What is Microbiology?

Essentially, microbiology is the study of biological organisms that

are too small to be seen with the naked eye (without using such
tools as the magnifying glass or microscope etc). Microbiology is
therefore dedicated to studying the lives and characteristics of a
wide variety of organisms ranging
from bacteria and archaea to parasitic worms in their
environments.
Although microbiology is, for the most part, described as the study
of microorganisms (those that cannot be seen with the naked eye),
such groups as algae and fungi contain organisms that do not
necessarily require the use of special tools to observe them.
Therefore, microbiology also encompasses a number of organisms
that fall outside the traditional definition.

Branches of Microbiology

The different branches of microbiology are classified into pure and

applied sciences as well as taxonomy.

Bacteriology
Bacteriology is the branch of microbiology concerned with the
study of bacteria. This branch is further divided into a number of
specializations that include marine bacteriology, sanitary
bacteriology, industrial bacteriology, agricultural bacteriology, and
systematic bacteriology among others.
Here, this branch of microbiology gives focus to such aspects as
types of bacteria and their characteristics, diseases, and
application among others.
Mycology
Unlike bacteriology which is the study of bacteria, which
are prokaryotic organisms, mycology deals with the study of fungi
which are eukaryotic in nature. Found in many types of
environments, the different types of fungi (mold and yeast) can be
highly beneficial or harmful.
Mycology gives focus to the different properties of these organisms
(characteristics, taxonomy, etc) which has it turn made it possible
to use them in various industries ranging from breweries to food
and medicine.
Those who specialize in mycology are known as mycologists.

Protozoology
Protozoology is one of the newer branches of microbiology based
on taxonomy. It is the sub-discipline that deals with the study
of protozoa. Like fungi, these are eukaryotic organisms that include
such groups as amoeboids, ciliates, sporozans , and flagellates.
Given that a good number of these organisms have been
associated with animals and human diseases, protozoologists not
only focus on their taxonomy and morphological aspects for
classification purposes, but also for medical significance.
Some common examples of diseases caused by protozoa include
malaria, sleeping sickness as well as amoebic dysentery.

Phycology

Like mycology, phycology is one of the branches of microbiology

that is concerned with the study of multicellular organisms. Unlike
mycology, however, phycology deals with the study of different
types of algae that can be found in different types of environment.
While they may exist as small microorganisms found floating in the
ocean, some algae grow to form large seaweeds found in the
aquatic environments.
Apart from being part of the food chain, algae are also involved in
the production of oxygen which makes them important in
microbiology.
Those who study phycology (e.g. Carl Adolph Agardh) are known
as phycologists.

Parasitology
Parasitology is a wide field of microbiology that deals with the study
of parasites. For the most part, parasitology is concerned with
organisms found in three major groups including
protozoa, helminths (worms) and arthropods.
Given that parasitology is concerned with disease-causing
organisms (as well as vectors) it has been influenced by a number
of other disciplines including immunology and biochemistry among
others.
Like mycology and phycology, parasitology entails the study of
both unicellular and multicellular organisms.
Those who study parasitology are known as parasitologists.

Immunology
Immunology is the sub-discipline that deals with the study of the
immune system. It has been one of the most important areas of
study since the 18th Century whose efforts are directed towards
enhancing the immune system to protect the body from diseases.
It is worth noting that while diseases are caused by various
organisms and foreign substances, they can also result from the
immune system itself in cases of autoimmunity.
By studying the relationship between the body, pathogens and the
immune system, researchers have made significant strides and
breakthroughs that have made it possible to eradicate diseases
that were once common in society.
These efforts continue to be seen in studies regarding such
diseases and Ebola among others outbreaks identified in different
parts of the world.
A person who studies immunology is known as an immunologist.

Virology
Virology is the branch of microbiology that is concerned with the
study of viruses. Unlike most of the other organisms which are
either described as being unicellular or multicellular, viruses are
acellular microbes with simple structures and need host cells to
multiply.
Given that viruses need host cells to multiply, they also, end up
affecting the cells and consequently causing disease.
In virology, researchers also focus on such aspects as
biochemistry, distribution, molecular biology as well as the
evolution of viruses which makes
it's possible to not only understand them, but also develop cures
to some of the most serious diseases caused by these parasites
(AIDs etc).

Nematology
Nematology is the sub-disciplines that deal with the study of
multicellular nematodes. Also known as roundworms, nematodes
include a variety of organisms (worms) found in a variety of
environments on earth (they can be found in soil, mud, sands,
mountains, etc).
According to studies, nematodes are some of the most abundant
organisms on our planet. Nematology, as a branch of microbiology,
has allowed for the classification of these worms based on their
general morphology, habitats as well as whether or not they cause
diseases, etc.
Those who study nematology are known as nematologists.

Apart from taxonomy, microbiology is also classified into pure

sciences.

