Scope and History of Microbiology - Ohio State University at Mansfield

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Microbiology

What is Microbiology?


Microbiology is the Science that studies
Microorganisms.


Microorganisms, roughly, are those living things
that are too small to be seen with the naked eye.


Microorganisms cannot be distinguished
Phylogenetically from “Macroorganisms”


For example, many fungi are microorganisms, as
well as all bacteria, all viruses, and most protists.


Microbiology is more a collection of techniques:



Aseptic technique



Pure culture technique



Microscopic observation of whole organisms


A microbiologist usually first isolates a specific
microorganism from a population and then
cultures it.

Scale of Microbes

Types of Microorganisms


Bacteria


a.k.a., eubacteria (“true” bacteria)


a.k.a., domain Bacteria


Archaeabacteria


a.k.a., domain Archaea


Single
-
celled members of domain Eukarya.


Protozoa


Microscopic Algae


Microscopic Fungi


Viruses

Types: Bacteria

Description
:

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

Types
:

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

Nutrient Type
:
chemoheterotrophs, photoheterotrophs,
chemoautotrophs, photoautotrophs

Durable state
:

endospores (some)

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

Rob
-
Shaped Bacteria

Spherical Bacteria

Spiral
-
Shaped Bacteria

Spirochete:

Borrelia burgdorferi

Types: Cyanobacteria

Description
:

blue
-
green algae

Types
:

photosynthetic aquatic procaryotes, green lake scum,
cell walls

Nutrient Type
:
photoautotrophs

Durable state
:

?

Diseases
:
none

Types: Algae

Description
:

photosynthetic aquatic eucaryotes, cell walls, both
unicellular and multicellular types

Types
:

brown, red, green, diatoms, dinoflagellates, euglenoids

Nutrient Type
:
photoautotrophs

Durable state
:
?

Diseases
:
Some poisonings associated with unicellular types:
Alexandrium

causes Paralytic Shellfish Poisoning (PSP),
Dinophysis

causes
Diarrhetic Shellfish Poisoning (DSP),
Pseudo
-
nitzschia multiseries

causes
Amnesic Shellfish Poisoning (ASP) [some would describe some as protists]

Types: Fungi

Description
:

yeasts (unicellular fungi), molds (filamentous
fungi)

Types
:

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

Nutrient Type
:
chemoheterotrophs

Durable state
:

spores

Diseases
:
mycoses: candida, ringworm (pictured), athlete's
foot, jock itch, etc.


Types: Helminths

Description
:

Flatworms (platyhelminths), roundworms
(nematodes)

Types
:

metazoan (multicellular animal) parasites, engulfers
and absorbers

Nutrient Type
:
chemoheterotrophs

Durable state
:
?

Diseases
:
trichinosis, hook worm, tape worm (pictured are
scolex
-
heads of), etc.

Types: Protozoa (Protists)

Description
:

Unicellular and slime molds, flagellates, ciliates

Types
:

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

Nutrient Type
:
chemoheterotrophs (some classifications
include some photoautotrophs as well)

Durable state
:

cysts (some)

Diseases
:
malaria, giardiasis, amoebic dysentery, etc. (shown
are harmless
--
to us
--
protist components of pond water:
Amoeba
,
Blepharisma
,
Paramecium
,
Peranema
, &
Stentor
)

Types: Viruses

Description
:

Not cells but enveloped or non
-
enveloped

Types
:

acellular, obligate intracellular parasites

Nutrient Type
:
not applicable

Durable state
:

virion particles, some can encase in durable
state of host

Diseases
:
common cold, flu, HIV, herpes, chicken pox, etc.

Binomial Nomenclature (1/3)

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
)

Binomial Nomenclature (2/3)

Both the genus and species names are always
italicized

(or
underlined)

always underline if writing 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

Binomial Nomenclature (3/3)

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.
!

Failure to employ correct binomial nomenclature on exams will
result in the subtraction of one point (on 200
-
Point Scale) per
erroneous usage

When in doubt, write the whole thing out (and
underline
)!

Various Binomials

Bacillus anthracis

Bacillus subtilis

Bdellovibrio
spp.

Brodetella pertusis

Chlamydia trachomatis

Clostridium botulinum

Clostridium perfringens

Clostridium tetani

Corynebacterium diphtheriae

Escherichia coli

Gardinerella vaginalis

Helicobacter pylori

Haemophilus influenzae

Klebsiella pneumoniae

Lactococcus

lactis

Legionella spp.

Listeria monocytogenes

Borrelia burgdorferi

Mycobacterium leprae

Mycobacterium tuberculosis

Mycoplasma pneumoniae

Neiseria meningitidis

Pasteurella pestis

Proteus vulgaris

Pseudomonas aeruginosa

Rickettsia prowazekii

Rickettsia rickettsii

Salmonella typhi

Serratia marcescens

Shigella dysenteriae

Staphylococcus aureus

Streptococcus pneumoniae

Treponema pallidum

Vibrio cholerae

Yersinia pestis

Neiseria gonorrhoeae

Cheat Sheet (1/2)

Bacillus anthracis

Bacillus subtilis

Bdellovibrio
spp.

Brodetella pertusis

Chlamydia trachomatis

Clostridium botulinum

Clostridium perfringens

Clostridium tetani

Corynebacterium diphtheriae

Escherichia coli

Gardinerella vaginalis

Helicobacter pylori

Haemophilus influenzae

Klebsiella

pneumoniae

Lactococcus

lactis

Legionella spp.

Listeria monocytogenes

Borrelia burgdorferi

Anthrax


Not pathogenic

Not pathogenic (to us, at least)

Lyme disease

Trachomas (blindness), etc.

