Historical Development and Divisions in Divisions of Microbiology

Microbiology
Based on Types of Microbes being studied
Microbiology is the study of organisms that are too (Pure Microbiology)
small to be seen by the naked eye, o Bacteriology – deals with bacteria
this includes: o Mycology – deals with fungi
• bacteria o Virology – deals with virus
• fungi o Protozoology –deals with protozoa
• viruses • which include some clinically
• protists are eukaryotic unicellular important microbes such as the
microscopic organisms that are not amoeba that causes diarrhea.
considered an animal plant or fungus o Phycology/Algology– deals with algae
o Parasitology- deals with parasites
 study of viruses (not technically classified as • that involves both multicellular
living organisms but do contain genetic parasites such as intestinal worms
material) and unicellular parasites such as
 all aspects of these microorganisms such as those that causes malaria.
their behavior, evolution, ecology, o Nematology- deals with nematodes
biochemistry, and physiology, along with the
pathology of diseases that they cause. Based on the study of microbes that integrate
✓ In clinical microbiology, the isolation and other fields of study (Integrative Arrangement)
identification of microorganisms that cause
diseases in humans is of primary Microbiology can also be classified according to its
importance. application or integration with other fields:
o Medical Microbiology- deals with pathogenic
1st Microorganism on Earth microbes
o Earth was formed about 4.5 billion years • the focus is on organisms that cause
ago diseases in humans and are
• first 800 million to 1 billion years of clinically important this concerns the
Earth’s existence - no life on this nature distribution pathogenesis and
planet treatment of microbial infection.
o Fossils of primitive microbes (as many as o Agricultural Microbiology –study of roles of
11 different types) found in ancient rock microbes in agriculture from the point of
formations in northwestern Australia to view of both harm and usefulness
about 3.5 billion years ago o Industrial Microbiology –study of microbes
o Animals appeared on Earth - 900 and 650 in industrial production (ex. Alcohol,
million years ago antibiotics)
o Humans (homo sapiens) - existed for only o Food and Dairy Microbiology –study of food
the past 100,000 years or so borne microbial diseases and their control
o First microbes on earth - Archaea and • in food microbiology the focus is on
Cyanobacteria microorganisms that are found to
contaminate food or those that are
we can see that microbes were some of the first used in the manufacture of food.
living organisms that inhabited the planet way o Aquatic Microbiology – study of
before humans did. microorganisms found in water
o Aero Microbiology –study of airborne
microorganisms
 o Environmental Microbiology –study of role region take for example the skin and
of microbes in maintaining the quality of the gastrointestinal tract they can
environment also be classified as opportunistic
o Geochemical Microbiology – deals with the pathogens or those that do not
role of microbes in coal, gas and mineral cause disease in healthy individuals
formation but may cause infection in
o Biotechnology –study of manipulation of immunocompromised individuals or
microbes at the genetic and molecular level they can be classified as true
to generate useful products (ex. Insulin) pathogens that cause disease in
• in biotechnology involving virtually all of its susceptible hosts.
microorganism useful products are o Unique physiology and metabolic pathways
synthesized by the genetic to survive
manipulation of microorganisms. For
example, genes coding for the Main roles of a diagnostic or clinical microbiologist
hormone insulin is inserted into host
organisms such as yeast or bacteria ✓ Now your role as a future medical
the said organisms will then produce technologist is to properly isolate correctly
insulin which will then be collected identify and analyze the microorganisms in
and be available for diabetic patients your sample to aid with the diagnosis and
o Immunology – deals with study of immune treatment of your patient.
responses to organisms
• the focus is on the ability of the body Knowledge of microbial structure and physiology
to ward of infections caused by is extremely important to clinical microbiologists
organisms. in 3 areas:
o Culture of organisms from patient
Significance of Microbiology specimens
• you must be knowledgeable and
Microorganisms are diverse when it comes skillful when it comes to culture and
to the resources they need and the location in isolation of organisms from different
which they can be found. Some can be found in the clinical samples.
environment, in the lakes, and rivers, and some in o Classification and identification of
the human body. organisms after they have been isolated
• you would then need to use different
Microorganism evolved to survive techniques such as microscopy and
o Various ecologic niches and habitats biochemical testing for identification.
o Some grow rapidly, some grow slowly o Prediction and interpretation of antimicrobial
o Some can replicate with a minimal number susceptibility patterns
of nutrients. Others require enriched • once identified, its susceptibility to
nutrients to survive different antibiotics will then be
o Variation exists in atmospheric growth determined.
conditions, temperature requirements, and
cell structure HISTORICAL DEVELOPMENT
o Inhabit the human body as normal biota
Anton van Leeuwenhoek was considered to be the
(normal flora), as opportunistic pathogens,
first true microbiologist and the father of
or as true pathogens
bacteriology.
• those that can be found in the
o “Beasties” in a water droplet
human body can be classified as
o “Father of Protozoology and
normal flora or microorganisms that
Bacteriology”
are the normal inhabitants of a body
ANIMALCULE- The word was invented by 17th-century Dutch
scientist Antonie van Leeuwenhoek to refer to the microorganisms he observed in rainwater.
Contributions of Leeuwenhoek: ✓ Observed spontaneous existence of fishes
1. Contributed the first microscope. from dried ponds, when the pond was filled
2. 1st person to observe microorganisms with rain.
(1673) • simple invertebrates could arise
3. Provided accurate description of bacteria through spontaneous generation.

