microbiologist – a scientist who studies microbes

■ Bacteriologist – a scientist who specializes in bacteriology
■ Phycologists – scientists specializing in the field of phycology or
algology
■ Protozoologists – explore the area of protozoology
■ Mycologists – who specialize in the study of fungi (mycology)
■ Virologists – encompasses the study of viruses and their effects on
living cells of all types (virology)
CELL STRUCTURE
AND TAXONOMY
 INTRODUCTION

■ Cell – fundamental unit of any

living organism
■ Metabolism – refers to all of the
chemical reactions that occur
within a cell
■ The less complex cells which
include Bacteria and Archaea are
called prokaryotes or
prokaryotic cells. The more
complex cells, containing a true
nucleus many membrane-bound
organelles are called eukaryotes
or eukaryotic cells.
 EUKARYOTIC
CELL STRUCTURE
 Eukaryotic Cell Structure

■ Cell Membrane – the cell is

enclosed and held intact by this.
■ It is like a “skin” around the cell,
separating the contents of the cell
from the outside world.
■ It regulates the passage of
nutrients, waste products and
secretions into and out of the cell.
■ It has the property of selective
permeability, only certain
substances may enter and leave
the cell
 Eukaryotic Cell Structure

2. Nucleus(pl.,nuclei)
■ It controls the function of the
entire cell and can be thought of
as the “command center” of the
cell.
Nucleoplasm (a type of protoplasm)
■ it is the gelatinous matrix or base
material of the nucleus.
Chromosomes
■ These are embedded or suspended
in the nucleoplasm.
 Eukaryotic Cell Structure

Nuclear membrane
■ The membrane that serves as a “skin”
around the nucleus. It contains
holes(nuclear pores) through which
large molecules can enter and exit the
nucleus.
Genes
■ These are located along the DNA
molecules.
■ These are sometimes described as
“beads on a string”, each bead (gene)
is actually a particular segment of the
DNA molecule.
 Eukaryotic Cell Structure

Gene products
■ Each gene contains the genetic information that enables the cell to produce one or
more
Three types of Ribonucleic Acid(RNA)
■ A. Ribosomal ribonucleic acid
■ B. Transfer Ribonucleic acid
■ C. Messenger Ribonucleic acid

Genotype(genome)
■ The organism’s complete collection of genes
 Eukaryotic Cell Structure

■ Different species have

different numbers & sizes of
chromosomes.

Nucleolus
■ It is here that rRNA molecules
are manufactured
 Eukaryotic Cell Structure

3. Cytoplasm
■ It is a semifluid, gelatinous, nutrient
matrix.
■ These are found insoluble storage
granules and various cytoplasmic
organelles, including endoplasmic
reticulum, ribosomes, Golgi
complexes, mitochondria, centrioles,
microtubules, lysosomes and other
membrane-bound vacuoles.
■ The semifluid portion is sometimes
referred to as cytosol
 Eukaryotic Cell Structure

4. Endoplasmic Reticulum
■ It is a highly convoluted system of
membranes that are interconnected
and arranged to form a transport
network of tubules and flattened
sacs within the cytoplasm.
Rough endoplasmic reticulum
■ It has a rough, granular appearance
when observed by transmission
electron microscopy
Smooth endoplasmic reticulum
■ Ribosomes are not attached
 Eukaryotic Cell Structure

5. Ribosomes
■ They consist mainly of rRNA and protein and
play an important part in the
synthesis(manufacture) of proteins.
Polyribosomes or polysomes
it is held together by a molecule of messenger
RNA (mRNA)
■ Each eukaryotic ribosome is composed of two
subunits – a large subunit (60S subunit) and a
small subunit (40S subunit) – that are
produced in the nucleolus.
■ Subunits are then transported to the
cytoplasm where they remain separate until
such time as they join together with an mRNA
molecule to initiate protein synthesis
 Eukaryotic Cell Structure

