Microorganism usually require a microscope to be seen.

Although
microbes are the cause of epidemics of infectious disease, there are many
positive examples of human-microbe interactions. Microbes have incredible
diversity and possess ecological importance.
-Tortora et al., 2019

At the end of this unit, you will be able to:

1. Know the basic concepts of Microbiology
2. Learn the history of Microbiology.

Multiple Choice ANSWERS:

Directions: Write your answer on the box provided.
1.
2.
1.Which of the following is NOT true of microorganisms? 3.
a.. They produce antibiotics.
4.
b. They are used in production of many types of food and beverages.
c. They decompose dead organisms. 5.
d. They all cause disease in humans.

2. Microorganisms are found:

a. In and on the bodies of warm-blooded mammals.
b. In soil.
c. In air.
d. Microorganisms are found in all of the above places.

3. Microbiology is the study of microorganisms which include all of the following except:
a. Bacteria
b. Viruses
c. Plants
d. Protozoa

4. Which of the following fields is concerned with the study fungi?

a. Bacteriology
b. Physiology
c. Virology
d. Mycology

5. Microorganisms are nearly ubiquitous (found everywhere) in the environment.

A. True
B. False

Thank you for answering the test.

If you got a score below 5, go to the following links

The Fundamentals of Microbiology

https://www.youtube.com/watch?v=Ye7zdnZ5RuY&ab_channel=Fis
heriesScienceEdu,

for further information

The next section is the content of this unit. It contains vital information
on the basics of Microbiology. Please read the content.
I. MICROBES IN OUR LIVES
Microbes, also called microorganisms, are minute living things that individually are usually
too small to be seen with the unaided eye. The group includes bacteria, fungi (yeasts and
molds), protozoa, and microscopic algae. It also includes viruses, those noncellular
entities sometimes regarded as straddling the border between life and nonlife. Often
associated only with infections and inconveniences such as spoiled food, microorganisms
are however important in maintaining Earth’s ecological balance.

The Microbiome
Everyone has microorganisms in and on the body. An adult human is composed of about
30 trillion body cells and harbors another 40 trillion bacterial cells, these make up the
normal microbiota or human microbiome. The normal microbiota is needed to maintain
good health.
Figure 1. Examples of Organisms that Occur as Members of the Microbiota of the Human
Gastrointestinal Tract and their Location

Note: A Photo of Examples of organisms that occur as members of the microbiota of the human
gastrointestinal tract and their location. Adapted from “Medical Microbiology and Immunology 6th Edition
(p.54)” by Goering et al. Copyright 2019 by Elsevier Limited.
Humans and many other animals depend on these microbes to maintain good health.
▪ Bacteria in our intestines, including E. coli, aid digestion and even synthesize some
vitamins that our bodies require, including B vitamins for metabolism and vitamin
K for blood clotting.
▪ They also prevent growth of pathogenic (disease-causing) species that might
otherwise take up residence, and they seem to have a role in training our immune
system to know which foreign invaders to attack and which to leave alone.

Our bodies begin to be populated with bacteria, even before birth. As newborns, we
acquire viruses, fungi, and bacteria. Microbes can colonize only those body sites that can
supply the appropriate nutrients. Temperature, pH, and the presence or absence of
chemical compounds are some factors that influence what types of microbes can flourish.
Figure 2. Several Types of Bacteria Found as Part of the Microbiota in an Infant’s
Intestine.

Note: A Photo Several types of bacteria

found as part of the microbiota in an
infant’s intestine. Adapted from
“Microbiology An Introduction 13th Edition
(p. 2)” by Tortora et al. Copyright 2019 by
Pearson Education, Inc.

To determine the makeup of typical microbiota of various areas of the body, and to
understand the relationship between changes in the microbiome and human diseases, is
the goal of the Human Microbiome Project, which began in 2007. Likewise, the National
Microbiome Initiative (NMI) launched in 2016 to expand our understanding of the role
microbes play in different ecosystems, including soil, plants, aquatic environments, and
the human body.
NAMING AND CLASSIFYING MICROORGANISMS

Nomenclature
The system of nomenclature (naming) for organisms in use today was established in 1735
by Carolus Linnaeus. Scientific names are latinized because Latin was the language
traditionally used by scholars. Scientific nomenclature assigns each organism two names:
a. genus- (plural: genera) is the first name and the first letter is always capitalized
b. specific epithet- (species name) and is not capitalized.

