The Microbial World and You

1. The Microbial World and You Chapter 1

2. Microbes in Our Lives • Microbes (microorganisms) • Too small to be seen with the unaided eye • Ubiquitous • Includes viruses, Bacteria, Fungi, Protozoa • Pathogenic microbes represent only a small number of all known microorganisms • Most microbes are beneficial and crucial for life • Basis of food chain in aquatic environments • Recycle chemical nutrients (saprobes) • Commercial uses – vitamins, alcohols, drugs, food and beverages and much, much more

3. Naming Microorganisms • Binomial system of nomenclature • Developed by Carolus Linnaeus (1735) • All organisms are assigned two names • Genus and specific epithet (species name) • Staphylococcus aureus(Staphylococcusaureus) • Escherichia coli (Escherichiacoli) • Penicilliumchrysogenum(Penicilliumchrysogenum)

4. Three Domains of Life • Carl Woese (1978) – classification based on cellular organization of organisms • Bacteria – Prokaryotic with Peptidoglycan cell walls • Archaea – prokaryotic without peptidoglycan cell walls • Eukarya – Eukaryotic • Protists, Fungi, Plants, and Animals

5. Check Your Understanding • What are microbes? How can they impact our lives (for better and worse)? • Differentiate between a pathogenic and non-pathogenic organism. • Distinguish between a genus and specific epithet. • Compare and contrast the three domains of life.

6. Types of microorganisms

7. Bacteria (Bacterium) • Prokaryotic • Peptidoglycancell wall • Reproduce via binary fission • Motile species move via flagella Haemophlusinfluenzae

8. Archaea • Prokaryotic • May possess cell walls, but lack peptidoglycan as a cell wall component • Not known to cause disease • Commonly found in extreme environments • Methanogens • Extreme Halophiles • Extreme Thermophiles

9. Fungi (Fungus) • Eukaryotic • Molds, yeast, true fungi • Cell wall composed primarily of chitin • Unicellular or multicellular • Multicellular forms consist of hyphae arranged into mycelia • Can reproduce asexually or sexually Mucorsp.

10. Protozoa • Eukaryotic • Unicellular • Move via flagella, cilia, or pseudopods • Used for classification • Can reproduce asexually or sexually Naegleriafowleri

11. Algae (Alga) • Photosynthetic eukaryotes • Important members in the balance of nature • Reproduce sexually and asexually • Cell wall composed primarily of cellulose Volvoxsp.

12. Viruses • Most can only be seen with an electron microscope • Acellular • Consist of DNA or RNA surrounded by a protein coat • Can only reproduce after entering a host cell and commandeering its cellular machinery • Parasitic Human Immunodeficiency Virus

13. Helminths • Flatworms and roundworms • Eukaryotic • Multicellular animal parasites • Classified on differences in mouth structures and larvae • Requires a microscope to see

14. Check Your Understanding • Which groups of microbes are prokaryotic? Which are eukaryotic? • Differentiate between the true bacteria and the prokaryotic Archaea. • Distinguish between the major groups of eukaryotic microbes. • How are virus unique among the other microbes?

15. A Brief History of Microbiology

16. The First Observations • Robert Hooke (1665) – “cells” after viewing cork • Anton van Leeuwenhoek (1673-1723) • Constructed over 400 microscopes (~300X magnification) • First to view and draw living microbes (“animalcules”) from rainwater, feces, plaque scrapings from teeth • Cell Theory – all living things are composed of cells

17. Disproving Spontaneous Generation • Rudolf Virchow (1858) – Biogenesis • Living cells can only come from other living cells • Louis Pasteur (1861-1914) • Used aseptic techniques to finally put to rest the debate over spontaneous generation • Repeated John Needham’s (1745) experiments • Used Swan-necked to further validate the results • Discovered microorganisms are responsible for fermentation • Developed pasteurization to prevent wine spoilage

18. Pasteur’s Experimental Design

19. Germ Theory of Disease • Joseph Lister (1860s) – used phenols to disinfect surgical equipment between patients • Greatly reduced post-operative infections • Robert Koch (1876) – Koch’s Postulates • Bacillus anthraciswas isolated from infected cattle • B. anthraciswas then cultured outside infected animal • B. anthraciswas inoculated into a healthy animal and caused the same disease affects originally seen • B. anthraciswas re-isolated from newly infected animal

20. Vaccination • Edward Jenner (1796) used cowpox to protect patients against the deadly smallpox epidemic • Basis for immunity • Protection from a disease provided by vaccination or natural recovery from the disease itself • Actual mechanism for immunity provided by vaccinations was discovered by Pasteur (1880) • Lab strains of microbes can become avirulent, but still provide immunity against pathogenic strains

21. Check Your Understanding • What is the Cell Theory? • Compare spontaneous generation and biogenesis. • How did Pasteur disprove the theory of spontaneous generation? What were some of his other contributions to the field of microbiology? • What is the germ theory of disease? What is the importance of Koch’s postulates? Explain his four postulates in your own words. • Explain Jenner’s contribution to microbiology.

