Important words and
concepts from Chapter 1, Black, 2002 (3/28/2003):
by Stephen T. Abedon (abedon.1@osu.edu)
for Micro 509
at the Ohio State University
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Course-external links are
in brackets Click [index] to access site index Click here to access text’s website Vocabulary
words
are found below |
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(1) Chapter title: Scope and History of Microbiology
(a)
Throughout this course
(i.e., these notes) I will be doing my best to supply you with links to
supplemental material found on the World Wide Web
(i)
If
you have additional interest in presented material or need additional exposure
to concepts, consider following these links (on line, of course)
(ii)
I
will regularly include Google searches that may be followed for
abundant additional information on material—however, always keep in mind that
your first, best reference will usually be your text book
(iii)
There
also exists an index to this site called MicroPort
that is found at http://www.phage.org/microbiology.htm
or by pressing [index]
throughout these notes
(b)
Studying tips:
(i)
Read
over assigned material in your text before coming to lectures
·
Read
your text well so that, minimally, you have made an attempt at understanding
the presented concepts
(ii)
Read
over the supplied lecture notes (i.e., these)
·
Read
lecture notes well so that you have made an attempt at understanding the
presented concepts
·
Make
an effort to memorize the supplied vocabulary
(iii)
Come to class prepared to ask questions
(iv)
After
class, organize the material, integrating the notes that you take during class
(v)
REMEMBER,
CLASS ONLY MEETS TWICE A WEEK SO BLOWING OFF A LECTURE OR NOT STUDYING
PRIOR TO AND AFTER A LECTURE IS EQUIVALENT TO BLOWING OFF HALF OF A WEEK OF
STUDYING
(vi)
Study
for the first exam in this course harder than you have ever studied for an exam
before
·
Triage
the material you will be studying such that you don’t waste your time studying
the material you already know/understand
·
Make
sure that you have extensively been through the material and have organized it before
you begin to study
·
Don’t
put off your studying to the last minute
·
Don’t
count organizing and learning your material as exam study time—studying for an
exam involves making sure that you have memorized and can lucidly regurgitate
the material, not simply becoming familiar with it
·
Simply
reading over notes again and again is not necessarily equivalent to doing the
hard work of learning
(vii)
Don’t
forget that labs are worth a good chunk of your grade
·
Don’t
blow off labs
·
Read
labs before you come to laboratories and as you are doing them
·
Also
read your lab schedule for tips on how to do labs
·
Labs
are much (much, much) easier to do when you are familiar with them; I will be
able to tell when you are unfamiliar with labs; I will reserve the right to
quiz on lab preparation if I get the impression that students are coming to
laboratories unprepared
·
Answer
questions and make notes while the material is still fresh in your mind
(c)
For tips on how to study for microbiology, see: [microbiology and "study
tips" (Google Search)]
[microbiology study tips
(need to skip down a bit to find) (Gary E. Kaiser)]
(d)
Links to other on-line microbiology courses (and course-like sites): [microbiology and course
(Google Search)]
[Microbiology Webbed Out
(Kenneth Todar)]
(e)
Microbiology link collections can be found at: [microbiology links
(Google Search)]
(a)
Microbiology
is "the study of microbes, organisms
so small that a microscope is needed to study them."
(b)
Microbiology,
as a science, may be differentiated along organism lines ("the variety of
kinds of microbes") and in terms of techniques and goals ("the kind
of work microbiologists do")
What is Microbiology? |
|
·
Microbiology is the study of microorganisms ·
Microorganisms, roughly, are living things that are
too small to be seen with the naked eye ·
Microorganisms cannot be distinguished
phylogenetically from “macroorganisms” (see variety of microorganisms, below) ·
Microbiology is more a collection of techniques:
aseptic technique, pure culture technique, microscopic observation of whole
organisms, etc. ·
Microbiologists isolate specific, culturable
microorganisms from wild populations, then study them (or, alternatively,
study them in situ without culturing them) |
(c)
[Microbiology is the study of
organisms too small to be seen with the naked eye. Originally, emphasis was
placed on harmful microorganisms which cause disease or spoilage of beverages
and food, but it is now recognized that many microbes have essential roles in
our ecosystem or can be used to accomplish beneficial tasks. Human history is
full of examples of major devastations caused by bacteria and viruses. Some of
these historically important diseases still occur, such tuberculosis and yellow
fever. Microorganisms are evolving to cause new infectious disease problems
such as Lyme disease and AIDS, which capture public attention. Control and
eradication of infectious diseases remain important goals of many
microbiologists. The recognition that microorganisms were responsible for what
was earlier thought to be "spontaneous generation" opened the door to
industrial (pharmaceutical, chemical, energy) and food microbiology,
technologies which contribute substantially to today's way of life.