The organism is referred to by both the genus and the specific epithet, and both names
italicized. For instance, Lactobacillus casei is a probiotic strain with health benefits.
Lactobacillus is the genus, casei is the specific epithet or species name. When
handwritten, you can underline the genus and species name separately, Lactobacillus
casei.

By custom, after a scientific name has been mentioned once, it can be abbreviated with
the initial of the genus followed by the specific epithet. So since the scientific name of the
probiotic strain was already mentioned above, you can write L.casei in the succeeding
sentences.

Scientific names can, among other things, describe an organism, honor a researcher, or
identify the habitat of a species, see table below.
Table 1. Scientific Name Examples
Types of Microorganisms
a. Bacteria
▪ Bacteria (singular: bacterium) are relatively simple, single-celled (unicellular)
organisms. Because their genetic material is not enclosed in a special nuclear
membrane, bacterial cells are called prokaryotes, from Greek words meaning
prenucleus. Prokaryotes include both bacteria and archaea.
Figure 3. (a) The Rod-shaped Bacterium Haemophilus influenzae, One of the Bacterial
Causes of Pneumonia. (b) Diagrammatic Structure of a Generalized Bacterium

b.

Note: A Photo of The rod-shaped

bacterium Haemophilus influenzae, one
of the bacterial causes of pneumonia.
Adapted from “Microbiology An
Introduction 13th Edition (p.5)” by Tortora
et al. Copyright 2019 by Pearson
a. Education, Inc.

▪ Bacteria are classified according to their cell wall as Gram-positive or Gram-

negative.
o Gram staining is a basic microbiological procedure for identification of
bacteria
o The main structural component of the cell wall is ‘peptidoglycan’
(mucopeptide or murein), a mixed polymer of hexose sugars (N-
acetylglucosamine and N-acetylmuramic acid) and amino acids.
o In Gram-positive bacteria, the peptidoglycan forms a thick (20–80 nm) layer
external to the cell membrane, and may contain other macromolecules.
o In Gram-negative species, the peptidoglycan layer is thin (5–10 nm) and is
overlaid by an outer membrane, anchored to lipoprotein molecules in the
peptidoglycan layer.
b. Archaea
▪ Archaea consist of prokaryotic cells; they lack peptidoglycan in their cell walls.
▪ Archaea are often found in extreme environments, are divided into three main
groups:
o methanogens-produce methane as a waste product from respiration
o extreme halophiles (halo - salt; philic - loving) live in extremely salty
environments such as the Great Salt Lake and the Dead Sea. -
o extreme thermophiles (therm - heat) live in hot sulfurous water, such as
hot springs at Yellowstone National Park
▪ Archaea are not known to cause disease in humans.

Figure 4. A Scanning Electron Micrograph of Archaea Methanocaldococcus villosus.

Note A Photo of A scanning electron micrograph showing the archaea Methanocaldococcus villosus. Adapted
from “What is a Microbe? https://ocean.si.edu/oceanlife/microbes/marine-microbes. Photo Courtesy of Gerhard
Wanner, University of Munich, Germany
FUNGI
▪ Fungi such as mushrooms, molds, and yeasts, have eukaryotic cells (cells with a
true nucleus). Organisms in the Kingdom Fungi may be unicellular or multicellular.
• Fungi are distinct from plants and animals, have a thick chitin-containing cell wall,
and grow as filaments (hyphae) or single-celled yeasts.
▪ The unicellular forms of fungi, yeasts, are oval microorganisms that are larger than
bacteria. The most typical fungi are molds.

Figure 5. Mucor, a Common Bread Mold

Note: A Photo of Mucor, a common bread

mold. Adapted from “Microbiology An
Introduction 13th Edition (p.5)” by Tortora
et al. Copyright 2019 by Pearson
Education, Inc.

▪ Fungi obtain nutrients by absorbing organic material from their environment.