Some of the most common categories include:

· Microbial cytology - deals with the structure and function of the
organisms
· Microbial physiology - is the branch of microbiology that deals
with the different parts and normal functions of the organisms
(functioning of the different parts of the organism)
· Microbial ecology - branch that deals with the
surroundings/habitat of the organism. This makes it possible to
understand how the organism interacts and affects its surroundings
· Microbial genetics - is concerned with the genetic makeup of
the organism. It is used to identify the different strains and
phenotypes of an organism and classify the organisms as such
 History of Microbiology

 Robert Hooke (1635 - 1703) was a “polymath’ he made many

scientific discoveries in the 17th century, including making
one of the first microscopes and also using a copy of one of
Leeuwenhoek’s microscopes to see and draw details of the
structure of plant cells and some microbes.
 Antony van Leeuwenhoek (1632-1723) made the first useful
microscopes in the 19th century, they were fiendishly difficult
to make and use, they were essentially a lens held in a metal
clip, the lens was made from a tiny drop of molten glass, and
he used such a microscope to see the first microscopic cells.
 Ilya Metchnikoff (1845-1916) was the first to realize that
animals such as us had a defence system against infection,
what we now call the immune system
 Paul Ehrlich (1854-1915), searched for the “magic bullet”
against infectious disease, he synthesized the first successful
(but very toxic) drug against a disease – syphilis, it was an
arsenic derivative he called salvarsan. Gerhardt Domagk
(1895-1964) developed the first useful drug against a variety
of bacterial infections, the first sulfa drug –prontosil.
Ironically, he died of an infection!
 Sir Alexander Fleming (1881-1955) and Selman Waksman
(1888-1973) discovered the first relatively safe and effective
 antibiotics (of natural origin) – isolated from microorganisms.
Fleming discovered penicillin, Waksman discovered
streptomycin and a number of other antibiotics.
 Louis Pasteur (1822-1895) was a chemist, he made many
great discoveries, and he performed a crucial experiment
using a swan necked flask that proved that new life did not
just spontaneously arise from substances like rotting meat.
For centuries before Pasteur, many people believed in
Spontaneous Generation- the belief that life is generated
spontaneously from dead organic matter.
 Robert Koch (1843-1910) and his colleagues made many
important discoveries in microbiology, Koch initiated the use
of the seaweed polysaccharide gel called agar as a stable
material for the formation of a gel on which separated and
pure (single species) colonies of bacteria and fungi could be
grown (actually it was the wife of a colleague of his who
suggested it), this was a critical advance, and he also stated
and used his Koch’s postulates (discussed later) required to
prove that a given organism caused a given disease.
 Applied Microbiology

Whereas taxonomy classification gives focus to the organism and

its general characteristics, applied microbiology is focused on how
various organisms can be used (applied) in given processes or the
impact they can have in different industries.

Some of the most important branches of microbiology based on

application include:
Food microbiology
Research studies focus on a variety of microorganisms that
contaminate/damage food and those that can be used for food
processing/modification among others. As such, microbiology gives
special attention to such microorganisms as molds, yeasts, and
bacteria among others that either benefit or have negative effects
on the quality of food material with public health concern in mind.
* Food microbiology is connected to several other fields
(immunology and molecular biology etc) and entails such aspects
as food processing and preservation, food ingredients, production
and fermentation among others.
Medical Microbiology
This is the branch of microbiology that is concerned with the
diagnosis, prevention and treatment of diseases caused by
different types of organisms (infection agents). This sub-discipline
is therefore related to a number of other fields including virology,
bacteriology, immunology, and germicrobiology.
Industrial microbiology
This branch of microbiology is concerned with the use of given
microorganisms for industrial production. Here, research studies
are directed towards the use of these organisms to increase and
maximize yields in industries like fuel, pharmaceutical, and
chemicals among others. Here, the use of microorganisms makes
it possible to mass produce for a big market.
Agricultural microbiology
Agricultural microbiology is concerned with microbes associated
with plants and animal diseases and production. As such, it is not
only concerned with the medical significance of these organisms,
but also their economic importance for farmers and the industry as
a whole. In the process, agricultural microbiology is aimed to solve
issues identified in agricultural practices while helping increase
yields for farmers.
Some of the other branches of microbiology based on application
include:
· Soil microbiology - This is the branch of microbiology that deals
with the study of soil microorganisms and how they impact soil
properties
· Pharmaceutical microbiology - Concerned with the use of
microorganisms for inhibiting contamination as well as the
development of pharmaceuticals
· Veterinary microbiology - Focus on microbes that cause
diseases
· Microbial biotechnology - Area of microbiology and
biotechnology aimed at using microbes for beneficial purposes: It
is aimed at enhancing microbial application in the day to day life. A
good example of this is the research study currently being
conducted (at the time of writing) to use given bacteria to replace
the traditional sewage systems by the Gates Foundation.
 Dental Caries

Cavities of the teeth, known clinically as dental caries, are

microbial lesions that cause damage to the teeth. Over time, the
lesion can grow through the outer enamel layer to infect the
underlying dentin or even the innermost pulp. If dental caries are
not treated, the infection can become an abscess that spreads to
the deeper tissues of the teeth, near the roots, or to the
bloodstream.

