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 Contents

CHAPTER 1 Introduction to Microbes and Their

Building Blocks
CHAPTER 2 Tools of the Laboratory: Methods for the
Culturing and

Microscopic Analysis of Microorganisms

CHAPTER 3 Bacteria and Archaea

CHAPTER 4 Eukaryotic Cells and Microorganisms
CHAPTER 5 Viruses and Prions
CHAPTER 6 Microbial Nutrition and Growth
CHAPTER 7 Microbial Metabolism
CHAPTER 8 Microbial Genetics and Genetic
Engineering
CHAPTER 9 Physical and Chemical Control of
Microbes
CHAPTER 10 Antimicrobial Treatment
CHAPTER 11 Interactions Between Microbes and
Humans
CHAPTER 12 Host Defenses I: Overview and Innate
Defenses
CHAPTER 13 Host Defenses II: Adaptive Immunity
and

Immunization

CHAPTER 14 Disorders in Immunity

CHAPTER 15 Diagnosing Infections
CHAPTER 16 Infectious Diseases Affecting the Skin
and Eyes
CHAPTER 17 Infectious Diseases Affecting the
Nervous System

CHAPTER 18 Infectious Diseases Affecting the

Cardiovascular and
Lymphatic Systems

CHAPTER 19 Infectious Diseases Affecting the

Respiratory Systems
CHAPTER 20 Infectious Diseases Affecting the
Gastrointestinal Tract
CHAPTER 21 Infectious Diseases Affecting the
Genitourinary System
CHAPTER 22 One Health: The Interconnected
Health of the
Environment, Humans, and Other Animals
Contributions by Ronald M. Atlas, University of
Louisville
 Chapter Highlights

Chapter 1 New infographic about the types of

microorganisms we
will study in the book. Added section on the cautions
we should take
about research on the microbiome: that it is big but
many results
are still preliminary.
Chapter 3 I describe my own recent experience with
C. diff.
Throughout the book, the genus Clostridium has been
updated to
Clostridioides in the case of C. diff.
Chapter 4 Emphasis on the rise of fungal infections in
immunocompromised persons. “The progress of
these infections in
immunosuppressed people was vividly described:
They’ll just rot
you down quick as a flash,” said one of the authors.”
Chapter 5 New infographic explaining cytopathic
effects.
Chapter 6 Made illustrations of levels of oxygen
growth clearer.
Clarified the illustration of serial dilution counting of
growth.
Chapter 7 The commentaries on the (often difficult)
figures are
particularly helpful in this chapter.
Chapter 8 A comment on the flow-of-genetic-
information figure,
emphasizing how the knowledge of the regulatory
RNAs is new, and
how science works. Same type of commentary about
mutations.
More epigenetic discussion. A commentary about the
similarity
between binary fission and PCR processes.
Discussion of using DNA
for information storage.
Chapter 10 New discussion about how the
microbiome affects
efficacy of antimicrobial drugs. FDA ban of
antimicrobials in
agriculture.
Chapter 11 New sites of the microbiome: placenta,
etc. Changes in
epidemiology of hospital-acquired infections (HAIs).
Important
information about the emergence of Candida auris.

Chapter 12 Comment bubble points out the discovery

of lymphatic
system in brain. Made figures of phagocytosis and of
interferon
much clearer, with commentary bubble on the latter.
Chapter 13 More explanation on the figure of genetic
rearrangements for antibody diversity.
Chapter 14 Added the newly appreciated influence of
T cells on
allergies.
Chapter 15 Explanation of the NAAT (nucleic acid
amplification
techniques) and how they relate to the techniques we
have already
described. The new practice of PCR’ing tissue
samples.
Chapter 16 Measles epidemics due to lack of
vaccinations.
Malassezia association with pancreatic cancer.
Chapter 17 Demoted Zika virus disease from a
Highlight disease;
latest data about acute flaccid myelitis. Highlighted
the Global Polio
Eradication Initiative. Updated the arbovirus
epidemiology.
Chapter 18 Did some clarification of the size of
insects involved in
various diseases. Ebola updates.
Chapter 19 COVID-19 featured as a highlight disease.
Added
Candida auris otitis media; expanded and updated
discussion of
influenza vaccines; new epidemiology of whooping
cough; use of
gene amplification and antibiotic susceptibility testing
for
tuberculosis; new section on novel coronaviruses.
Chapter 20 Thirty-state Campylobacter outbreak from
handling
puppies; rise of antibiotic resistance in Helicobacter;
new
infographic about foodborne disease outbreaks.
Chapter 21 A commentary that helps students
understand data
reported as “per 100,000 people.”
Chapter 22 Critical information and graphics
describing how the
COVID-19 pandemic illustrates the principles of One
Health. Added
discussion of the emergence of Candida auris and the
influence of
climate change; the creep northward of mosquito and
tick-borne

diseases; hepatitis A epidemic in the United States;

wildfires in
California and Australia; longer duration of mosquito-
borne disease
Season.