✓ he was the first to observe living John Needham, in 1745 published experiments
microorganisms using his self-made claiming the spontaneous generation of
microscope with 50 to 300 times microorganisms in decayable fluids.
magnification. ✓ he experimented by boiling broth placing it
 he used the term besties or animal tools to on a flask and sealing it he then observed
describe the microorganisms. that the broth eventually became cloudy and
concluded that microorganisms generated
The following are early theories that tries to explain spontaneously but it may be that the broth
how individuals contract diseases and infections: was not sufficiently boiled to kill all the pre-
existing microbes in the first place.
Hippocrates, father of medicine, observed that ill
health resulted due to changes in air, winds, water, Lazzaro Spallanzani, opposed this view who
climate, food, nature of soil and habits of people. boiled beef broth for an hour, sealed the flasks, and
observed no formation of microbes.
Varro, disease was caused by animated particles  Spallanzani improved on the experiments
invisible to naked eyes but which were carried in by Needham
the air through the mouth and nose into the body. ✓ he boiled the broth completely sealed the
flask and observe no formation of microbes.
Fracastorius, agents of communicable disease
were living germs, that could be transmitted by Franz Schulze, Theodore Schwann, Georg
direct contact with humans and animals, and Friedrich Schroder and Theodor von Dusch
indirectly by objects; but no proof because of attempted to counter such arguments.
lacking experimental evidence.
John Tyndall, in 1877 proved and was able to
Roger Bacon, postulated that invisible explain satisfactorily the need for prolonged heating
living creatures produced disease. to eliminate microbial life from infusions.
✓ showed that dust carry organisms that could
Kircher, finding minute worms in the blood of contaminate sterile broth and explained that
plague victims, but with the equipment available to prolonged exposure to heat is necessary to
him, it is more likely that what he observed were kill off microorganisms.
only blood cells.
o Intermittent heating, now called
tyndallization, killed both heat-stable form
There are also theories on the origins of life on and a heat-sensitive form of bacteria.
earth: Theory of Abiogenesis • tyndalization is a form of sterilization
that uses moist heat for consecutive
Theory of spontaneous generation – living days to eradicate microorganisms.
things originated from non-living things
• postulates that life arises from non- Francesco Redi (1626-1697): first tried to set an
living matter experiment to disprove spontaneous generation /
life comes from pre-existing life
Aristotle, founder theory spontaneous generation  Redi was one of the first to disprove the
theory of spontaneous generation
 ▪ it is then concluded that microorganisms
can be present in the dust that flowed in the
air and may contaminate a sterile broth.

