What is Microbiology?

Transcription

1 Microbiology

2 What is 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 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.

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 Spiral-Shaped Bacteria Spirochete: Borrelia burgdorferi

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 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 Bacillus subtilis Bdellovibrio spp. Borrelia burgdorferi Brodetella pertusis Chlamydia trachomatis Clostridium botulinum Clostridium perfringens Clostridium tetani Corynebacterium diphtheriae Escherichia coli Gardinerella vaginalis Helicobacter pylori Haemophilus influenzae Klebsiella pneumoniae Lactococcus lactis Legionella spp. Listeria monocytogenes Mycobacterium leprae Mycobacterium tuberculosis Mycoplasma pneumoniae Neiseria gonorrhoeae Neiseria meningitidis Pasteurella pestis Proteus vulgaris Pseudomonas aeruginosa Rickettsia prowazekii Rickettsia rickettsii Salmonella typhi Serratia marcescens Shigella dysenteriae Staphylococcus aureus Streptococcus pneumoniae Treponema pallidum Vibrio cholerae Yersinia pestis

19 Cheat Sheet (1/2) Bacillus anthracis Bacillus subtilis Bdellovibrio spp. Borrelia burgdorferi Brodetella pertusis Chlamydia trachomatis Clostridium botulinum Clostridium perfringens Clostridium tetani Corynebacterium diphtheriae Escherichia coli Gardinerella vaginalis Helicobacter pylori Haemophilus influenzae Klebsiella pneumoniae Lactococcus lactis Legionella spp. Listeria monocytogenes Anthrax Not pathogenic Not pathogenic (to us, at least) Whooping cough (pertusis) Lyme disease Trachomas (blindness), etc. Botulism Gas gangrene & food poisoning Tetanus Diphtheria Typhoid fever Vaginitis Stomach ulcer Lung, ear infection, meningitis Atypical pneumoniae (common) Yogurt Legionnaire s disease Damage to fetus

20 Cheat Sheet (2/2) Leprosy Tuberculosis Atypical pneumonia Gonorrhea Meningitis Plague (older name) Wound infection Opportunist (e.g., burns) Typhus Rocky Mountain Spotted Fever Typhoid fever Nosocomial infections Traveler s diarrhea TSS, food poisoning, etc. Most-common pneumonia Syphilis Cholera Plague (newer name) Mycobacterium leprae Mycobacterium tuberculosis Mycoplasma pneumoniae Neiseria gonorrhoeae Neiseria meningitidis Pasteurella pestis Proteus vulgaris Pseudomonas aeruginosa Rickettsia prowazekii Rickettsia rickettsii Salmonella typhi Serratia marcescens Shigella dysenteriae Staphylococcus aureus Streptococcus pneumoniae Treponema pallidum Vibrio cholerae 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 Leeuwenhoek s Microscope RBCs

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 spontaneousgeneration 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 points noncomp = 300 points) = 1100 points Extra stuff: Daily reading and lecture quizzes (½ pt/question) 30% rule on all exam questions See syllabus for details:

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