Chapter 1: Humans and the Microbial World

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. Nosocomial Infections

Microscope of Antony van Leeuwenhoek (1632-1723) Microbiology, b. 1674 Microscope of Antony van Leeuwenhoek (1632-1723)

Microscope of Antony van Leeuwenhoek (1632-1723) Note that images will dissolve in if you are responsible for them and/or I’ll circle or “square” in blue the parts of these images you are particularly responsible for). Microbiology, b. 1674 Note that “blue” text you are very responsible for, “black” less so, and “red” only in the form of bonus questions. 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.” Microbiology b. >3 billion BC 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: Redi’s 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 Pastuer (1861) Refuted Spont. Gen.

Origin of Microbes: Pasteur’s Swan-Necked Flasks

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

Origin of Microbes: Pasteur’s Swan-Necked Flasks No Turbidity w/o Contamination! Remains sterile. Bacteria, fungal spores, and dust adhere to glass. Contamination of culture Heat to sterilize (doesn’t always work). Broth turbidity indicates bacterial growth.

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. Problem of Endospores

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 Types of Microorganisms

Relationship of Microbes

Comparing Domains

Scale of Microbes Don’t worry about these bacterial names, just “microscopes” and relative sizes.

Scale of Microbes

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.

Rod-Shaped Bacteria

Spherical Bacteria

Spiral-Shaped Bacteria Borrelia burgdorferi Spirochete:

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 usage—don’t 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 scolex-heads 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 Smallpox is a Disease with a Viral Etiology

Other “Agents”

Microbes & Ecology Microbes are produces—they provide energy to ecosystems, especially aquatic 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)

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 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) 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 Impact of Infectious Disease

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: 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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