6. Golgi Complex
■ It is also known as a Golgi
apparatus or Golgi body, connects
or communicates with the ER.
■ This stack of flattened,
membranous sacs completes the
transformation of newly
synthesized proteins into mature,
functional ones and packages them
into small membrane-enclosed
vesicles for storage within the cell
or export outside the cell.
 Eukaryotic Cell Structure

7. Lysosomes and Peroxisomes

■ Lysosomes – are small vesicles that originate at the Golgi complex
■ Autolysis – breaking down worn out parts of the cell and may destroy
the entire cell if the cell is damaged or deteriorating.
■ Peroxisomes – membrane-bound vesicles in which hydrogen
peroxide is both generated and broken down. These are found in most
eukaryotic cells but prominent in mammalian liver cells.
Lysosomes and Peroxisomes
 Eukaryotic Cell Structure

■ The energy necessary for cellular

function is provided by the
formation of high-energy
phosphate molecules such as ATP
– these are the major energy-
carrying or energy-storing
molecules within cells.
8. Mitochondria – referred to as the
“power plants”, “powerhouses”,
“energy factories” of the eukaryotic
cell because this is where most of the
ATP molecules are formed by cellular
respiration.
 Eukaryotic Cell Structure

9. Plastids – these are membrane-

bound structures containing various
photosynthetic pigments
Chloroplasts – one type of plastid,
contain a green, photosynthetic
pigment called chlorophyll. They are
found in plant cells and algae.
■ Photosynthesis – the process by
which light energy is used to
convert carbon dioxide and water
into carbohydrates and oxygen. It is
the conversion of light energy into
chemical energy.
 Eukaryotic Cell Structure

10. Cytoskeleton
■ It is present throughout the
cytoplasm, it is a system of
fibers
Three types:
■ Microtubules
■ Microfilaments(actin
filaments)
■ Intermediate filaments
■ Microtubules and
microfilaments are essential
for various activities such as
cell division, contraction,
motility and the movement of
chromosomes within the cell.
■ Microtubules are slender,
hollow tubules composed of
spherical protein subunits
called tubulins.
 Eukaryotic Cell Structure

11. Cell Wall

■ Cell walls of algae contain a
polysaccharide – cellulose – that is
not found in the cell walls of any
other microorganisms. It is also
found in the cell walls of plants.
■ Cell walls of fungi contain a
polysaccharide – chitin – that is
not found in the cell walls of any
other microorganisms. It is also
found in the exoskeletons of
beetles and crabs.
 Eukaryotic Cell Structure

12. Flagella (sing., flagellum) –

long, thin structures
■ Flagellates – flagellated
protozoa
■ Flagella – are referred to as
organelles of locomotion (cell
movement).
■ Cilia (sing,.cilium) – they are
also organelles of locomotion, but
they tend to be shorter(more hair-
like), thinner and more numerous
than flagella.
 PROKARYOTIC
CELL STRUCTURE
Prokaryotic Cell Structure

■ Prokaryotic cells are about 10 times

smaller than eukaryotic cells.
Prokaryotes are very simple cells when
compared with eukaryotic cells and yet
they are able to perform the necessary
processes of life.
■ Reproduction of prokaryotic cells is by
binary fission

1. Cell Membrane – similar in structure and

function to the eukaryotic cell membrane.
Mesosomes – inward foldings of the cell
membranes where cellular respiration takes
place in bacteria.
Prokaryotic Cell Structure

2. Chromosome
■ It consists of a single, long, supercoiled, circular DNA molecules which
serves as the control center of the bacterial cell.
■ Plasmid or extra-chromosomal DNA – small, circular molecules of
double-stranded DNA that are not part of the chromosome that may
also be present in the cytoplasm of prokaryotic cells. They have also
been found in yeast cells.
Prokaryotic Cell Structure

