Humans and the Microbial World

Nosocomial Infections

A Nosocomial Infection is a hospital- or clinicacquired 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.

Microbiology, b. 1674

Microscope of Antony van Leeuwenhoek (1632-1723)

Microbiology, b. 1674

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Microscope of Antony van Leeuwenhoek (1632-1723)

 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).

What is Microbiology?

Microbiology b. >3 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.

Origin of Microbes: Redis Exp.

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

Pastuer (1861) Refuted Spont. Gen.

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

Origin of Microbes: Pasteurs Swan-Necked Flasks

Origin of Microbes: Pasteurs Swan-Necked Flasks

Remains sterile. Bacteria, fungal spores, and dust adhere to glass. Contamination of culture Broth turbidity indicates bacterial growth.

Heat to sterilize (doesnt always work).

Origin of Microbes: Pasteurs Swan-Necked Flasks

Remains sterile. Bacteria, fungal spores, and dust adhere to glass. Contamination of culture Broth turbidity indicates bacterial growth.

Heat to sterilize (doesnt always work).

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.

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

Relationship of Microbes

Comparing Domains

Scale of Microbes

Dont worry about these bacterial names, just microscopes and relative sizes.

Scale of Microbes

Types: Bacteria
Description: eubacteria, archaeabacteria, Gram-negative, Grampositive, 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.

Rod-Shaped Bacteria

Spherical Bacteria

Spiral-Shaped Bacteria
Spirochete: Borrelia burgdorferi

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 (e.g., coli) 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 1000-Point Scale) per erroneous usagedont let this happen to you!!!!!! When in doubt, write the whole thing out (and underline)!

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

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]

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.

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 scolexheads of), etc.

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)

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.

Types: Viruses

Other Agents

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)

Mycorrhizal Fungi

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 speciallyformulated 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 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)

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)

MicroDude Comes to Work

Important Point: