Microbiology

1. Microbiology

2. 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?

3. Scale of Microbes

4. 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

5. 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.

6. Rob-Shaped Bacteria

7. Spherical Bacteria

8. Spirochete: Borrelia burgdorferi Spiral-Shaped Bacteria

9. Types: Cyanobacteria Description: blue-green algae Types: photosynthetic aquatic procaryotes, green lake scum, cell walls Nutrient Type: photoautotrophs Durable state: ? Diseases: none

10. 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]

11. 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.

12. 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.

13. 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)

14. 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.

15. 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)

16. 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

17. 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)!

18. 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

19. 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

20. 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

21. 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)

22. 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.

23. 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)

24. 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)

25. Brueghel: The Triumph of Death (1560)

26. 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….

27. Hooke’s Microscope

28. RBCs Leeuwenhoek’s Microscope

29. Edward Jenner – Smallpox Vaccine (1796)

30. 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

31. Redi’s Experiment

32. 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!

33. Pasteur’s Swan-Necked Flasks

34. 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.

35. MicroDude Comes to Work

36. 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

37. 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

38. Link to Next Presentation

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