Tooth decay results from the metabolic activity of microbes that

live on the teeth. A layer of proteins and carbohydrates forms when
clean teeth come into contact with saliva. Microbes are attracted
to this food source and form a biofilm called plaque. The most
important cariogenic species in these biofilms is Streptococcus
mutans. When sucrose, a disaccharide sugar from food, is broken
down by bacteria in the mouth, glucose and fructose are
produced. The glucose is used to make dextran, which is part of
the extracellular matrix of the biofilm. Fructose is fermented,
producing organic acids such as lactic acid. These acids dissolve
the minerals of the tooth, including enamel, even though it is the
hardest material in the body. The acids work even more quickly on
exposed dentin (Figure 1). Over time, the plaque biofilm can
become thick and eventually calcify. When a heavy plaque deposit
becomes hardened in this way, it is called tartar or dental
calculus (Figure 2). These substantial plaque biofilms can include
a variety of bacterial species,
including Streptococcus and Actinomyces species.

Some tooth decay is visible from the outside, but it is not always
possible to see all decay or the extent of the decay. X-ray imaging
is used to produce radiographs that can be studied to look for
deeper decay and damage to the root or bone (Figure 2). If not
detected, the decay can reach the pulp or even spread to the
bloodstream. Painful abscesses can develop.

To prevent tooth decay, prophylactic treatment and good hygiene

are important. Regular tooth brushing and flossing physically
removes microbes and combats microbial growth
and biofilm formation. Toothpaste contains fluoride, which
becomes incorporated into the hydroxyapatite of tooth enamel,
protecting it against acidity caused by fermentation of mouth
microbiota. Fluoride is also bacteriostatic, thus slowing enamel
degradation. Antiseptic mouthwashes commonly contain plant-
derived phenolics like thymol and eucalyptol and/or heavy
metals like zinc chloride (see Using Chemicals to Control
Microorganisms). Phenolics tend to be stable and persistent on
surfaces, and they act through denaturing proteins and disrupting
membranes.

Regular dental cleanings allow for the detection of decay at early

stages and the removal of tartar. They may also help to draw
attention to other concerns, such as damage to the enamel from
acidic drinks. Reducing sugar consumption may help prevent
damage that results from the microbial fermentation of sugars.
Additionally, sugarless candies or gum with sugar alcohols (such
as xylitol) can reduce the production of acids because these are
fermented to nonacidic compounds (although excess consumption
may lead to gastrointestinal distress). Fluoride treatment or
ingesting fluoridated water strengthens the minerals in teeth and
reduces the incidence of dental caries.

If caries develop, prompt treatment prevents worsening. Smaller

areas of decay can be drilled to remove affected tissue and then
filled. If the pulp is affected, then a root canal may be needed to
completely remove the infected tissues to avoid continued spread
of the infection, which could lead to painful abscesses.
 Periodontal Disease

In addition to damage to the teeth themselves, the surrounding

structures can be affected by microbes. Periodontal disease is the
result of infections that lead to inflammation and tissue damage in
the structures surrounding the teeth. The progression from mild to
severe periodontal disease is generally reversible and
preventable with good oral hygiene.

Inflammation of the gums that can lead to irritation and bleeding

is called gingivitis. When plaque accumulates on the teeth,
bacteria colonize the gingival space. As this space becomes
increasingly blocked, the environment becomes anaerobic. This
allows a wide variety of microbes to colonize,
including Porphyromonas, Streptococcus, and Actinomyces.
The bacterial products, which
include lipopolysaccharide (LPS), proteases, lipoteichoic
acids, and others, cause inflammation and gum damage
(Figure 3). It is possible that methanogenic archaeans
(including Methanobrevibacter oralis and
other Methanobrevibacter species) also contribute to disease
progression as some species have been identified in patients
with periodontal disease, but this has proven difficult to
study.[1] [2] [3] Gingivitis is diagnosed by visual inspection,
including measuring pockets in the gums, and X-rays, and is
usually treated using good dental hygiene and professional dental
cleaning, with antibiotics reserved for severe cases.

Over time, chronic gingivitis can develop into the more serious
condition of periodontitis (Figure 4). When this happens, the
gums recede and expose parts of the tooth below the crown. This
newly exposed area is relatively unprotected, so bacteria can grow
on it and spread underneath the enamel of the crown and
cause cavities. Bacteria in the gingival space can also erode
the cementum, which helps to hold the teeth in place. If not
treated, erosion of cementum can lead to the movement or loss of
teeth. The bones of the jaw can even erode if the infection spreads.
This condition can be associated with bleeding and halitosis (bad
breath). Cleaning and appropriate dental hygiene may be sufficient
to treat periodontitis. However, in cases of severe periodontitis, an
antibiotic may be given. Antibiotics may be given in pill form or
applied directly to the gum (local treatment). Antibiotics given can
include tetracycline, doxycycline, macrolides or β-lactams.
Because periodontitis can be caused by a mix of microbes, a
combination of antibiotics may be given.