Introduction to Microbes and Their

Building Blocks

IN THIS CHAPTER...
1.1 Microbes: Tiny but Mighty
1. List the various types of microorganisms that can
colonize humans.
2. Describe the role and impact of microbes on the
earth.
3. Explain the theory of evolution and why it is called
a theory.
4. Explain the ways that humans manipulate
organisms for their own uses.
5. Summarize the relative burden of human disease
caused by microbes.
6. Differentiate among bacteria, archaea, and
eukaryotic microorganisms.
7. Identify two acellular infectious agents that are
studied in microbiology.
8. Compare and contrast the relative sizes of the
different microbes.
1.2 Microbes in History
9. Make a time line of the development of
microbiology from the 1600s to today.
10. List some recent microbiology discoveries of
great impact.
11. Identify the important features of the scientific
method.
1.3 Macromolecules: Superstructures of Life
12. Name the four main families of biochemicals.
13. Provide examples of cell components made from
each of the families of biochemicals.
14. Differentiate among primary, secondary, tertiary,
and quaternary levels of protein structure.
15. List the three components of a nucleotide.
16. Name the nitrogen bases of DNA and RNA.
17. List the three components of ATP.
18. Recall three characteristics common to all cells.

1.4 Naming, Classifying, and Identifying

Microorganisms
19. Differentiate among the terms nomenclature,
taxonomy, and classification.
20. Create a mnemonic device for remembering the
taxonomic categories.
21. Correctly write the binomial name for a
microorganism.
22. Draw a diagram of the three major domains.
23. Explain the difference between traditional and
molecular approaches to taxonomy.

At the beginning of every chapter in this book, a

different health care worker will tell you a story
about something “microbiological” that happened to
him or her in the line of duty. For this first
chapter, though, I am claiming “dibs” as author and
am going to introduce myself to you by telling
you about the first day of class in my course.
Long ago I noticed that students have a lot of
anxiety about their microbiology course. I know
that starts you out with one strike against you
because attitudes are powerful determinants of our
success. So on the first day of class I often spend
some time talking with students about how much
they already know about microbiology.
Sometimes I start with “How many of you have taken
your kids for vaccinations?” since in the
classes I teach very many students are parents.
Right away students will tell me why they or friends
they know have not vaccinated their children, and I
can tell them there’s a sophisticated
microbiological concept they are referencing, even if
they aren’t naming it: herd immunity,
discussed in chapter 11 of this book.
Of course, nowadays, everyone has some type of
experience with COVID-19, and the virus that
causes it, SARS-CoV-2. The whole world has
undergone a crash course in infection, and in
epidemiology. This course will help you sort out all of
the information that has been pouring out
about COVID-19.
Think about how many times you have taken
antibiotics in the past few years. What is special
about antibiotics that they are only given to treat
infections?
What is the most unusual infection you have ever
encountered among family or friends or
patients you have cared for?

Case File Wrap-Up appears at the end of the

chapter.
Source: CDC/Janice Haney Carr (Staphylococcus
aureus and Legionella); Source: Dr. Erskine Palmer
& Byron Skinner/CDC
(rotavirus); Source: Dr. Stan Erlandsen/CDC
(Giardia sp. cyst); Science Photo Library RF/Getty
Images (white blood cell); Steve
Gschmeissner/Science Photo Library/Getty Images
(fallopian tube, SEM); NIAID, NIH, Rocky Mountain
Laboratories (Salmonella
typhimurium); Jerome Wexler/Science Source
(Eutrophic pond with floating masses); ©Michael
Williams (photo of Kelly Cowan with
student)

