Chapter 1: Humans and the Microbial World

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Chapter 1Humans and theMicrobial World
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Nosocomial Infections

• A Nosocomial Infection is a hospital- or
  clinic-acquired Infectious Disease.
• Nobody goes into medicine in order to prevent
  Nosocomial Infections.
• Nevertheless, to practice medicine you must be
  able to prevent Nosocomial Infections.
• To prevent Nosomial Infections you need to have
  some understanding of microbiology.
• Oh yes, and Infectious Disease, in general, is
  kind of important to medicine, too.
• At the very least, you should be striving to Do
  No Harm!
• And avoiding harming by infection requires some
  reasonable knowledge of microbiology.

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Microbiology, b. 1674
Microscope of Antony van Leeuwenhoek (1632-1723)
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Microbiology, b. 1674
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Microscope of Antony van Leeuwenhoek (1632-1723)
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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 (i.e., in pure culture).

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Microbiology b. gt3 billion BC

• It is generally believed that microorganisms
  have existed on earth for several billion years,
  and over time, plants and animals have evolved
  from microorganisms.

• Above is a fossil cyanobacterium that is 950
  million years old.
• Microorganisms are very diverse in all their
  aspects appearance, metabolism, physiology, and
  genetics. They are far more diverse in these
  terms than plants and animals.

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Origin of Microbes Redis Exp.
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Origin of Microbes 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

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Pastuer (1861) Refuted Spont. Gen.

• Pasteur filtered air through cotton plug showing
  that filterable particles cause contamination of
  sterile broths.
• Swan-necked flask experiments

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Origin of Microbes Pasteurs Swan-Necked Flasks
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Origin of Microbes Pasteurs Swan-Necked Flasks
Remains sterile.
Contamination of culture
Bacteria, fungal spores, and dust adhere to glass.
Heat to sterilize (doesnt always work).
Broth turbidity indicates bacterial growth.
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Origin of Microbes Pasteurs Swan-Necked Flasks
No Turbidity w/o Contamination!
Remains sterile.
Contamination of culture
Bacteria, fungal spores, and dust adhere to glass.
Heat to sterilize (doesnt always work).
Broth turbidity indicates bacterial growth.
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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.

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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 and other Agents

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Relationship of Microbes
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Comparing Domains
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Scale of Microbes
Dont worry about these bacterial names, just
microscopes and relative sizes.
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Scale of Microbes
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Types Bacteria
Description eubacteria, archaeabacteria,
Gram-negative, Gram-positive, acid fast,
cyanobacteria
Types prokaryotes, 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.
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Rod-Shaped Bacteria
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Spherical Bacteria
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Spiral-Shaped Bacteria
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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)
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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 (e.g., coli) is never abbreviated
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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 1000-Point Scale) per erroneous
usagedont let this happen to you!!!!!!
When in doubt, write the whole thing out (and
underline)!
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Types Cyanobacteria
Description also called blue-green algae,
cyanobacteria are a kind of bacteria (more
specifically, a kind of eubacteria)
Types photosynthetic aquatic procaryotes, green
lake scum, cell walls
Nutrient Type photoautotrophs
Durable state ?
Diseases none
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Types Algae
Description photosynthetic aquatic eukaryotes,
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
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Types Fungi
Description yeasts (unicellular fungi), molds
(filamentous fungi)
Types eucaryotes, nutrient absorbers, dry
conditions, plant decomposers, cell walls, 100
human pathogens
Nutrient Type chemoheterotrophs
Durable state spores (not endospores)
Diseases mycoses candida, ringworm (pictured),
athlete's foot, jock itch, etc.
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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.
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Types Protozoa (Protists)
Description Unicellular and slime molds,
flagellates, ciliates
Types eucaryotes, parasites (most not),
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)
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Types Viruses
Description Viruses are not cells but some
viruses do have lipid envelopes
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.
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Types Viruses
Smallpox is a Disease with a Viral Etiology
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Other Agents
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Microbes Ecology

• Microbes are producesthey provide energy to
  ecosystems, especially aquatic ecosystems
• Microbes are fixersthey make nutrients available
  from inorganic sources, e.g., nitrogen
• Microbes are decomposersthey free up nutrients
  from no longer living sources
• Microbes form symbioses (such as mycorrhizal
  fungi associated with plant rootsthough somewhat
  macroscopic, the bacteria found in legume root
  nodules, etc.)
• Microbes serve as emdosymbionts (e.g.,
  chloroplasts and mitochondria)

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Mycorrhizal Fungi
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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 BugsPlus 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.
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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 wasnt so long ago that humans didnt
  know this)
• Nevertheless, most microorganisms, including most
  bacteria, do not cause diseases in any organism
  (including in humans)

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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

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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).
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Brueghel The Triumph of Death (1560)
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MicroDude Comes to Work
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Important Point
If you are having trouble understanding lecture
material Try reading your text before
attending lectures. And take the time to read it
well!
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