Microbiology by Madame Dela Cruz

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WhatisMicrobiology? Microbiology is the Science that studiesMicroorganisms.

Microorganisms, roughly, are those living thingsthat are too small to be seen with the naked eye.Microorganisms cannot be distinguishedPhylogenetically from MacroorganismsFor example, many fungi are microorganisms, aswell 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 specificmicroorganism from a population and then

cultures it.

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ScaleofMicrobes

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Types ofMicroorganisms

Bacteria a.k.a., eubacteria (true bacteria) a.k.a., domain Bacteria

Archaeabacteria

a.k.a., domain ArchaeaSingle-celled members of domain Eukarya.

Protozoa Microscopic Algae Microscopic Fungi

Viruses

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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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Spherical Bacteria

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Spiral-Shaped Bacteria

Spirochete:

Borreliabu rgdorferi

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Types: Cyanobacteria

Description: blue-green algae

Types: photosynthetic aquatic procaryotes, green lake scum,

cell wallsNutrient Type: photoautotrophs

Durable state: ?

Diseases: none

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Types: Algae

Description: photosynthetic aquatic eucaryotes, cell walls, bothunicellular 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 causesDiarrhetic 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 (filamentousfungi)

Types: eucaryotes, absorbers, dry conditions, plant

decomposers, cell walls, ~100 human pathogensNutrient Type: chemoheterotrophs

Durable state: spores

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

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Types: Helminths

Description: Flatworms (platyhelminths), roundworms(nematodes)

Types: metazoan (multicellular animal) parasites, engulfers

and absorbersNutrient Type: chemoheterotr ophs

Durable state: ?

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

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Types: Protozoa (Protists)

Description: Unicellular and slime molds, flagellates, ciliates

Types: eucaryotes, parasites, engulfers and absorbers, wet

conditions, no cell wall, ~30 human pathoge nsNutrient Type: chemoheterotrophs (some cl assificationsinclude some photoautotrophs as well)

Durable state: cysts (some)

Diseases: malaria, giardiasis, amoebic dysentery, etc. (shownare harmless--to us--protist components of pond water:

Amoeba , Blepharisma , Paramecium , Peranema , & Stentor )

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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 durablestate 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 thegenus 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 nolonger actually describes a species)

When both genus and species names are present, the genusname 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 isnot acceptable unless you have already written Escherichiacoli 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 usedin 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 anypotential for confusion (e.g., Enterococcus vs. Escherichia )

These rules are to be followed when employing binomialnomenclature even in your speech. It is proper to refer toEscherichia coli as E. coli or even as Escherichia , but it is notproper to call it coli or E.C. !

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

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Various BinomialsBacillus anthracis

Bacillus subtilisBdellovibrio spp.

Brodetella pertusisChlamydia trachomatis

Clostridium botulinumClostridium perfringensClostridium tetani Corynebacterium diphtheriaeEscherichia coli

Gardinerella vaginalisHelicobacter pylori Haemophilus influenzaeKlebsiella pneumoniaeLactococcus lactis

Legionella spp.Listeria monocytogenes

Borrelia burgdorferi

Mycobacterium leprae

Mycobacterium tuberculosisMycoplasma pneumoniae

Neiseria meningitidisPasteurella pestis

Proteus vulgarisPseudomonas aeruginosaRickettsia prowazekii Rickettsia rickettsii Salmonella typhi

Serratia marcescensShigella dysenteriaeStaphylococcus aureusStreptococcus pneumoniaeTreponema pallidum

Vibrio choleraeYersinia pestis

Neiseria gonorrhoeae

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Cheat Sheet (1/2)Bacillus anthracis

Bacillus subtilisBdellovibrio spp.

Brodetella pertusisChlamydia trachomatis

Clostridium botulinumClostridium perfringensClostridium tetani Corynebacterium diphtheriaeEscherichia coli

Gardinerella vaginalisHelicobacter pylori Haemophilus influenzaeKlebsiella pneumoniaeLactococcus lactis

Legionella spp.Listeria monocytogenes

Borrelia burgdorferi

Anthrax

Not pathogenicNot pathogenic (to us, at least)

Lyme diseaseTrachomas (blindness), etc.

