Important words and concepts from Chapter 1, Black, 2002 (3/28/2003):

by Stephen T. Abedon ( for Micro 509 at the Ohio State University



Course-external links are in brackets

Click [index] to access site index

Click here to access text’s website

Vocabulary words are found below



(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 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


(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)]

(2) What is Microbiology?

(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)]


Supplemental Material – Types of Microorganisms & their General Properties




Nutrition type


durable state:

some diseases:


brown, red, green, diatoms, dinoflagellates, euglenoids

photosynthetic aquatic eucaryotes, cell walls, unicellular and multicellular





eubacteria, archaeabacteria, Gram-negative, Gram-positive, acid fast, cyanobacteria

procaryotes, absorbers, wet conditions, animal decomposers, cell walls, unicellular


photohetero- chemoauto- photoauto-

endospores (some)

tetanus, botulism, gonorrhea, chlamydia, tuberculosis, etc., etc., etc.


blue-green algae

photosynthetic aquatic procaryotes, green lake scum, cell walls





yeasts (unicellular fungi), molds (filamentous fungi)

eucaryotes, absorbers, dry conditions, plant decomposers, cell walls, ~100 human pathogens



mycoses: candida, ringworm, athlete's foot, jock itch, etc.


Flatworms (platyhelminths), roundworms (nematodes)

metazoan (multicellular animal) parasites, engulfers and absorbers



tape worm, trichinosis, hook worm, etc.


Unicellular and slime molds, flagellates, ciliates

eucaryotes, parasites, engulfers and absorbers, wet conditions, no cell wall, ~30 human pathogens


cysts (some)

malaria, giardiasis, amoebic dysentery, etc.


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]

(5) Algae (chapters 4, 11)

(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]

(6) Fungi (chapters 4, 11)

(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]

(8) Protozoa (chapters 4, 11)

(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]

(10) Arthropods

(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]

(11) Binomial nomenclature

(a)                    Homo sapiens and Escherichia coli are both examples of binomial nomenclature, the naming of organism using two names


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




Micrococcus luteus



Bacillus anthracis



Bacteroides fragilis

various infections from fecal contamination


Bordetella pertussis

whooping cough (pertussis)


Borrelia burgdorferi

Lyme disease


Campylobacter spp.



Chlamydia trachomatis

trachoma, nongonococcal urethritis


Clostridium botulinum (difficile, tetani)

botulism, tetanus, gas gangrene


Corynebacterium diphtheriae



Enterobacter aerogenes

opportunistic infections


Escherichia coli

opportunistic infections of colon and other sites


Gardnerella vaginalis



Haemophilus influenzae

respiratory infections, meningitis, conjunctivitis


Helicobacter pylori

peptic ulcer disease


Klebsiella pneumoniae

respiratory and urinary tract infections


Legionella spp.

pneumonia and other respiratory infections


Moraxella lacunata



Mycobacterium tuberculosis (leprae, paratuberculosis, smegmatis)

tuberculosis, leprosy (Hanson's disease)


Mycoplasma pneumoniae

walking pneumonia


Neisseria gonorrhoeae

gonorrhea; meningitis & nasopharylngeal infections by other species





Proteus vulgaris

urinary tract infections, especially nosocomial


Pseudomonas aeruginosa

urinary tract infections, burns, and wounds


Rickettsia prowazekii (rickettsii)

typhus, Rocky Mountain spotted fever


Salmonella typhimurium

typhoid fever, enteritis, and food poisoning


Serratia marcescens

opportunistic infections


Shigella dysenteriae (sonnei)

bacillary dysentery


Staphylococcus aureus

skin abscesses, opportunistic infections such as toxic shock syndrome


Streptococcus pyogenes

strep throat and other infections, puerperal fever = childbirth fever


Streptomyces spp.



Treponema pallidum



Vibrio cholera



Yersinia pestis




(d)                    [binomial nomenclature (Google Search)] binomial nomenclature (MicroDude)] [index]

(12) History of microbiology

(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

(ii)                    Anton van Leeuwenhoek

(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]

(13) Hooke, Robert (~1665)

(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]

(15) Germ theory of disease

(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

(v)                    Alexander Fleming

(vi)                  Etc.

(e)                    [germ theory of disease (Google Search)] [index]

(16) Redi, Francesco

(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


Fermentation products (ethanol, acetone, etc.)


Wine, cheese, yogurt, bread, half-sour pickles, etc.


Recombinant products (e.g., human insulin)



(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]

(23) Chemotherapy

(a)                    Chemotherapy is the treatment of disease using chemicals administered to the diseased body

(b)                    [antimicrobial therapy (MicroDude)] [index]

(24) Antibiotic

(a)                    A kind of antibacterial chemotherapeutic derived from natural sources (e.g., other bacteria)

(b)                    [antimicrobial therapy (MicroDude)] [index]

(25) Molecular genetics

(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]

(26) Molecular biology

(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

(d)                    Bacteria

(e)                    Binomial nomenclature

(f)                      Chemotherapy

(g)                    Flemming, Alexander

(h)                    Fungi

(i)                      Germ theory of disease

(j)                      Helminths

(k)                    History of microbiology

(l)                      Hooke, Robert

(m)                  Jenner, Edward

(n)                    Koch, Robert

(o)                    Lister, Joseph

(p)                    Microbes

(q)                    Microorganisms

(r)                     Molecular biology

(s)                     Molecular genetics

(t)                      Pasteur, Louis

(u)                    Protozoa

(v)                    Redi, Francesco

(w)                  Semmelweis, Ignazp

(x)                    van Leeuwenhoek, Anton

(y)                    The variety of kinds of microbes

(z)                     Viruses

(aa)                 What is Microbiology?