Microorganisms in soil and water are essential in the transformation of carbon,
nitrogen, oxygen, sulfur and iron to products needed by plants and animals. In
various ways, microbes participate in environmental cycling and degradation and
global change. In the last few decades, microorganisms have been recognized as
ideal model systems for the study of basic biological processes. ¶ More
recently, microbiologists have brought an exciting dimension to the study of
biology through the use of genetic engineering techniques and highly specific
protein (antibody) molecules. Accomplishments in these areas already have led
to enormous benefits for the human race, but there are many more challenges to
be conquered through these kinds of studies. In the future, studies in space
microbiology may help to reveal if there is life on other planets and the role
of microorganisms in closed systems. Today, one can truly say that the
potential for microbiology to benefit human and animal health and life has
never been better. (CSU Department of Microbiology)]
(d)
[microbiology (Google Search)] [index]
(3) The variety of kinds of
microbes (microbes,
microorganisms)
(a)
Microbes are typically (but certainly not
always) either unicellular organism (e.g., bacteria) or acellular
"organisms" (e.g., viruses)
(b)
Typically
a microbiologist will differentiate microbes into the following categories:
(i)
Bacteria
(ii)
Algae
(iii)
Fungi
(iv)
Viruses
(v)
Protozoa
(vi)
Helminths
(c)
We
will consider all of these types, though with particular emphasis on the
bacteria and the viruses
(d)
Additional,
external links: [index]
(i)
[microbe and SEM
(links to electron microscopic images of microbes) (Google Search)]
(ii)
[big picture of infectious
diseases (Gary E. Kaiser)]
(iii)
[microbe portrait gallery
(pictures of microbes) (Microbe World)]
(iv)
[universal tree (MicroDude)]
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Supplemental
Material – Types of Microorganisms & their General Properties |
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organism: |
types: |
description: |
Nutrition type (-trophs): |
durable state: |
some diseases: |
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algae: |
brown, red, green,
diatoms, dinoflagellates, euglenoids |
photosynthetic aquatic
eucaryotes, cell walls, unicellular and multicellular |
photoauto- |
--- |
--- |
|
bacteria: |
eubacteria,
archaeabacteria, Gram-negative, Gram-positive, acid fast, cyanobacteria |
procaryotes, absorbers,
wet conditions, animal decomposers, cell walls, unicellular |
chemohetero- photohetero- chemoauto-
photoauto- |
endospores (some) |
tetanus, botulism,
gonorrhea, chlamydia, tuberculosis, etc., etc., etc. |
|
cyano-bacteria: |
blue-green algae |
photosynthetic aquatic
procaryotes, green lake scum, cell walls |
photoauto- |
--- |
--- |
|
fungi: |
yeasts (unicellular
fungi), molds (filamentous fungi) |
eucaryotes, absorbers, dry
conditions, plant decomposers, cell walls, ~100 human pathogens |
chemohetero- |
spores |
mycoses: candida,
ringworm, athlete's foot, jock itch, etc. |
|
helminths: |
Flatworms
(platyhelminths), roundworms (nematodes) |
metazoan (multicellular
animal) parasites, engulfers and absorbers |
chemohetero- |
--- |
tape worm, trichinosis,
hook worm, etc. |
|
protozoa: |
Unicellular and slime
molds, flagellates, ciliates |
eucaryotes, parasites,
engulfers and absorbers, wet conditions, no cell wall, ~30 human pathogens |