BotulismGas gangrene & food poisoningTetanusDiphtheriaTyphoid fever

VaginitisStomach ulcer Lung, ear infection, meningitisAtypical pneumoniae (common)Yogurt

Legionnaires diseaseDamage to fetus

Whooping cough (pertusis)

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Cheat Sheet (2/2)Leprosy

TuberculosisAtypical pneumonia

MeningitisPlague (older name)

Wound infectionOpportunist (e.g., burns)TyphusRocky Mountain Spotted Fever Typhoid fever

Nosocomial infectionsTravelers diarrheaTSS, food poisoning, etc.Most-common pneumoniaSyphilis

CholeraPlague (newer name)

Gonorrhea

Mycobacterium leprae

Mycobacterium tuberculosisMycoplasma pneumoniae

Neiseria meningitidisPasteurella pestis

Proteus vulgarisPseudomonas aeruginosaRickettsia prowazekii Rickettsia rickettsii Salmonella typhi

Serratia marcescensShigella dysenteriaeStaphylococcus aureusStreptococcus pneumoniaeTreponema pallidum

Vibrio choleraeYersinia pestis

Neiseria gonorrhoeae

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Microbes & Ecology

Microbes are producesthey provide energy to ecosystemsMicrobes are fixersthey make nutrients available from

inorganic sources, e.g., nitrogen

Microbes are decomposersthey free up nutrients from nolonger living sources

Microbes form symbioses (such as mycorrhizal fungiassociated with plant rootsthough somewhat macroscopic,the bacteria found in legume root nodules, etc.)

Microbes serve as emdosymbionts (e.g., chloroplasts andmitochondria)

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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 Bugs+Plus provides easy tofollow step-by-step instructions, containers of

specially-formulated wet and dry nutrients anda container of microbes cultured for their

ability to digest oil and other petroleumderivatives.

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Microbes & Disease

Microbes both cause and prevent diseasesMicrobes produce antibiotics used to treat diseases

The single most important achievement of modern medicineis the ability to treat or prevent microbial disease

Most of this course will consider the physiology of microbesand their role in disease

The Germ Theory of Disease = Microbes cause disease!

(yes, it wasnt so long ago that humans didnt know this)

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Infectious diseases are diseases caused bymicrobes200,000 deaths per year in U.S. from infectiousdiseases~20 million died from influenza (a diseasecaused by a virus) in 1918New infectious diseases still being discovered

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Normal FloraThese are the ~harmless microorganisms found on your body.

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

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Brueghel: The Triumph of Death (1560)

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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) = Kochs postulates

Dmitri Iwanowski (1990s) = Inference of virusesAlexander Fleming (1920s) = Penicillin

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

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Hookes Microscope

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Leeuwenhoeks Microscope

RBCs

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Edward Jenner Smallpox Vaccine (1796)

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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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Redis Experiment

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Problems Translating to Microbes

Hard to kill endosporesboiled broths not always sterilizedConcerns (invalid) that boiling altered broths so as to prevent

spontaneous generation

Concerns (invalid) that absence of air preventedspontaneous generation

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

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

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Origin of Microbes: Pasteurs Swan-Necked Flasks

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Origin of Microbes: Pasteurs Swan-Necked Flasks

Heat tosterilize(doesnt

always work).

Bacteria,fungal spores,

and dustadhere to

glass.

Remainssterile.

Contaminationof culture

Broth turbidityindicates bacterial

growth.

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Origin of Microbes: Pasteurs Swan-Necked Flasks

Heat tosterilize(doesnt

always work).

Bacteria,fungal spores,

and dustadhere to

glass.

Remainssterile.

Contaminationof culture

Broth turbidityindicates bacterial

growth.

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Pasteurs Swan-Necked Flasks

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ProblemofEndospores 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 formendospores, not all bacteria can .Endospores represent a bacterial durable state

and are very difficult to kill.John Tyndal (1876) discovered that there existdifferences in the ability of heat to kill different kindsof bacteria-containing cultures.

Ferdinand Cohn (1876) showed that this differencewas due to endospores and Robert Koch (1877) showed that the bacterium Bacillus anthracis forms endospores as part of its transmission.

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President Garfields VertebraeOn the morning of July 2, 1881, Charles Guiteau

fired two shots at President James Garfield as heentered a Washington, DC train station. One shotgrazed Garfield's hand. The second entered thePresident's spine near the right 11th rib but didnot exit.

Th e x-ray, which would easily have pinpointed the

bullet's location, had not yet been discovered. Sothe President's physicians did what all competentphysicians had routinely done in such cases.They probed the entry wound with specialinstruments designed for that purpose - butwithout success.

The bullet remained lost inside the President.Medical historians believe Garfield could havesurvived his injury if the attending physicians hadwashed their hands and used sterile instruments.In 1881, though, such antisepsis techniques werestill under debate within the American medicalprofession.

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MicroDude Comes to Work