3. Cytoplasm – it consists of water, enzymes, dissolved oxygen, waste

products, essential nutrients, proteins, carbohydrates and lipids
4. Cytoplasmic Particles – prokaryotic ribosomes are smaller than
eukaryotic ribosomes but their function is the same.
5. Bacterial Cell Wall – the main constituent is a complex
macromolecular polymer known as peptidoglycan(also known as
murein), consisting of many polysaccharide chains linked together by
small peptide chains.
Prokaryotic Cell Structure

■ Gram-positive bacteria –
have a thick layer of
peptidoglycan combined with
teichoic acid and lipoteichoic
acid molecules.
■ Gram-negative bacteria –
have a much thinner layer of
peptidoglycan but this layer is
covered with a complex layer
of lipid macromolecules,
usually referred to as the
outer membrane.
Prokaryotic Cell Structure

6. Glycocalyx (Slime Layers and

Capsules)
■ Glycocalyx – is a slimy, gelatinous
material produced by the cell
membrane and secreted outside of
the cell wall.
Two types:
■ A. slime layer – is not highly
organized and is not firmly attached to
the cell wall. It easily detaches and
drifts away.
■ B. capsule – highly organized and
firmly attached to the cell wall. `
Prokaryotic Cell Structure

■ It can be detected using a capsule

staining procedure, which is a type of
negative stain.
■ S-colonies – encapsulated bacteria
usually produce colonies on nutrient agar
that are smooth, mucoid and glistening.
■ R-colonies – non-encapsulated bacteria
tend to grow as dry, rough colonies
■ Capsules serve an anti-phagocytic
function, protecting the encapsulated
bacteria from being phagocytized
(ingested) by phagocytic white blood
cells. Thus, they are able to survive longer
in the human body than non-capsulated
bacteria.
Prokaryotic Cell Structure

7. Flagella (sing., flagellum) – these are thread-like, protein appendages

that enable bacteria to move.
The number and arrangement of flagella possessed by a certain species
of bacterium are characteristic of that species.
■ Peritrichous bacteria – bacteria possessing flagella over their entire
surface (perimeter)
■ Lophotrichous bacteria – bacteria with a tuft of flagella at one end
■ Amphitrichous bacteria – bacteria having one or more flagella at
each end
■ Monotrichous bacteria - bacteria possessing a single polar
flagellum
Prokaryotic Cell Structure

■ Flagella stain – the number

of flagella that a cell
possesses and their locations
on the cell can be determined
using this stain.
■ Bacterial flagella consist of
three, four or more threads of
protein twisted like a rope.
They do not contain
microtubules and their
flagella are not membrane-
bound.
Prokaryotic Cell Structure

8. Pili(Fimbriae)
■ Pili(sing.,pilus) or
fimbriae(sing.,fimbria) are hair-like
structures, most often observed on
Gram-negative bacteria. They are
composed of polymerized protein
molecules called pilin.
Two types of pili
■ a. one type merely enables bacteria to
adhere or attach to surfaces
■ B. The other type(sex pilus) facilitates
transfer of genetic material from one
bacterial cell to another following
attachment of the cells to each other.
Prokaryotic Cell Structure

9. Spores (Endospores)
■ These are bacterial spores that
enables bacteria to survive in adverse
conditions such as temperature
extremes, desiccation and lack of
nutrients.
■ The process by which they are formed
is called sporulation.
■ Spores are resistant to heat, cold,
drying and most chemicals. It have
been shown to survive for many years
in soil or dust, and some are quite
resistant to disinfectants and boiling.
 SUMMARY OF STRUCTURAL DIFFERENCES
BETWEEN PROKARYOTIC AND EUKARYOTIC
CELLS
Prokaryotic Cell
■ Do not have true nucleus
■ Have complex cell walls
consisting proteins, lipids and
polysaccharides.
■ Possess no membranes other
than the cell membrane that
encloses the cytoplasm.
Eukaryotic Cell
■ True nucleus
2 types:
1. ANIMAL CELL – do not have a cell wall
2. PLANT CELL – have a simple cell wall that
usually contains cellulose
■ Contain membranous structures and
many membrane-bound organelles
■ Ribosomes (80S ribosomes) are larger and
denser than those found in prokaryotes.
Prokaryotic Cell Reproduction