▪ Fungi can reproduce sexually or asexually. They obtain nourishment by absorbing
organic material from their environment— whether soil, seawater, freshwater, or
an animal or plant host.
PROTOZOA
▪ Protozoa are unicellular eukaryotes, ranging in size from 2 to 100 nm.
▪ Protozoa move by pseudopods, flagella, or cilia.
▪ Amoebae move by using extensions of their cytoplasm called pseudopods (false
feet).
▪ Other protozoa have long flagella or numerous shorter appendages for locomotion
called cilia. Protozoa have a variety of shapes and live either as free entities or as
parasites (organisms that derive nutrients from living hosts) that absorb or ingest
organic compounds from their environment.
Figure 6. An Amoeba Approaching a Food Particle.

Note: A Photo An amoeba approaching a

food particle. Adapted from “Microbiology
An Introduction 13th Edition (p.5)” by
Tortora et al. Copyright 2019 by Pearson
Education, Inc.

▪ Many protozoal species are free-living, but others are important parasites of
humans.
▪ Some free-living species can infect humans opportunistically. Protozoa continue
to multiply in their host until controlled by its immune response or by treatment and
thus may cause particularly severe disease in immunocompromised individuals.
ALGAE
▪ Algae are unicellular or multicellular eukaryotes that obtain nourishment by
photosynthesis (unicellular ones are the algae of interest of microbiologists)
▪ Exhibit both sexual and asexual reproductive forms.
▪ The cell walls of many algae are composed of a carbohydrate called cellulose.
▪ Algae are abundant in freshwater and saltwater, in soil, and in association with
plants.
▪ As photosynthesizers, algae need light, water, and carbon dioxide for food
production and growth, but they do not generally require organic compounds
▪ Algae produce oxygen and carbohydrates that are used by other organisms.
▪
Figure 7. The Pond Alga, Volvox.

Note: A Photo The pond alga Volvox.

Adapted from “Microbiology An
Introduction 13th Edition (p.5)” by Tortora
et al. Copyright 2019 by Pearson
Education, Inc.
VIRUSES
▪ Viruses are noncellular entities that are parasites of cells.
▪ Viruses consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat.
An envelope may surround the coat.
▪
Figure 8. Zika virus (ZikV).

Note: A Photo The pond alga Volvox.

Adapted from “Microbiology An
Introduction 13th Edition (p.5)” by Tortora
et al. Copyright 2019 by Pearson
Education, Inc.

▪ Viruses are considered to be living only when they multiply within host cells they
infect.
▪ Viruses are metabolically inert and can replicate only after infecting a host cell and
parasitizing the host’s ability to transcribe and / or translate genetic information.
▪ Viruses infect every form of life. They cause some of the most common and many
of the most serious diseases of humans, including cancer.
▪ Some insert their genetic material into the human genome and others can remain
latent in different cell types and then reactivate at any time, but especially if the
body is stressed or the immune system is compromised.
Figure 9. Stages in the Infection of a Host’s Cell and Replication of a Virus.

Note: A Photo Stages in the infection of a

host’s cell and replication of a virus.
Adapted from “Medical Microbiology and
Immunology 6th Edition (p.28)” by
Goering et al. Copyright 2019 by Elsevier
Limited.

▪ Viruses are difficult targets for antiviral agents as it is difficult to target only those
cells infected by the virus. However, many can be controlled by vaccines.
HELMINTHS
▪ Helminths are parasitic worms.
▪ Three groups:
o Tapeworms (Cestoda)
o Flukes ((Trematoda)
o Roundworms (Nematoda)
▪ Helminths are often large organisms with a complex body organization. Although
invading larval stages may measure only 100–200 μm, adult worms may be
centimetres or even metres long.
▪
Figure 10. Filariform Larvae, the Infective Stage of Strongyloides stercoralis

Note: A Photo of Filariform larvae, the infective stage of Strongyloides stercoralis. Courtesy of Peter
Chiodini. Adapted from “Medical Microbiology and Immunology 6th Edition (p.28)” by Goering et al.
Copyright 2019 by Elsevier Limited.
▪ Infection can occur after transmission of helminths which occurs in four distinct
way:
o swallowing infective eggs or larvae via the fecal–oral route
o swallowing infective larvae in the tissues of another host
o active penetration of the skin by larval stages
o the bite of an infected blood-sucking insect vector.