Major contribution of Louis Pasteur

Theory of Biogenesis

1. Microbial theory of fermentation

• he described that certain
✓ he placed fresh meat into two containers microorganism convert
leaving one open and the other sealed with carbohydrates into alcohol
cloth. Days later, he observed that the anaerobically a process called
exposed meat contained maggots and the fermentation
sealed one does not. He then demonstrated
that maggots came from flies that laid eggs 2. Principles and practice of sterilization and
on the meat disproving the theory of pasteurization
spontaneous generation. • he also emphasized the use of heat
in the preparation of wine to avoid
Louis Pasteur, disproved the theory of spoilage by the contamination of
abiogenesis or the theory of spontaneous unwanted microorganisms in a
generation. process called pasteurization
 Take note that the phrase “theory of
abiogenesis” and “theory of spontaneous 3. Control of diseases of silkworms
generation,” are used interchangeably
4. Development of vaccines against anthrax
and rabies.
• he also developed vaccines against
deadly infections such as anthrax
and rabies

o Designed a large curved flask (Pasteur 5. Discovery of streptococci

goose neck flask) and placed a sterile
growth broth medium. Air freely moved The Germ Theory of Disease
through the tube; but dust particles were The germ theory of disease is put forth to try and
trapped in the curved portion of flask. explain that microbes are responsible for infectious
o Microbial growth in the broth was not seen. diseases.
In his experiment, a sterile broth is placed in a
plastic with an s-shaped neck that is designed for Robert Koch, the discoverer of the causative agent
free movement of air while keeping the dust of anthrax and tuberculosis, gave postulates
particles from reaching the broth proving that germs indeed cause infections.
✓ no growth has been observed as the dust • The said microorganism must be present in
particles are trapped in the curvature of the all of the cases of the disease but must be
neck. absent from a healthy host.
✓ however, when the necks of the flask are • The microorganism must be able to be
broken off exposing the sterile broth to the isolated from the deceased host and can be
air above, microbial growth was observed. grown in pure culture.
• The same disease must be manifested
when the isolated microorganism is
inoculated into a healthy host and the same
 microorganism must be isolated again from 3. Many species are species specific. eg.
the inoculated host. Brucella abortus cause abortion in animals
but no report in humans.
4. Certain diseases develop only when an
opportunistic pathogen invades or found its
way into the system of an
immunocompromised host.

Personalities With Great Contribution to

Microbiology

The following are some of the most important

personalities and their contribution in the field of
microbiology:
Today, additional postulate is mentioned
Robert Koch is the proponent of the germ theory
e.g. Specific antibody to the bacterium should be
detectable in the serum during the disease.
Karl Landsteiner, apart from his discovery of the
major blood groups he also provided basis for
immunologic reactions

It has not been possible to fulfil every one

Alexander Fleming is famous for his accidental
of Koch’s postulates, but by adhering to
discovery of the antibiotic penicillin produced by the
them as closely as possible, serious errors
have been prevented. fungus penicillium no tattoo

Selman A Waksman discovered the streptomycin

another postulate has been added and that is and neomycin antibiotics
specific antibody against the microbe must be
present in the serum sample of the deceased host Susumu Tonegawa described the involvement of
genes in the production of antibody against foreign
Exceptions of Koch’s Postulates: substances
1. Many healthy people carry pathogens but
do not exhibit symptoms of the disease. Luc Montagneir is known for his discovery of the
• first some hosts can be carriers human immunodeficiency virus that causes aids
harboring microorganisms without
showing and or having signs and MICROBIAL TAXONOMY
symptoms.
2. Some microbes are very difficult or We all know that there are a lot of different
impossible to grow in vitro (in the laboratory) microbes that exist in virtually all places on earth
in artificial media. eg. Treponema pallidum. even in the human body.
• second some microbes are Naturally, microbiologists devised a way in
challenging to isolate and be grown order to characterize and arrange known microbes
in artificial media. Classic example is into categories so as to facilitate a more organized
the treponema pallidum, the way of studying microbial life. This is what microbial
bacterium that causes syphilis. taxonomy is all about.
o Diagnostic procedures for
syphilis typically relies on Taxonomy
microscopic and serologic Greek - taxes: arrangement; Greek - nomos: law
techniques.
 ➢ taxonomy is then a set of rules that arrange ❖ some microbes require additional
organisms in groups or classifications called nutrients than others
taxa (categories) ~ plural:taxon • Physiologic and biochemical characteristics,
❖ is determined different biochemical
Involves 3 structured, interrelated categories: tests
1. classification • Susceptibility or resistance to antibiotics or
2. nomenclature chemicals
3. identification ❖ their response to different antibiotics
or chemicals
Genotype - based on similarities and differences
genetic makeup Formal levels of bacterial classification in
• Base sequencing of DNA or RNA successively smaller taxa or subsets
• DNA base composition ratio to measure the
degree of relatedness

