Microbiology

 Microbiology is the Science that studies

What is Microbiology? 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.
Rod-Shaped Bacteria
Spherical Bacteria
 Spirochete:
Borrelia burgdorferi
Spiral-Shaped Bacteria
 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 binomial 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.!

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

 Various Binomials
Bacillus anthracis
Bacillus subtilis
Bdellovibrio spp.
Borrelia burgdorferi
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
Mycobacterium leprae
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Neiseria gonorrhoeae
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
 Cheat Sheet (1/2)
Bacillus anthracis Anthrax
Bacillus subtilis Not pathogenic
Bdellovibrio spp. Not pathogenic (to us, at least)
Borrelia burgdorferi Whooping cough (pertusis)
Brodetella pertusis Lyme disease
Chlamydia trachomatis Trachomas (blindness), etc.
Clostridium botulinum Botulism
Clostridium perfringens Gas gangrene & food poisoning
Clostridium tetani Tetanus
Corynebacterium diphtheriae Diphtheria
Escherichia coli Typhoid fever
Gardinerella vaginalis Vaginitis
Helicobacter pylori Stomach ulcer
Haemophilus influenzae Lung, ear infection, meningitis
Klebsiella pneumoniae Atypical pneumoniae (common)
Lactococcus lactis Yogurt
Legionella spp. Legionnaire’s disease
Listeria monocytogenes Damage to fetus
 Cheat Sheet (2/2)
Leprosy
Tuberculosis
Atypical pneumonia
Gonorrhea
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)
Mycobacterium leprae
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Neiseria gonorrhoeae
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
 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)
Impact of Infectious Disease
 Infectious diseases are diseases caused by
microbes
 200,000 deaths per year in U.S. from infectious
diseases
 ~20 million died from influenza (a disease
caused by a virus) in 1918
 “New” infectious diseases still being discovered
 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!
Origin of Microbes: Pasteur’s Swan-Necked Flasks
Origin of Microbes: Pasteur’s Swan-Necked Flasks

Remains
sterile.

Bacteria, Contamination
Heat to fungal spores, of culture
sterilize and dust
(doesn’t adhere to Broth turbidity
always work). glass. indicates bacterial
growth.
Origin of Microbes: Pasteur’s Swan-Necked Flasks

Remains
sterile.

Bacteria, Contamination
Heat to fungal spores, of culture
sterilize and dust
(doesn’t adhere to Broth turbidity
always work). glass. indicates bacterial
growth.
Pasteur’s Swan-Necked Flasks
Problem of Endospores  Pasteur was fortunate to have worked with broths
prepared from non-soil or -plant associated substances
(e.g., hay).
 Those substances contain bacteria that can form
endospores, not all bacteria can.
 Endospores represent a bacterial durable state
and are very difficult to kill.
 John Tyndal (1876) discovered that there exist
differences in the ability of heat to kill different kinds
of bacteria-containing cultures.
 Ferdinand Cohn (1876) showed that this difference
was due to endospores and Robert Koch (1877)
showed that the bacterium Bacillus anthracis
forms endospores as part of its transmission.
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