chemohetero- |
cysts (some) |
malaria, giardiasis,
amoebic dysentery, etc. |
|
viruses: |
Enveloped, non-enveloped |
acellular, obligate
intracellular parasites |
not applicable |
virion particles, encased
in durable state of host |
common cold, flu, HIV,
herpes, chicken pox, etc. |
(4) Bacteria (chapters 4,
6,
7,
8,
9)
(a)
The
bacteria have the following characteristics:
(i)
Relatively
small
(ii)
Single-celled
(iii)
No
nucleus or other membrane-bound organelles
(iv)
Simple
morphologies
(v)
Primarily
synthesizers or absorbers (i.e., not engulfers)
(b)
Most
bacteria do not cause human diseases,
but most infectious diseases are caused by bacteria
(and viruses)
(c)
More
typically, bacteria are beneficial, whether to ecosystems or
directly to individual organisms
(d)
[bacteria (Google Search)] [index]
(a)
The
algae have the following characteristics:
(i)
Both
unicellular and multicellular types
(ii)
Generally
aquatic
(iii)
Contain
nucleus and other membrane-bound organelles
(iv)
Photosynthetic
(b)
Algae
typically are beneficial (to ecosystems) though
some can cause damage
(c)
Only
a few contribute to human disease
(d)
[algae (Google Search)] [eukaryotic microorganisms and parasites, algae (supplementary lecture) (MicroDude)]
[index]
(a)
The
fungi generally have the following characteristics:
(i)
Both
unicellular and multicellular types
(ii)
Generally
not aquatic (i.e., prefer dryer environments)
(iii)
Contain
nuclei and other membrane-bound organelles
(iv)
Nutrient
absorbers (not photosynthetic and not engulfers)
(v)
Decomposers
(b)
Single-celled
fungi are called yeasts
(c)
Multicelled
fungi are called molds
(d)
There
are a number of fungi-caused human diseases (e.g., athletes foot, Candida yeast
infections)
(e)
In
the environment fungi serve as plant symbionts and decomposers
(f)
[fungi or fungus (Google Search)] [eukaryotic microorganisms and parasites, fungi (supplemental lecture) (MicroDude)]
[index]
(7) Viruses (chapters 8,
10)
(a)
Viruses
are not cells
(b)
Instead
they are acellular, obligate intracellular
parasites (i.e., they must invade a cell to replicate)
(c)
Generally
viruses are much smaller than cellular organisms
(d)
Viruses
either cause diseases or are sufficiently benign that they infect without
causing damage to the host; in some cases viruses can be beneficial to their
hosts (e.g., lysogenic conversion)
(e)
[virology and introduction
(Google Search)]
[viruses (MicroDude)] [index]
(a)
The
protozoa generally have the following characteristics:
(i)
Unicellular
(ii)
Aquatic
(or, minimally, grow and reproduce in moist environments)
(iii)
Contain
nucleus and other membrane-bound organelles
(iv)
Mostly
engulfers though some absorbers and, depending on the classification scheme,
also photosynthesizers
(b)
The
absorbers tend to be parasitic and cause disease
(c)
[protozoa, parasitology (Google Search)] [eukaryotic microorganisms and parasites, protozoa (supplemental lecture) (MicroDude)]
[index]
(9) Helminths (chapter 11)
(a)
These
are parasitic worms (as well numerous non-parasitic types)
(b)
Parasitic
worms are a province of microbiology because
(i)
They
share with other microorganisms their capacity to cause infectious disease
(ii)
They
are studied using techniques which overlap those employed to study other
microorganisms (e.g., microscopes)
(c)
Helminths,
however, are certainly not as small as the more-typical objects of microbiological
study (i.e., bacteria, viruses, protozoa, etc.)
(d)
[helminths, parasitic worms (Google Search)] [eukaryotic microorganisms and parasites (MicroDude)]
[multicellular parasites (supplemental lecture)
(MicroDude)]
[index]
(a)
Though
not considered microorganisms, arthropods (e.g., insects) are important vectors
of infectious-disease propagation
(b)
For
example, mosquitoes transmit malaria, which is caused by a protozoa
(c)
[arthropod vector,
arthropod vectors (Google Search)] [eukaryotic microorganisms and parasites (MicroDude)]
[arthropod vectors (supplemental lecture) (MicroDude)]
[index]
(a)
Homo sapiens and Escherichia coli
are both examples of binomial nomenclature, the naming of organism using two names
(b)
Binomial Nomenclature |
|
Failure
to employ correct binomial nomenclature on exams will result in the
subtraction of one point (on 200-Point Scale) per erroneous usage |
|
·
Examples: Escherichia coli, E. coli, Escherichia
spp., and “the genus Escherichia” ·
The genus name (Escherichia) is always
capitalized ·
The species name (coli) is never capitalized ·
The species name is never used without the genus
name (e.g., coli standing alone, by itself, is a mistake!) ·
The genus name may be used without the species name
(e.g., Escherichia may stand alone, though when doing so it no longer
actually describes a species) ·
When both genus and species names are present, the
genus name always comes first (e.g., Escherichia coli, not coli
Escherichia) ·
When both genus and species names are present, the
species name always directly follows the genus name ·
Both the genus and species names are always italicized
(or underlined)—always underline if are writing out binomials by hand ·
The first time a binomial is used in a work, it must be spelled out in its
entirety (e.g., E. coli standing alone in a manuscript is not
acceptable unless you have already written Escherichia coli in the
manuscript) ·
The next time a biniomial is used it may be
abbreviated (e.g., E. for Escherichia) though this is done
typically only when used in combination with the species name (e.g., E.
coli) ·
The species name is never abbreviated ·
It is a good idea to abbreviate unambiguously if
there is any potential for confusion (e.g., Enterococcus vs. Escherichia) ·
These rules are to be followed when employing
binomial nomenclature even in your speech. It is proper to refer to Escherichia
coli as E. coli or even as Escherichia, but it is not
proper to call it coli or E.C.! |
(c)
Examples
of bacteria binomials:
|
Binomial
Examples—Supplemental Material We will
be learning these in Chapter 9 Click on
speaker icons for some pronunciations |
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Binomials
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Disease
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various infections from fecal contamination |
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Campylobacter spp. |
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opportunistic infections |
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opportunistic infections of colon and other sites |
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respiratory infections, meningitis, conjunctivitis |
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respiratory and urinary tract infections |
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Legionella spp. |
pneumonia and other respiratory infections |
|
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Mycobacterium tuberculosis (leprae, paratuberculosis, smegmatis) |
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gonorrhea;
meningitis & nasopharylngeal infections by other species |
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urinary tract infections, especially nosocomial |
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urinary tract infections, burns, and wounds |
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typhoid fever,
enteritis, and food poisoning |
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opportunistic infections |
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bacillary dysentery |
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skin abscesses, opportunistic infections such as toxic shock syndrome |
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strep throat and
other infections, puerperal fever =
childbirth fever |
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Streptomyces spp. |
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(d)
[binomial nomenclature
(Google Search)]
binomial nomenclature (MicroDude)]
[index]
(a)
We
will briefly outline the history of microbiology in terms of the achievements
of a few individuals (yes, this will be on the test) including
(i)
Robert
Hooke
(iii)
Those
individuals involved directly in defining the germ theory of disease
Microbes and Ecology |
|
·
Microbes are produces—they provide energy to
ecosystems ·
Microbes are fixers—they make nutrients available
from inorganic sources, e.g., nitrogen ·
Microbes are decomposers—they free up nutrients
from no longer living sources ·
Microbes form symbioses (such as mycorrhizal fungi
associated with plant roots, the bacteria found in legume root nodules, etc.)