Page 4
1.1 Microbes: Tiny but Mighty

Mycobacterium tuberculosis bacteria

Source: CDC/Janice Carr
Microbiology is a specialized area of biology that
deals with living things ordinarily too small to be
seen without magnification. Such microscopic
organisms are collectively referred to as
microorganisms (my′′-kroh-or′-gun-izms), microbes,
or several other terms depending on the kind
of microbe or the purpose. There are several major
groups of microorganisms that we’ll be studying.
They can be either cellular or noncellular. The
cellular microorganisms we will study are bacteria,
archaea, fungi, and protozoa. Another cellular
organism that causes human infections is not
technically a microorganism. Helminths are
multicellular animals whose mature form is visible to
the naked eye. Acellular microorganisms causing
human disease are the viruses and prions. Table
1.1 gives you a first glimpse at these
microorganisms. There is another very important
group of
organisms called algae. They are critical to the
health of the biosphere but do not directly infect
humans, so we will not consider them in this book.
Each of the other seven groups contains members
that colonize humans, so we will focus on them.
The nature of microorganisms makes them both very
easy and very difficult to study—easy because
they reproduce so rapidly and we can quickly grow
large populations in the laboratory, and difficult
because we usually can’t see them directly. We rely
on a variety of indirect means of analyzing them in
addition to using microscopes.
Table 1.1 The Types of Microorganisms We Will
Study in this Book

Page 5

Important Note to Students!

This is your author here. I wanted to alert you right
up front that you should look at the figures and read
the tables in the chapters. I know that it
is human nature to skip these when you see the
reference in the main text (like “figure 1.4”) and just
move on with the next sentence. But in
this book I made a real point to put a lot of
information in the figures and tables because it is
easier to digest things such as processes and
categories when they are presented in a more visual
format. And there are a lot of “processes” and
“categories” in biology! So I opted for a bit
less text, and a bit more pictures and tables. So be
sure to make it a point to stop by and examine these
visual features. Thanks! Kelly
Microbes and the Planet
For billions of years, microbes have extensively
shaped the development of the earth’s habitats and
the
evolution of other life forms. It is understandable that
scientists searching for life on other planets first
look for signs of microorganisms.
Single-celled organisms appeared on this planet
about 3.8 billion years ago according to the fossil
record. One of these organisms—referred to as
LCA, or the Last Common Ancestor—eventually led
to

the appearance of two newer single cell types,

called bacteria and archaea. A little bit later this
single-
celled ancestor gave rise to eukaryotic (yoo-kar′-ee-
ot-ic) cells. The type of cell known as LCA no

longer exists. Only its “offspring”—bacteria, archaea,

and eukaryotes—remain. Eu-kary means “true
nucleus,” and these were the only cells containing a
nucleus. Bacteria and archaea have no true
nucleus. For that reason, they have traditionally
been called prokaryotes (pro-kar′-ee-otes), meaning
“prenucleus.” But researchers are suggesting we no
longer use the term prokaryote to lump them
together because archaea and bacteria are so
distinct genetically. Some scientists have started
calling
them akaryotes, meaning “no nucleus.” If you
consider the seven types of microorganisms we will
be
dealing with in this book, you will recognize bacteria
and archaea as each having their own domain.
The protozoa, fungi, and helminths are all in the
domain Eukarya. Viruses and prions do not appear
on
the tree of life because they are not cells, and not
considered living. That sounds strange, but we will
delve into that in the virus chapter, which comes
later.
Figure 1.1 depicts the resulting tree of life—a
diagram of all organisms on the planet. There are
two
important things to note about this figure. First, all of
biologic life falls into these three categories,
known as domains. Most of the organisms you are
familiar with (animals, plants, etc.) are in one
category, Eukarya. Second, these three domains all
emerged from a single common cell type (the
“stem” at the bottom).
Bacteria and archaea are predominantly single-
celled organisms. Many eukaryotic organisms are
also single-celled, but the eukaryotic cell type also
developed into highly complex multicellular
organisms such as worms and humans. In terms of
numbers, eukaryotic cells are a small minority
compared to the bacteria and archaea, but their
larger size (and our own status as eukaryotes!)
makes
us perceive them as dominant to—and more
important than—bacteria and archaea.

Figure 1.1 The tree of life: A phylogenetic system. A

system for representing the origins of cell lines and
major
taxonomic groups. There are three distinct cell lines
placed in superkingdoms called domains. ©McGraw-
Hill Education
Page 6

Figure 1.2 Evolutionary time line.