Figure 11. How Helminth Parasites Enter the Body

Note: A Photo of How helminth parasites enter the body. Adapted from “Medical Microbiology
and Immunology 6th Edition (p.41)” by Goering et al. Copyright 2019 by Elsevier Limited.
ARTHROPODS
▪ Phylum Arthropoda is the largest in the animal kingdom.
▪ Examples with which most people will be familiar are crustaceans, centipedes,
insects, ticks and mites.
▪ Blood feeders include mosquitoes, midges, biting flies, bugs, fleas and ticks.
▪ Mosquitoes are temporary ectoparasites, feeding for only a few minutes
▪ Ticks feed for much longer.
▪ The louse Pediculus humanus and the crab louse Phthirus pubis spend almost all
of their lives on humans, feeding on blood and reproducing on the body or in
clothing.
▪ The scabies mite Sarcoptes scabiei lives permanently on humans, burrowing into
the superficial layers of skin to feed and lay eggs.

Figure 12. Sarcoptes scabiei, the Scabies Mite

Note: A Photo of Filariform larvae, the

infective stage of Strongyloides
stercoralis. Courtesy of Peter Chiodini.
Adapted from “Medical Microbiology and
Immunology 6th Edition (p.28)” by
Goering et al. Copyright 2019 by Elsevier
Limited.

▪ Arthropods transmit pathogens of all major groups, from viruses to worms and
some (e.g. mosquitoes and ticks) transmit a wide variety of organisms.
CLASSIFICATION OF MICROORGANISMS
▪ In 1978, Carl Woese devised a system of classification based on the cellular
organization of organisms. It groups all organisms in three domains as follows:
o Bacteria (cell walls contain a protein–carbohydrate complex called
peptidoglycan)
o Archaea (cell walls, if present, lack peptidoglycan)
o Eukarya, which includes the following:
▪ Protists (slime molds, protozoa, and algae)
▪ Fungi (unicellular yeasts, multicellular molds, and mushrooms)
▪ Plants (mosses, ferns, conifers, and flowering plants)
▪ Animals (sponges, worms, insects, and vertebrates)
A BRIEF HISTORY OF MICROBIOLOGY

The First Observations

▪ Robert Hooke (1665) reported that life’s smallest structural units were “little
boxes,” or “cells.”, using his improved microscope.
▪ Hooke’s observations laid the groundwork for development of the cell theory, the
concept that all living things are composed of cells.
▪ Anton van Leeuwenhoek, using a simple microscope, was the first to observe
microorganisms (1673). He wrote about the “animalcules” he saw through his
simple, single lens microscopes. Van Leeuwenhoek made detailed drawings of
organisms he found in rainwater, feces, and material scraped from teeth. These
drawings have since been identified as representations of bacteria and protozoa
Figure 13. Anton van Leeuwenhoek’s Microscopic Observations

Note: A Photo of Anton van Leeuwenhoek’s microscopic observations. Adapted from “Microbiology An Introduction
13th Edition (p.7)” by Tortora et al. Copyright 2019 by Pearson Education, Inc.
The Debate over Spontaneous Generation
▪ Until the mid-1880s, many people believed in spontaneous generation, the idea
that living organisms could arise from nonliving matter.
▪ Francesco Redi demonstrated that maggots appear on decaying meat only when
flies are able to lay eggs on the meat (1668).
▪ John Needham claimed that microorganisms could arise spontaneously from
heated nutrient broth (1745).
▪ Lazzaro Spallanzani repeated Needham’s experiments and suggested that
Needham’s results were due to microorganisms in the air entering his broth (1765).
▪ Rudolf Virchow introduced the concept of biogenesis: living cells can arise only
from preexisting cells (1858).
▪ Louis Pasteur demonstrated that microorganisms are in the air everywhere and
offered proof of biogenesis (1861).
▪ Pasteur’s discoveries led to the development of aseptic techniques used in
laboratory and medical procedures to prevent contamination by microorganisms.

Figure 14. Pasteur’s Set-Up Disproving Spontaneous Generation

Note: A Photo of Pasteur’s Set-Up Disproving Spontaneous Generation. Adapted from “Microbiology An Introduction
13th Edition (p.8)” by Tortora et al. Copyright 2019 by Pearson Education, Inc.
The First Golden Age of Microbiology

▪ The science of microbiology advanced rapidly between 1857 and 1914.