·
Microbes serve as emdosymbionts (e.g., chloroplasts
and mitochondria) |
(b)
[microbiology and history
(Google Search)]
[significant events of the last
125 years (American Society for Microbiology)] [index]
(a)
Builder
of the first (or, at least, an early) compound microscope
(b)
Coined
the term “cell”
(c)
[Perhaps his most famous microscopical observation was
his study of thin slices of cork. He wrote: '…I could exceedingly plainly
perceive it to be all perforated and porous… these pores, or cells, …were
indeed the first microscopical pores I ever saw, and perhaps, that were ever
seen, for I had not met with any Writer or Person, that had made any mention of
them before this.' Hooke had discovered plant cells -- more precisely, what
Hooke saw were the cell walls in cork tissue" (Enter Evolution: Theory and
History)]
(d)
[Robert Hooke (Google Search)] [Robert Hooke (1635-1703) (Enter Evolution: Theory and
History)] [index]
(14) van Leeuwenhoek, Anton (mid
to late 1600s, early 1700s)
(a)
The
first microbiologist (Leeuwenhoek is more-or-less pronounced layu-wen-hook)
(b)
First
to use microscopes to view microorganisms
(c)
[van Leeuwenhoek (Google Search)] [Antony van Leeuwenhoek
(1632-1723) (Enter Evolution: Theory and
History)] [history of the microscope
(Brian J. Ford)] [Leeuwenhoek microscope
(Molecular Expressions Museum of Microscopy)]
[Leeuwenhoek's perception of the spermatozoa
(niclely places Leeuwenhoek in his time) (Zygote)] [index]
(a)
The
germ theory of disease is the idea that diseases may be caused by microscopic
organisms (i.e., not visible to the naked eye), a.k.a., microbes
Microbes and Disease |
|
·
Microbes both cause and prevent diseases ·
Microbes produce antibiotics used to treat diseases ·
The single most important achievement of modern
medicine is the ability to treat or prevent microbial disease ·
Most of this course will consider the physiology of
microbes and their role in diseases |
(b)
The
germ theory of disease was not quick to catch on because of the contrasting
concept of spontaneous generation which is an idea that life can arise
spontaneously from no longer living things; for example,
(i)
The
"spontaneous" clouding of clear broth
(ii)
The
occurrence of maggots on meat
(c)
The
idea of spontaneous generation was debunked by experiments by
(i)
Francesco
Redi
(ii)
Louis
Pasteur
(iii)
Etc.
(d)
Others
that contributed to the development and practical application of the germ
theory of disease include
(i)
Robert
Koch
(ii)
Ignaz
Semmelweis
(iii)
Joseph
Lister
(iv)
Edward
Jenner
(vi)
Etc.
(e)
[germ theory of disease
(Google Search)]
[index]
(a)
Showed
that meat protected from flies via a gauze barrier did not develop maggots,
hence were not spontaneously generated
(b)
[Redi’s experiment seemed to
show spontaneous generation to be false. However, the Dutch merchant Anton van
Leewenhoek’s… microscope supported spontaneous generation, because it revealed
an entire world of microorganisms. Many people thought microorganisms were
simple enough to be produced from non-living material, Redi, believed that
microorganisms were spontaneously generated. For a period of time, people
believed that simply placing a piece of hay in water could produce certain
bacteria. (Chronology of Spontaneous
Generation)]
(c)
[Francesco Redi (Google Search)] [Redi, Fransesco (Catalog of the Scientific
Community in the 16th and 17th Centuries)] [index]
(17) Pasteur, Louis (mid to late
1800s)
(a)
Building
on the experiments of others, Pasteur showed that boiled broth did not become
cloudy (turbid) when air but not dust could contact the broth
(b)
Built
elegant "swan-necked" flasks which trapped dust (and microorganisms)
along their curved necks, thus showing that neither air nor broth were
sufficient to allow the generation of microorganisms (it is the microorganisms,
e.g., bacteria, that scatter light thereby producing turbidity in broth
cultures)
(c)
Pasteur
additionally showed that cotton plugs (a primitive air-filtration device) could
prevent microbes from reaching otherwise air-exposed sterile broths
Applied Microbiology |
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(d)
Note
