SE 404 - Microbiology and Parasitology
Reviewer Notes
SECTION 1. INTRO TO MICROBIOLOGY
Chapter 1. Microbiology — The Science 2. ACELLULAR MICROBES - are
called the non living microbes or
BIOLOGY - the study of living organisms “infectious particles” such as viroids,
prions, and viruses.
MICROBIOLOGY - the study of microbes,
microscopic organisms, and certain non Discussion Notes:
living entities - Acellular Microbes are basically just
particles/molecules first before
MICROBES - are ubiquitous living and non invading a living cell. In which, they
living organisms that cannot be seen by the live and reproduce there.
naked eye but with an instrument called
microscope. From the word “micro” - Acellular Microbes can also cause
(extremely small). cell death and take certain traits
from the living cell it’s invading
The two categories of Microbes in terms of
life are Cellular and Acellular Microbes: MICROSCOPE - is an optimal instrument
1. CELLULAR MICROBES - are called used to observe very small objects
the living microbes or simply,
“microorganisms”. Examples of
these include bacteria, archaea,
some algae, protozoa, and fungi.
Discussion Notes:
- Archaea is one of the three domains
of life along with Bacteria and
Eukarya.
- Archaea can be found in extreme
environments/conditions such as GERMS - the non-scientific or common
extreme pH conditions, high acidity, name used for microbes
permafrost, and higher temperatures
while Bacteria can be found The two categories of Microbes in terms of
everywhere virtually or ubiquitous. its ability to cause diseases are Pathogens
and Nonpathogens:
- Similarly to Eukaryotic Organisms 1. PATHOGENS - the scientific term
(has nucleus and membrane bound used to describe disease-causing
organelles), Archaea also possesses microbes. Only 3% of microbes are
these. pathogenic.
2. NONPATHOGENS - are microbes caused by a bacteria called
that do not cause diseases. The vast Clostridium perfringens
majority of microbes are
nonpathogens where some are even 2. MICROBIAL INTOXICATION -
beneficial. occurs when a pathogen produces a
toxin in vitro by a person ingesting
INDIGENOUS MICROBIOTA (Human the toxin which the latter causes
Microbiome or Human Bioneme) - are the diseases. These cannot be
microbes that live on or in the human body. transmitted to others unless they
● OPPORTUNISTIC PATHOGENS ingested the same trigger or
(Opportunists) - are microbes that microbe. Examples are the ff:
don’t cause diseases in ordinary
conditions but have the potential to a. Staphylococcal Food
cause disease themselves when Poisoning - is a
opportunity presents itself. gastrointestinal illness
caused by the
Discussion Notes: Staphylococcus aureus
- Opportunistic Pathogens find bacteria whenever a person
opportunity whenever there’s touches a food with the
“Immunocompromise”. This is when bacteria on their skin. Then,
the body experiences a person ate that food with
poor/compromised health conditions the bacteria on it.
or low immune system
b. Foodborne Botulism - is a
The two categories of diseases caused by rare and serious fatal
Pathogens disease that is caused by the
1. INFECTIOUS DISEASES - occurs ingestion of potent
when a pathogen colonizes a neurotoxins, botulinum
person’s body which then toxins, and the bacteria
reproduces and infects the body Clostridium botulinum from
causing a disease. This can then be contaminated foods like
transmitted to others by direct improperly canned goods.
contact from the infected body.
Examples are the ff: Why Study Microbiology?
a. MRSA (Methicillin-resistant 1. Microorganisms are essential for life.
Staphylococcus aureus) These microbes actually produce
Infection - caused by a more oxygen in the atmosphere than
staph bacteria (harmless plants (photosynthetic algae and
bacteria found on the skin) bacteria like cyanobacteria) .
that became resistant to Making them a producer of oxygen
many staph antibiotics in photosynthesis.
b. Gas gangrene - is a highly
lethal infection of soft tissue
2. Microbes are also used in the cycle, the nitrates are converted
process of decomposition of dead back to nitrogen gas by other
organisms and living organisms’ bacteria.
waste products. These are called the
decomposers or saprophytes: Microbial Ecology - is the study of
relationships between microbes and
Saprophyte – an organism that lives the environment. This is represented
on dead or decaying organic matter in plant cropping and composting.