✓ taxonomy is based on similarities and

differences in the genotype and the
phenotype
✓ the term genotype is based on the genetic
makeup of an organism

Phenotype (readily observable physical and

functional features expressed by its genotype)
✓ the phenotype however, is about the This is a diagram showing each taxon each
observable characteristics or features of an of which is successively smaller than the one
organism that resulted from the expression preceding it for microbes.
of its genes the taxon are of the following:
1) Kingdom
Below are Phenotypic Characteristics: 2) Division/ Phylum
• Macroscopic (colony morphology on media) 3) Subphylum
❖ morphology of the organism as seen 4) Class
macroscopically from a culture 5) Family
media 6) Genus
• Microscopic (size, shape, arrangement into 7) Specific Epithet
groups or chains of organisms) morphology 8) Subspecies
❖ microscopic morphology of the
organism as observed under the `First is the domain followed by kingdom, division,
microscope that which include its class, order, family, tribe, genus, and species below
size shape. Is it round or elongated? the species level further subclassifications are also
arrangement or the bacterial cells used such as subspecies~ serotype and biotype
found singly in pairs tetrads or in and it all depends on the minor characteristics of
groups or clusters. the organism in question.
• Staining characteristics (gram-positive or
gram-negative)
❖ the staining characteristics or how
the microorganisms picked up the
stain that was applied to them before
microscopy
• Nutritional requirements
 Diagnostic microbiologists / three (occasionally
four or five) categories:
Even though there are several taxon in
taxonomy microbiologists use only a handful of
them when describing microorganisms that would
be the family, the genus, the species, and the
strain
1. Family - similar to a human “clan”
2. Genus (genera) - equivalent to a human
last name
There are three domains which are the most 3. Species (epithet) - equivalent to a human
inclusive and largest of all the taxon. first name
4. Strain
Eukaryotic organisms such as fungi, plants, Ex. Staphylococcus (genus) aureus (species
animals, humans, and protists belong under the epithet) belongs to the family Micrococcaceae
domain Eukarya
Strain is a sub-level below the species taxa it is
Bacteria are placed either in the domain bacteria given when an isolated organism from one source
or archaea has minor difference in characteristics with another
• Bacteria under the domain archaea are organism of the same species that is obtained from
some of the most robust microbes as they another source.
are lovers of the extremes and are found
in extreme environmental conditions. for example:
• a Staphylococcus aureus isolated from
✓ Bacteria are in domains Bacteria and patient A and is resistant to the antibiotic
Archaea, separate from the animals; plants penicillin
and protists are in domain Eukarya • Staphylococcus aureus is also isolated from
✓ Bacteria and Archaea include unicellular patient B but the organism is susceptible to
prokaryotic organisms. penicillin
✓ we can conclude that the S. aureus from
patient a and patient b are strains of the
SOME IMPORTANT MILESTONES IN TAXONOMY
same species

Carolus Linnaeus~ a french naturalist is

DICHOTOMOUS KEY
considered to be the “father of modern taxonomy”
as he was the first to devise the system of
The dichotomous key is a useful technique in
classification for organisms.
classifying organisms based on known criteria each
category may be posed or asked as a question.
o it is a dichotomous key because there are
always two options based on the
characteristics of an organism.
o by choosing the correct characteristic at
each stage, one would be able to classify an
organism under scrutiny the stages and
therefore the characteristics start from
general and then become more
*mas malake in another file* subsequently specific.
 ✓ Means of assigning an organism to a • to be able to follow a dichotomous key for
specific taxonomic category typically the identification of microbes, one must be
involves the use of specific criteria that may knowledgeable with the shape, staining
posed as questions (e.g. What does the characteristics, biochemical reactions, and
organism look like etc.) sensitivity to antibiotics of the microbes
 Relevant criteria may be arranged as a among others.
dichotomous key.
✓ Questions are arranged hierarchically with NOMENCLATURE
more general questions are asked first, with
questions becoming more specific asked Standard rules for denoting bacterial names:
subsequently. o family name is capitalized and has an “-
aceae” ending (Micrococcaceae)
❖ bacterial family names have
capitalized first letters and always
end with a c e a e