that Pasteur was fortunate that the foods he boiled into broths did not contain
bacterial spores since such spores are resistant to killing by boiling
(e)
Pasteur
invented pasteurization, the heating of foods to eliminate harmful
microorganisms while retaining not-harmful microorganisms
(f)
He
was responsible for the association of specific microbes with diseases
(g)
He
development the rabies vaccine (as well as other vaccines)
(h)
(discovered
Staphylococcus, Streptococcus and Pneumococcus)
(i)
[Louis Pasteur (Google Search)] [Louis Pasteur (1822-1895)
(Access Excellence)]
[index]
(18) Koch, Robert (late 1800s,
early 1900s)
(a)
Identified
the bacteria
that cause anthrax, tuberculosis, cholera
(b)
Contributed
significantly to the development of pure culture technique
(c)
Introduction
of agar to microbiology
(d)
Koch's Postulates, a way of ascribing a
particular infectious disease to a particular,
causing microorganism
(e)
[Robert Koch (Google Search)] [Robert Koch (1843-1910)
(Medicine Through Time)]
[index]
(19) Semmelweis, Ignaz (mid-late 1800s)
(a)
Instituted
hand washing as a means of minimizing surgical infection (a means of aseptic
technique)
(b)
"Recognized
a connection between autopsies and puerperal (childbed) fever. Many physicians
went directly from performing autopsies to examining women in labor without so
much as washing their hands. When Semmelweis attempted to encourage more
sanitary practices, he was ridiculed and harassed until he had a nervous
breakdown and was sent to an asylum. Ultimately, he suffered the curious irony
of succumbing to an infection caused by the same organism that produces
puerperal fever."
(c)
[Ignaz Semmelweis (Google Search)] [index]
(20) Lister, Joseph (mid-late
1800s)
(a)
Building
on the work of Pasteur (anti-spontaneous generation) and Semmelweis (aseptic
technique), Lister instituted the use of chemical antimicrobials for the
"sanitization" of objects that come into contact with surgical wounds
(b)
Considered
the "father of antiseptic surgery"
(c)
[Joseph Lister (Google Search)] [index]
(21) Jenner, Edward (late 1700s)
(a)
Use
of cowpox virus to vaccinate against smallpox virus
(b)
[Edward Jenner (Google Search)] [index]
(22) Flemming, Alexander (early
1900s)
(a)
Discovered
penicillin, an antibiotic
(b)
[Alexander Flemming
(Google Search)]
[index]
(a)
Chemotherapy
is the treatment of disease using chemicals administered to the diseased body
(b)
[antimicrobial
therapy (MicroDude)] [index]
(a)
A
kind of antibacterial chemotherapeutic derived from natural sources (e.g.,
other bacteria)
(b)
[antimicrobial
therapy (MicroDude)] [index]
(a)
In
addition to the germ theory of disease, microorganisms
have served as important biochemical and genetic model systems
(b)
That
is, typically it is easier to study things in microorganisms than in larger
organisms because microorganisms generally are cheaper and easier to work with,
plus share many important characteristics with larger organisms
(c)
For
example, understanding the molecular role of DNA in the hereditary process
occurred as a consequence of studies employing microorganisms (indeed, Watson,
of Watson and Crick, studied the viruses of bacteria)
(d)
[Recombinant
DNA and engineering, DNA technology (MicroDude)] [index]
(a)
Molecular
biology is a field that evolved from molecular genetics
and microbiology
(b)
Molecular
biology (e.g., genetic engineering)
is a series of techniques including such things as gene cloning and DNA sequencing (which are techniques that have
traditionally employed microorganisms in their implementation)
(c)
These
are very important tools which are serving to revolutionize how people to and
what they can do in biology and medicine (including microbiology)
(d)
For
example, entire genomes of certain microorganisms (a number growing monthly)
have been completely sequenced
(e)
[molecular biology (MicroDude)] [index]
(27) Vocabulary [index]
(a)
Algae
(b)
Antibiotic
(c)
Arthropods
(f)
Chemotherapy
(h)
Fungi
(j)
Helminths
(l)
Hooke, Robert
(m)
Jenner,
Edward
(n)
Koch, Robert
(o)
Lister, Joseph
(p)
Microbes
(q)
Microorganisms
(t)
Pasteur,
Louis
(u)
Protozoa
(v)
Redi,
Francesco
(y)
The variety of kinds of microbes
(z)
Viruses