Fermentation and Pasteurization

▪ Pasteur found that yeasts ferment sugars to alcohol and that bacteria can oxidize
the alcohol to acetic acid, in the absence of air. This process, called fermentation,
is used to make wine and beer.
▪ A heating process called pasteurization is used to kill bacteria in some alcoholic
beverages and milk.

The Germ Theory of Disease

▪ The discovery that yeasts play a crucial role in fermentation alerted scientists to
the possibility that microorganisms might have similar relationships with plants and
animals—specifically, that microorganisms might cause disease. This idea was
known as the germ theory of disease.
▪ Agostino Bassi (1835) and Pasteur (1865) showed a causal relationship between
microorganisms and disease.
o Bassi had proved that another silkworm disease was caused by a fungus
 o Pasteur, after using Bassi’s data, found that the more recent infection was
caused by a protozoan, and he developed a method for recognizing afflicted
silkworm moths.
▪ Joseph Lister (1860s) introduced the use of a disinfectant to clean surgical
wounds in order to control infections in humans (1860s).
▪ Robert Koch proved that microorganisms cause disease. He used a sequence of
procedures, now called Koch’s postulates (1876), that are used today to prove
that a particular microorganism causes a particular disease.
Vaccination
▪ In 1798, Edward Jenner demonstrated that inoculation with cowpox material
provides humans with immunity to smallpox.
▪ About 1880, Pasteur discovered that avirulent bacteria could be used as a vaccine
for fowl cholera.
▪ Modern vaccines are prepared from living avirulent microorganisms or killed
pathogens, from isolated components of pathogens, and by recombinant DNA
techniques.
The Second Golden Age of Microbiology

▪ The Second Golden Age began with the discovery of penicillin’s effectiveness
against infections.

Figure 14. The Discovery of Penicillin

Note: A Photo of The Discovery of Penicillin Adapted from “Microbiology An Introduction 13th Edition (p.11)” by
Tortora et al. Copyright 2019 by Pearson Education, Inc.

▪ Two types of chemotherapeutic agents are:

o synthetic drugs (chemically prepared in the laboratory) and
o antibiotics (substances produced naturally by bacteria and fungi that inhibit
the growth of bacteria).
 ▪ Paul Ehrlich introduced an arsenic-containing chemical called salvarsan to treat
syphilis (1910).
▪ Alexander Fleming observed that the Penicillium fungus inhibited the growth of a
bacterial culture. He named the active ingredient penicillin (1928).
▪ Researchers are tackling the problem of drug-resistant microbes.
▪ Bacteriology is the study of bacteria, mycology is the study of fungi, and
parasitology is the study of parasitic protozoa and worms.
▪ The study of AIDS and analysis of the action of interferons are among the current
research interests in immunology.
▪ New techniques in molecular biology and electron microscopy have provided tools
for advancing our knowledge of virology.
▪ The development of recombinant DNA technology has helped advance all areas
of microbiology.

The Third Golden Age of Microbiology

▪ Microbiologists are using genomics, the study of all of an organism’s genes, to
study microbiomes in different environments.
▪ Through genomics, the study of all of an organism’s genes, scientists are able to
classify bacteria and fungi according to their genetic relationships with other
bacteria, fungi, and protozoa. These
Microbes and Human Welfare
▪ Microorganisms degrade dead plants and animals and recycle chemical elements
to be used by living plants and animals.
▪ Bacteria are used to decompose organic matter in sewage.
▪ Bioremediation processes use bacteria to clean up toxic wastes.
▪ Bacteria that cause diseases in insects are being used as biological controls of
insect pests. Biological controls are specific for the pest and do not harm the
environment.
▪ Using microbes to make products such as foods and chemicals is called
biotechnology.
▪ Using recombinant DNA, bacteria can produce important substances such as
proteins, vaccines, and enzymes.
▪ In gene therapy, viruses are used to carry replacements for defective or missing
genes into human cells.
▪ Genetically modified bacteria are used in agriculture to protect plants from frost
and insects and to improve the shelf life of produce.

Microbes and Human Disease

▪ The disease-producing properties of a species of microbe and the host’s

resistance are important factors in determining whether a person will contract a
disease.
▪ Bacterial communities that form slimy layers on surfaces are called biofilms.