o genus name is capitalized and followed by

the species epithet, which begins with a
lowercase letter; both the genus and the
species should be italicized in print but
underlined when written in script (e.g.,
Staphylococcus aureus or Staphylococcus
aureus)
❖ in the specific name of an organism
there should be two words
this is an example of a dichotomous key for vertebrates so that
you can grasp its concept and usefulness
❖ the first one is the genus name
followed by the species epithet.
• In each stage a question is asked and two The first letter of the genus name is
options were given answerable by yes or no capitalized while the species is
written in lowercase letters or no
• as we go through each level therefore each
capitalization.
question, we are able to classify the
❖ in print, the scientific name should
organisms based on their characteristics
be italicized. When written by hand,
the scientific name should be
underlined rules.

o abbreviated by using the first letter

(capitalized) of the genus followed by a
period (dot) and the species epithet
(S. aureus)
it should still be italicized or underlined
whichever is appropriate.

o first two letters or the first syllable are used

when two or more genera names begin with
Dichotomous Keys for Bacterial Identification are much the same first letter
more complicated but the concept is the same (Staph. and Strept. for Staphylococcus and
Streptococcus)
 o when the genus name followed by the word ❑ Eukaryotes - fungi, algae, protozoa,
species is encountered it usually denotes animals, and plants
the genus as a whole. ▪ eukaryotes or those with membrane
(Staphylococcus species) bound nucleus are categorized
under the domain Eukarya.
o when the genus name is followed by the ❑ Archaea (Archaeobacteria) - more closely
word sp for singular or spp for plural it related to eukaryotic cells / found in
usually denotes that the species epithet is microorganisms that grow under extreme
not specified environmental conditions / lack
❖ for example, Staphylococcus sp we peptidoglycan.
are referring to a single unspecified ▪ most resistant microorganism falls
species of bacterium under the under this domain.
genus staphylococcus.
Archaea (Greek: (archaics) ancient, origin from the
Classification by Phenotypic and Genotypic earliest cells)
Characteristics • has cell wall, plasma membrane, ribosomes
and flagella (no nucleus and membrane –
❑ Subspecies - based on phenotypic bound organelles)
differences (abbreviated “subsp.”) • Never contain peptidoglycan – contain
▪ phenotypic differences can be protein or glycoprotein wall structure known
denoted by the use of subspecies. as S-layer
❑ Serovarieties - based on serologic
differences (antigenic properties) Extremophiles - lovers of the extreme conditions
(abbreviated “serovar”) ❑ halophiles (salt-loving cells) in Utah’s Great
▪ differences based on serologic Salt Lake
reactions or antigen antibody related ▪ halophiles live in environments with
reactions can be denoted by the use high salinity or salt concentrations.
of severovarieties. ❑ thermophiles (heat-loving cells) in hot
❑ Biovarieties – based on biochemical or springs and deep ocean vents
physiological test result differences ▪ thermophiles or those that are found
(abbreviated “biovar”) in hot springs and deep ocean vents
▪ differences based on biochemical thrive in environments with extreme
tests are denoted using biovarieties. heat
❑ Phage typing - based on susceptibility to ❑ anaerobic methanogens give off swamp
specific bacterial phages gas and inhabit the intestinal tracts of
❑ Analysis of ribosomal RNA (rRNA) animals.

Classification by Cellular Type

Organisms can also be classified according

to the type of cell:
❑ Prokaryotes - domains Archaea and
Bacteria (Eubacteria)
▪ prokaryotes or simple cells lacking
membrane-bound nucleus fall under
the domains, bacteria and archaea.
▪ bacteria fall in either of these two
domains.