■ They reproduce by a process known as binary fission in which one

cell(parent cell) splits in half to become two daughter cells.
■ Before it can divide in half, its chromosome must be duplicated, so
that each daughter cell will possess the same genetic information as
the parent cell.
■ Generation time the time it takes for binary fission to occur, varies
from one bacterial species to another and also depends on the growth
conditions.
TAXONOMY
 TAXONOMY

■ It is the classification of living organisms.

Three areas:
■ 1. Classification
■ 2. Nomenclature
■ 3. Identification
 CLASSIFICATION

■ It is the arrangement of organisms into taxonomic groups (taxa) on

the basis of similarities or relationships. It include kingdom or
domains, divisions or phyla, classes, orders, families, genera and
species.
 NOMENCLATURE &
IDENTIFICATION
Nomenclature
■ It is the assignment of names to the various taxa according to
international rules.

Identification
■ It is the process of determining whether an isolate belongs to one of
the established, named taxa or represents a previously unidentified
species.
 MICROBIAL CLASSIFICATION

■ The science of taxonomy was established, based on the binomial system

of nomenclature developed in the 18th century by the Swedish Scientist
Carolus Linnaeus.
■ In the binomial system, each organism is given two names: a).
Genus(pl.,genera) and b). Specific epithet. When together they are
referred to as the species.
■ To express the genus, capitalize the first letter of the word and underline
or italicize the whole world – for example, Escherichia.
■ To express the species, capitalize the first letter of the genus name and
then underline or italicize the entire species name – for example,
Escherichia coli.
 MICROBIAL CLASSIFICATION
Acceptable terms aside from the proper scientific names of bacteria
■ - staphylococci(for Staphylococcus spp.)
■ - streptococci (for Streptococcus spp.)
■ - clostridia (for Clostridium spp.)
■ - pseudomonads(for Pseudomonas spp.)
■ - mycoplasmas (for Mycoplasma spp.)
■ -rickettsias (for Rickettsia spp.)
■ - chlamydias (for Chlamydia spp.)
 MICROBIAL CLASSIFICATION

Nicknames and slang terms frequently used within hospitals:

■ GC and gonococci (for Neisseria gonorrhea)
■ Meningococci (for Staphylococcus or staphylococcal)
■ Pneumococci (for S. pneumonia)
■ Staph (for Streptococcus or streptococcal)
■ Strep (for Streptococcus or streptococcal)
 MICROBIAL CLASSIFICATION

■ In 1969, Robert H. Whittaker proposed a Five-Kingdom System of

Classification, in which all organisms are placed into five kingdoms:
 Bacteria and archaea are in the Kingdom Prokaryotae (Monera)
 Algae and protozoa are in the Kingdom Protista (Protists)
 Fungi are in the Kingdom Fungi
 Plants are in the Kingdom Plantae
 Animals are in the Kingdom Animalia
 MICROBIAL CLASSIFICATION

■ In the late 1970’s, Carl R. Woese devised a Three-Domain System of

Classification – it is based on differences in the structure of certain
rRNA molecules among organisms in the three domains.
Two domains of prokaryotes:
■ A. Archaea and Bacteria
■ Eucarya or Eukarya
 MICROBIAL CLASSIFICATION

■ Archaea comes from archae, meaning “ancient”

■ Bacteria been referred to as eubacteria meaning “true” bacteria but
are now usually referred to as bacteria
■ Domain Eukarya is divided into four kingdoms: Kingdom Protista or
Prototista (algae & protozoa); Kingdom Plantae; Kingdom Fungi;
Kingdom Animalia