Botulism

Gas gangrene & food poisoning

Tetanus

Diphtheria

Typhoid fever

Vaginitis

Stomach ulcer

Lung, ear infection, meningitis

Atypical pneumoniae (common)

Yogurt

Legionnaire’s disease

Damage to fetus

Whooping cough (pertusis)

Cheat Sheet (2/2)

Leprosy

Tuberculosis

Atypical pneumonia

Meningitis

Plague (older name)

Wound infection

Opportunist (e.g., burns)

Typhus

Rocky Mountain Spotted Fever

Typhoid fever

Nosocomial infections

Traveler’s diarrhea

TSS, food poisoning, etc.

Most
-
common pneumonia

Syphilis

Cholera

Plague (newer name)

Gonorrhea

Mycobacterium leprae

Mycobacterium tuberculosis

Mycoplasma pneumoniae

Neiseria meningitidis

Pasteurella pestis

Proteus vulgaris

Pseudomonas aeruginosa

Rickettsia prowazekii

Rickettsia rickettsii

Salmonella typhi

Serratia marcescens

Shigella dysenteriae

Staphylococcus aureus

Streptococcus pneumoniae

Treponema pallidum

Vibrio cholerae

Yersinia pestis

Neiseria gonorrhoeae

Microbes & 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

though somewhat macroscopic,
the bacteria found in legume root nodules, etc.)


Microbes serve as emdosymbionts (e.g., chloroplasts and
mitochondria)

Microbes & Industry


Industry: Fermentation products (ethanol, acetone, etc.)


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


Biotech: Recombinant products (e.g., human insulin,
vaccines)


Environment: Bioremediation

Each carton of Bugs+Plus provides easy to
follow step
-
by
-
step instructions, containers of
specially
-
formulated wet and dry nutrients and
a container of microbes cultured for their
ability to digest oil and other petroleum
derivatives.


Microbes & 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 disease


The Germ Theory of Disease = Microbes cause disease!


(yes, it wasn’t so long ago that humans didn’t know this)

Normal Flora


These are the ~harmless microorganisms found
on

your body.

Every part of your body that normally comes in contact with
outside world (deep lungs and stomach are exceptions)

Brueghel: The Triumph of Death (1560)


Brief History Microbiology


Anton van Leeuwenhoek (1670s) = microscopy


Edward Jenner (1796) = vaccination against smallpox


Ignaz Semmelweis (1840s) = hand washing before surgery


Louis Pasteur (1860s) = repudiation spontaneous generation


Joseph Lister (1860) = father aseptic surgery


Robert Koch (1870s) = Koch’s postulates


Dmitri Iwanowski (1990s) = Inference of viruses


Alexander Fleming (1920s) = Penicillin


Stephen T. Abedon (2000s) = not one heck of a lot….

Hooke’s Microscope


Leeuwenhoek’s Microscope


RBCs

Edward Jenner


Smallpox Vaccine (1796)

Spontaneous Generation Myths


Snakes from horse hairs in stagnant water


Mice from grain and cheese wrapped in a sweater


Maggots from rotting meat


Fleas from hair


Flies from fresh and rotting fruit


Mosquitoes from stagnant pondwater


Eels from slimy mud at the bottom of the ocean


Locusts from green leaves


Raccoons from hollow tree trunks


Termites are generated from rotting wood


Redi’s Experiment

Problems Translating to Microbes


Hard to kill endospores

boiled broths not always sterilized


Concerns (invalid) that boiling altered broths so as to prevent
spontaneous generation


Concerns (invalid) that absence of air prevented
spontaneous generation


Concerns (invalid) that heating or chemically treating air
removed vital force from air thereby preventing spontaneous
generation


Basically, proponents of spontaneous generation had good
ol’ common sense on their side, but since their common sense
did not include any sense of microbiology, these spontaneous
-
generation proponents were remarkably incorrect!

Pasteur’s Swan
-
Necked Flasks


President Garfield’s Vertebrae

On the morning of July 2, 1881, Charles Guiteau
fired two shots at President James Garfield as he
entered a Washington, DC train station. One shot
grazed Garfield's hand. The second entered the
President's spine near the right 11th rib but did
not exit.

The x
-
ray, which would easily have pinpointed the
bullet's location, had not yet been discovered. So
the President's physicians did what all competent
physicians had routinely done in such cases.
They probed the entry wound with special
instruments designed for that purpose
-

but
without success.

The bullet remained lost inside the President.
Medical historians believe Garfield could have
survived his injury if the attending physicians had
washed their hands and used sterile instruments.
In 1881, though, such antisepsis techniques were
still under debate within the American medical
profession.

MicroDude Comes to Work

Course Structure


Grading:


3 midterms (200 points each x 3 = 600 points)


1 lab exams (200 points)


1 final exam (150 points comp + 150 points non
-
comp = 300 points)


600 + 200 + 300 = 1100 points


Extra stuff:


Daily reading
and

lecture quizzes (
½

pt/question)


“30% rule” on all exam questions


See syllabus for details:


www.phage.org/school_syllabus.htm

Laboratory Primer

Just reading a lab exercise is not the same as getting ready to
do a lab

you also need to outline for yourself, either mentally
or on paper, just what it is that you will be doing

I know that making such an outline with unfamiliar material is
not easy

that is why you need to
look at your lab schedule
,
where I attempt to guide you through what it is that you will
need to be doing

You have to try to remember that a culture that has settled will
need to be resuspended

and you have to not just go through
the motions: you actually need to resuspend it!

It may be that some of you have not had previous training in
using a microscope; after class today we therefore will have a
“microscope 101” session in B211

Link to Next Presentation

Acknowledgements

http://www.colby.edu/biology/BI163/Bacteriappt/bacteriaarchaea.ppt