Figure 15. Biofilm on a Piece of Plastic

 Note: A Photo of Biofilm on a Piece of Plastic.
Adapted from “Microbiology An Introduction
13th Edition (p.17)” by Tortora et al. Copyright
2019 by Pearson Education, Inc.

▪ An infectious disease is one in which pathogens invade a susceptible host, such

as a human or an animal.
▪ An emerging infectious disease (EID) is a new or changing disease showing an
increase in incidence in the recent past or a potential to increase in the near future.
o Zika Virus Disease
o Middle East Respiratory Syndrome (MERS)
o Influenza
o Antibiotic-Resistant Infections
o Ebola Virus Disease
o Marburg Virus
ACTIVITY 1

1. The genus name of a bacterium is “erwinia,” and the specific epithet is “amylovora.”
Write the scientific name of this organism correctly. Using this name as an example,
explain how scientific names are chosen.

2. Find at least eight supermarket products made by microorganisms. (Hint: The label will
state the scientific name of the organism or include the word culture, fermented, or
brewed.)

Thank you for completing the task. If you have not completed
the task or you have difficulty in accomplishing the activity, please
send me a message through our Google class or you may ask
clarifications through a text message or a private message in
Facebook

And now, you are ready for the learning assessment.

MULTIPLE CHOICE

Directions: Read the following statements and write the letter of your answer on the box
provided.
ANSWERS:
1.
1. Which of the following is a scientific name?
2.
a. Mycobacterium tuberculosis
3.
b. Tubercle bacillus
4.
2. Which of the following is not a characteristic of bacteria?
5.
a. are prokaryotic
6.
b. have peptidoglycan cell walls
7.
c. have the same shape 8.
d. grow by binary fission 9.
e. have the ability to move 10.
3. Which of the following is the most important element of
Koch’s germ theory of disease? The animal shows disease
symptoms when
a. the animal has been in contact with a sick animal.
b. the animal has a lowered resistance.
c. a microorganism is observed in the animal.
d. a microorganism is inoculated into the animal.
e. microorganisms can be cultured from the animal.
4. Recombinant DNA is
a. DNA in bacteria.
b. the study of how genes work.
c. the DNA resulting when genes of two different organisms are mixed.
d. the use of bacteria in the production of foods.
e. the production of proteins by genes.
5. Which of the following statements is the best definition of biogenesis?
a. Nonliving matter gives rise to living organisms.
b. Living cells can only arise from preexisting cells.
c. A vital force is necessary for life.
d. Air is necessary for living organisms.
e. Microorganisms can be generated from nonliving matter.
6. Which of the following is a beneficial activity of microorganisms?
a. Some microorganisms are used as food for humans.
b. Some microorganisms use carbon dioxide.
c. Some microorganisms provide nitrogen for plant growth.
d. Some microorganisms are used in sewage treatment processes.
e. all of the above
7. It has been said that bacteria are essential for the existence of life on Earth.
Which of the following is the essential function performed by bacteria?
a. control insect populations
b. directly provide food for humans
c. decompose organic material and recycle elements
d. cause disease
e. produce human hormones such as insulin
8. Which of the following is an example of bioremediation?
a. application of oil-degrading bacteria to an oil spill
b. application of bacteria to a crop to prevent frost damage
c. fixation of gaseous nitrogen into usable nitrogen
d. production by bacteria of a human protein such as interferon
e. all of the above
9. Spallanzani’s conclusion about spontaneous generation was challenged
because Antoine Lavoisier had just shown that oxygen was the vital component of air.
Which of the following statements is true?
a. All life requires air.
b. Only disease-causing organisms require air.
c. Some microbes do not require air.
d. Pasteur kept air out of his biogenesis experiments.
e. Lavoisier was mistaken.
 10. Which of the following statements about E. coli is false?
a. E. coli was the first disease-causing bacterium identified by Koch.
b. E. coli is part of the normal microbiome of humans.
c. E. coli is beneficial in human intestines.
d. E. coli gets nutrients from intestinal contents.
e. None of the above; all the statements are true.

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the activity, please send me a message through our Google class or
you may ask clarifications through a text message or a private
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Unit 2.