(photo): NASA/Goddard Space Flight Center
Figure 1.2 depicts the time line of appearances of
different types of organisms on earth. Starting
on the left, you see that the ancestor cell type was
here alone for quite a while before giving rise to the

three domains of life. Eukaryotes came along last,

and it took a very long time for single-celled
eukaryotes to develop into more complex eukaryotic
organisms (insects, reptiles, and mammals). On
the scale pictured in the figure, humans just barely
appeared in very recent earth history. Bacteria and
archaea preceded even the earliest animals by more
than 2 billion years. This is a good indication that
humans are not likely to—nor should we try to—
eliminate bacteria from our environment. They have
survived and adapted to many catastrophic changes
over the course of our geologic history.
Another indication of the huge influence bacteria
exert is how ubiquitous they are. Ubiquitous
means “found everywhere.” Microbes can be found
nearly everywhere, from deep in the earth’s crust,
to the polar ice caps and oceans, to inside the
bodies of plants and animals. Being mostly invisible,
the
actions of microorganisms are usually not as
obvious or familiar as those of larger plants and
animals.
They make up for their small size by their immense
numbers and by living in places that many other
organisms cannot survive. Above all, they play
central roles in the earth’s landscape that are
essential
to life. When we point out that single-celled
organisms have adapted to a wide range of
conditions over the
3.5 billion years of their presence on this planet, we
are talking about evolution. The presence of life in
its present form would not be possible if the earliest
life forms had not changed constantly, adapting to
their environment and circumstances. Getting from
the far left in figure 1.2 to the far right, where
humans appeared, involved billions and billions of
tiny changes, starting with the first cell that
appeared about a billion years after the planet itself
was formed.

Source: NASA

Page 7
You have no doubt heard this concept described as
the theory of evolution. Let’s clarify some
terms. Evolution is the accumulation of changes that
occur in organisms as they adapt to their
environments. It is documented every day in all
corners of the planet, an observable phenomenon
testable by science. Scientists use the term theory in
a different way than the general public does,
which often leads to great confusion. In science, a
theory begins as a hypothesis, or an educated
guess
to explain an observation. By the time a hypothesis
has been labeled a theory in science, it has
undergone years and years of testing and not been
disproved. It is taken as fact. This is much different
from the common usage, as in “My theory is that he
overslept and that’s why he was late.” The theory

of evolution, like the germ theory and many other

scientific theories, refers to a well-studied and well-
established natural phenomenon, not just a random
guess.

Medical Moment
Medications from Microbes
Penicillin is a worthy example of how
microorganisms can be used to improve human life.
Alexander Fleming, a Scottish bacteriologist,
discovered penicillin quite by accident in 1928. While
growing several bacterial cultures in Petri dishes, he
accidentally forgot to cover them.
They remained uncovered for several days. When
Fleming checked the Petri dishes, he found them
covered with mold. Just before Fleming
went to discard the Petri dishes, he happened to
notice that there were no bacteria to be seen around
the mold—in other words, the mold
was killing all of the bacteria in its vicinity.
Recognizing the importance of this discovery,
Fleming experimented with the mold (of the genus
Penicillium) and discovered that it
effectively stopped or slowed the growth of several
bacteria. The chemical that was eventually isolated
from the mold—penicillin—became
widely used during the Second World War and
saved many soldiers’ lives, in addition to cementing
Fleming’s reputation.
Q. Can you think of a logical reason that a microbe
(the fungus) would produce a chemical that harms
another microbe (the bacteria)?
Answer in Appendix B.
How Microbes Shape Our Planet
Microbes are deeply involved in the flow of energy
and food through the earth’s ecosystems. Most
people are aware that plants carry out
photosynthesis, which is the light-fueled conversion
of carbon
dioxide to organic material, accompanied by the
formation of oxygen (called oxygenic
photosynthesis). However, bacteria invented
photosynthesis long before the first plants appeared,
first as a process that
did not produce oxygen (anoxygenic
photosynthesis). This anoxygenic photosynthesis
later evolved
into oxygenic photosynthesis, which not only
produced oxygen but also was much more efficient
in
extracting energy from sunlight. Hence, these
ancient, single-celled microbes were responsible for
changing the atmosphere of the earth from one
without oxygen to one with oxygen. The production
of
oxygen also led to the use of oxygen for aerobic
respiration and the formation of ozone, both of which
set off an explosion in species diversification. Today,
photosynthetic microorganisms (mainly bacteria
and algae) account for more than 70% of the earth’s
photosynthesis, contributing the majority of the
oxygen to the atmosphere (figure 1.3).

Find the original Textbook (PDF) in the link below:

CLICK HERE