which also aids in fertilization by
returning inorganic nutrients to the Discussion Notes:
soil. - “Biological Waste Treatment”
requires a significant ratio of
Decomposition - process by which “Organic Matter” (Carbon)
substances are broken down into and “Nutrients” (Nitrogen and
simpler forms of matter. Phosphorus)
3. Microbes are also capable of - “Nitrogenous Compounds /
decomposing industrial wastes and Nitrogen Species” are
cleaning up toxic wastes which is a Ammonia (NH3) or
process known as Bioremediation. Ammonium (NH4), Nitrates
(NO3) and Nitrites (NO2)
For example, Pseudomonas putida
is a bacterium (microbe) used in oil - There are two processes in
spill remediation. the Nitrogen Cycle:
4. Microbes are also used in different A. NITRIFICATION - an
elemental cycles such as carbon, aerobic process by which
nitrogen, oxygen, sulfur, and reduced nitrogen compounds
phosphorus cycles. (usually Ammonia) are
converted to Nitrates and
Biogeochemical Cycle - is a Nitrites. This process does
general cycle of nutrients including not include the conversion of
carbon, nitrogen, hydrogen, oxygen, Nitrogen Gas to Ammonia for
sulfur, and phosphorus from the soil it does not use the Nitrifying
to the atmosphere and then back to Bacteria in its soil.
soil through various chemical
processes. B. DENITRIFICATION - is an
anaerobic process by which
Nitrogen Cycle - a process in which microbes convert all the
certain bacteria convert nitrogen gas nitrogenous compounds
from the air to ammonia (NH3) in the (usually Nitrates, Nitrites, and
soil. Then, the soil bacteria convert Urea) back to nitrogen gas
the ammonia to nitrites (NO2) and (N2)
nitrates (NO3). Completing the
- “Nitrifying Bacteria” are
oxygen-requiring microbes
used in Nitrification. While
“Denitrifying Bacteria” use
the redox of nitrates to
oxidize the carbon. Thus,
resulting in the creation of
nitrogen gas back in the
atmosphere.
- “Nitrogen Fixing Bacteria” are
5. Microbes like algae and bacteria
the microbes that convert
serve as foods by small creatures
Nitrogen Gas to Ammonia (or
which start the food chain among
the Fixed Nitrogen).
organisms.
“Plant-microbe Interaction”
occurs here.
Planktons - are microscopic
organisms in the ocean serving as
- Why is it essential to dig the
the starting point of many food
soil around plants? So that it
chains. Phytoplanktons are the tiny
causes more space for
marine plants and algae whilst
oxygen to be absorbed by
Zooplanktons are the tiny marine
the microbes to live in the
animals.
environment.
6. Microbes can also be found living in
- Nutrients like Nitrogen and
intestinal tracts of animals and in the
Phosphorus can benefit
digestion of food producing
plants but can also harm
beneficial substances. These are
aquatic life and environment
called the Gut Microbiota/
due to “Eutrophication”.
Microbiome (the small community/
composition of the gut).
- Bacteria does not only
depend on oxygen but also
7. Microbes have also been used as
“ATP (Adenosine
cell models so that it can represent
Triphosphate)” for energy
or act as a specific microcellular
and metabolism
process.
8. Biotechnology is the use of living
organisms or their derivatives to
make or modify useful products or
processes. Thus, making microbes
useful in various industries like food,
beverages, agriculture, and
medicine.
9. Microbes like some bacteria and First Microorganisms on Earth
fungi produce antibiotics to treat
patients with infectious diseases. 4.5 Billion Years Ago - formation of Earth.
For the first 800 million to 1 billion years,
Antibiotic - is a substance produced there are no signs of life
by a microbe that is effective in
killing or inhibiting the growth of 3.5 Billion Years Ago - dating of fossils of
other microbes. primitive microbes found in ancient
sandstone formation from northwestern
10. Microbes are also an essential part Australia
of the field of Genetic Engineering.
It is where gene/s from one 900 - 650 Million Years Ago - animals
organism is/are inserted into a emerged
bacterial or yeast cell. Because a
gene contains the instructions for the 100,000 Years Ago - human species,
production of a gene product specifically the present form Homo sapiens
(usually a protein), the cell that started to exist
receives a new gene can now
produce whatever product is coded 3180 B.C. - first found evidence of
for by that gene; so too can all of the pestilence (fatal epidemic disease like the
cells that arise from the original cell. bubonic plague) in Egypt
Discussion Notes: Infectious diseases of humans and animals
- These engineered microbes have existed for as long as animals and
then produce various useful humans exist.
substances such as insulin,
growth hormones, vaccines, Archaea and Cyanobacteria are the
and interferons. candidates for the first microbes on Earth
- Three steps of Genetic Pioneers in the Science of Microbiology
Engineering includes:
1. Collection of DNA Anton van Leeuwenhoek (1632 - 1723)
(deoxyribonucleic ● First person to see live bacteria and
acid) protozoa
● “Father of Microbiology”, “Father of
2. PCR (Polymerase Bacteriology” or “Father of
Chain Reaction) - Protozoology”
obtaining traits from ● Was not a trained scientist but had
an enzyme in order to hobbies like grounding tiny glass
multiply DNA lenses and then mounting in small
fragments metal frames which is now known as
single-lens microscope or simple
3. Amplification microscope
● He observed “animalcules” (tiny 73 deg Celsius to 75 deg Celsius for
living creatures) 15 seconds.
