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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”

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What is microbiology l.jpg

  • 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.

What is Microbiology?



Types of microorganisms l.jpg
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 l.jpg
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.




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Spirochete:

Borrelia burgdorferi

Spiral-Shaped Bacteria


Types cyanobacteria l.jpg
Types: Cyanobacteria

Description: blue-green algae

Types: photosynthetic aquatic procaryotes, green lake scum, cell walls

Nutrient Type: photoautotrophs

Durable state: ?

Diseases: none


Types algae l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Types: Viruses

Description: Not cells but enveloped or non-enveloped

Sorry, no images - I ran out of steam

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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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 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 200-Point Scale) per erroneous usage

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


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Various Binomials

Bacillus anthracis

Mycobacterium leprae

Bacillus subtilis

Mycobacterium tuberculosis

Bdellovibrio spp.

Mycoplasma pneumoniae

Note How Each is Italicized!

Borrelia burgdorferi

Neiseria gonorrhoeae

Brodetella pertusis

Neiseria meningitidis

Chlamydia trachomatis

Pasteurella pestis

Clostridium botulinum

Proteus vulgaris

Clostridium perfringens

Pseudomonas aeruginosa

Clostridium tetani

Rickettsia prowazekii

Corynebacterium diphtheriae

Rickettsia rickettsii

Escherichia coli

Salmonella typhi

Gardinerella vaginalis

Serratia marcescens

Helicobacter pylori

Shigella dysenteriae

Haemophilus influenzae

Staphylococcus aureus

Klebsiella pneumoniae

Streptococcus pneumoniae

Lactococcuslactis

Treponema pallidum

Legionella spp.

Vibrio cholerae

Listeria monocytogenes

Yersinia pestis


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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

Klebsiellapneumoniae

Atypical pneumoniae (common)

Lactococcuslactis

Yogurt

Legionella spp.

Legionnaire’s disease

Listeria monocytogenes

Damage to fetus


Cheat sheet 2 2 l.jpg
Cheat Sheet (2/2)

Leprosy

Mycobacterium leprae

Tuberculosis

Mycobacterium tuberculosis

Atypical pneumonia

Mycoplasma pneumoniae

Gonorrhea

Neiseria gonorrhoeae

Meningitis

Neiseria meningitidis

Plague (older name)

Pasteurella pestis

Wound infection

Proteus vulgaris

Opportunist (e.g., burns)

Pseudomonas aeruginosa

Typhus

Rickettsia prowazekii

Rocky Mountain Spotted Fever

Rickettsia rickettsii

Typhoid fever

Salmonella typhi

Nosocomial infections

Serratia marcescens

Traveler’s diarrhea

Shigella dysenteriae

TSS, food poisoning, etc.

Staphylococcus aureus

Most-common pneumonia

Streptococcus pneumoniae

Syphilis

Treponema pallidum

Cholera

Vibrio cholerae

Plague (newer name)

Yersinia pestis


Microbes ecology l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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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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….



Leeuwenhoek s microscope l.jpg

RBCs

Leeuwenhoek’s Microscope



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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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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!



President garfield s vertebrae l.jpg
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.



Course structure l.jpg
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


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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



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Acknowledgements

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


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