● Developed vaccines for chicken
Additional Notes: cholera, anthrax, swine erysipelas,
- From his observations, many and rabies
scientists postulated different
theories about these living creatures. Robert Koch (1843 - 1910)
It started with the “theory of ● German physician that made
spontaneous generation” or numerous contributions to
abiogenesis — the idea that life can microbiology
arise spontaneously from nonliving ● Made significant contributions to the
material. germ theory of disease
● Discovered that Bacillus anthracis
- However, between 1650 to 1850, the produced spores
theory was debated and was later ● Developed methods of fixing,
debunked by the works of Louis staining, and photographing bacteria
Pasteur and John Tyndall . ● Developed methods of cultivating
bacteria on solid media. These
- German Scientist Rudolf Virchow, methods enabled Koch to obtain
in 1858, proposed the theory that pure cultures (a condition in which
debunked the previous theory called only one type of organism is growing
biogenesis — proving that life can on a solid culture medium or in a
only arise from preexisting life liquid culture medium in the
laboratory; no other types of
Louis Pasteur (1822 - 1895) organisms are present) of bacteria.
● French chemist who made
numerous contributions to Koch’s Postulates
microbiology A scientific procedure, published in 1884,
● Investigated different fermentation proving that a microbe is the cause of a
products produced by various specific infectious disease.
microbes
● Discovery of organisms that can live 1. A particular microbe must be found
without oxygen where he introduced in all cases of the disease and must
the terms aerobes (organisms not be present in healthy animals or
requiring oxygen to live) and humans.
anaerobes (organisms that don’t)
● Developed the process of 2. The microbe must be isolated from
Pasteurization — a method to kill the diseased animal or human and
pathogens in many types of liquid grown in pure culture in the
which started because of wine laboratory.
spoilage. Today, it is acquired by
heating the liquid to 63 deg Celsius 3. The same disease must be
to 65 deg Celsius for 30 minutes or produced when microbes from the
pure culture are inoculated into
healthy susceptible laboratory host cells. This includes viruses,
animals. rickettsias, and chlamydia. In
addition, these can be grown instead
4. The same microbe must be in cell cultures (cultures of living
recovered from the experimentally animals, human or animal cells of
infected animals and grown again in various types), embryonated chicken
pure culture. eggs, or certain animals (“laboratory
animals”).
After completing these steps, the
microbe is said to have fulfilled Koch’s - Fastidious (fussy) is a characteristic
Postulates and has been proven to be the of microbes having complex and
cause of that particular infectious disease. demanding nutritional requirements
Koch’s Postulates not only helped to
prove the germ theory of disease, but also
gave a tremendous boost to the
development of microbiology by stressing
laboratory culture and identification of
microbes.
Circumstances do exist in which
Koch’s Postulates cannot be fulfilled like
opportunistic pathogens and certain
pathogens not growing on artificial media
like viruses, rickettsias, and chlamydias.
Additional Notes:
- Koch’s Postulate is also the
foundation of Modern Disease
Diagnosis — meaning that if there
are no microbes responsible for that
disease, it is not named as that
specific disease.
- In order to be infected with a
disease, there are always causative
agents that will trigger it (these are
usually microorganisms or particles
like viruses)
- Obligate Intracellular Pathogens
(or Obligate Intracellular
Parasites) are pathogens that can
survive and multiply only within living
Careers in Microbiology 2. What are obligate intracellular
pathogens?
MICROBIOLOGIST - a scientist that studies - Pathogens that can survive
microbiology. Within this, there are also and multiply only within living
various fields: host cells
● BACTERIOLOGIST - bacteriology
(bacteria) 3. Who introduced the terms “aerobes”
● PHYCOLOGIST - phycology (algae) and “anaerobes?”
● PROTOZOOLOGIST - protozoology - Louis Pasteur
(protozoa)
● MYCOLOGIST - mycology (fungi) 4. What are “anaerobes” and
● VIROLOGIST - virology (viruses) “aerobes”?
● PARASITOLOGIST - parasitology - Anaerobes are organisms
(parasites) that don’t require oxygen to
live while aerobes are the
Medical and Clinical Microbiology opposite
MEDICAL MICROBIOLOGY - involves the
study of pathogens, the disease they cause,
and the body’s defenses against disease. It
is concerned with epidemiology,
transmission of pathogens,
disease-prevention measures, aseptic
techniques, treatment of infectious
diseases, immunology, and production of
vaccines.
● CLINICAL MICROBIOLOGY or
DIAGNOSTIC MICROBIOLOGY -is
concerned with the laboratory
diagnosis of infectious diseases of
humans.
Increase your Knowledge:
1. Who is Rudolf Virchow?
- a German scientist that
proposed the theory that
debunked the theory of
spontaneous generation
(abiogenesis) which is
biogenesis. Stating that life
comes from preexisting life