22. The birth of modern chemotherapy

23. Chemotherapy • Use of chemical substances to treat disease • Relies on the fact that some chemicals are more poisonous to the microbes than the infected host • Antibiotics – chemicals naturally produced by bacteria and fungi to act against other microbes • Synthetic Drugs – chemotherapeutic agents prepared from chemicals in the lab

24. The First Synthetic Drug • Paul Erlich speculated on the existence of a “magic bullet” in medicine • A drug that could kill pathogens without harming the infected host • Discovered the compound salvarsan (1910), an effective chemotherapeutic against syphillis • Chemical derived from arsenic

25. Penicillin – The First Antibiotic • Discovered by Alexander Fleming (1928) • Produced by Penicilliumchrysogenum • Formerly known as P. notatum • Inhibited bacterial growth on media • Not clinically tested and mass produced until 1940s

26. Problems with Antibiotics • Some are as toxic, if not more so, to the host as to the microbe • Especially true with viral chemotherapeutics • Emergence of antibiotic-resistant strains of microbes • Produce chemicals that inactivate the antibiotic • Change in cell surface receptors that the antibiotic can bind to • Prevent antibiotic from accumulating in the microbe • Vancomycin-resistant Staphylococcus aureus and Enterococcus faecalis are two worrisome examples

27. Check Your Understanding • Differentiate between a synthetic drug and an antibiotic. • Explain the importance of Fleming’s discovery. • What mechanisms have pathogens developed to overcome antibiotics?

28. Modern Developments in microbiology

29. Bacteriology • Study of bacteria • Heide Schulz (1997) discovered a bacterium large enough to see with unaided eye • Thiomargarita namibiensis • Thiomargarita namibiensis

30. Mycology • Study of fungi • Fungal infections now account for 10% of nosicomial(hospital-acquired) infections • Coccidioidesimmitis infections have risen 10-fold in California • Causes coccidioidomycosis (flu-like symptoms with accompanying rash to pneumonia and death) and, rarely, meningitis in immunocompromised individuals

31. Parasitology • Study of protozoa and parasitic worms • Caduceus may have been designed based on method for removing guinea worms • 16-year old girl recently succumbed to a Naegleriafowleri infection • Received after swimming in the St. John’s River in Brevard County Dranunculusmedinensis

32. Immunology • Study of immunity and the human immune system • World Health Organization (WHO) effectively eradicated smallpox by the late 1970s • Additional vaccines have be developed for measles, mumps, chickenpox, tetanus, tuberculosis, influenza, polio, and hepatitis B • Interferons (1960s) inhibit the replication of viruses • Currently used in treatment of viral disease and cancer

33. Virology • Study of viruses • Infectious particles too small to be seen by the unaided eye were first proposed by Pasteur • Coined the term virus from Latin word for poison • Electron microscope (1940s) helped further the study of viruses by elucidating their structure

34. Recombinant DNA Technology • Paul Berg (1960s) first demonstrated ability to attach human or animal DNA to a bacterial plasmid • Allows bacteria to make the human or animal protein • Recombinant DNA • Microbial Genetics studies how inheritance of DNA occurs in microbes • Molecular Biology studies how genes are encoded in DNA and how DNA directs protein synthesis

35. Check Your Understanding • Differentiate between bacteriology, mycology, parasitology, immunology, and virology. • Describe some important “recent” developments that highlight the importance of each sub-discipline of microbiology. • Differentiate between microbial genetics from molecular biology.

36. Microbes and Human Wellfare

37. Aid in Recycling Elements • First identified by MartinusBeijerinck and Sergei Winogradsky (1880s) • Showed how bacteria recycle elements between soil and atmosphere • Microbial Ecology • Carbon, nitrogen, oxygen, sulfur, and phosphorus cycle all rely, at least partly, on microbes

38. Sewage Treatment • Sewage is 99.9% water • Combines physical processes with beneficial microbes to remove the remaining 0.1% of harmful substances • Organic materials are converted to CO2, nitrates, phosphates, sulfates, ammonia, methane, etc…

39. Bioremediation • Use of microbes to remove pollutants and toxic wastes produced by industry • Exxon Valdez (1989) and Deepwater Horizon (2010) • Commonly used microbes include Pseudomonas sp. and Bacillus sp. • Bacillus enzymes are used in detergents

40. Pest Control • Bacillus thuringiensis has been widely used to control caterpillars, bollworms, cabbage worms and other pests • Produce proteins toxic to insect digestive tract • Far less damaging to the environment that chemical insecticides such as DDT

41. Biotechnology • Recombinant DNA technology has been used to incorporate genes into microbes that normal lack those genes • Allows large-scale production of proteins • Human insulin • Gene Therapy seeks to replace defect genes with healthy ones • Duchenne’s Muscular Dystrophy • Cystic Fibrosis

42. Check Your Understanding • Identify several beneficial uses for bacteria. • What is biotechnology? How has it been beneficial to us?

43. Microbes and human disease

44. Normal Microbiota (Flora) • Organisms living naturally within our bodies • Provide competition to prevent colonization by harmful microbes • Produce useful substances such as vitamin K • Can cause disease when outside normal habitat • Depends on natural resistance of the subject

45. Biofilms • Collection of microbes on a solid surface • Plaque on teeth is the world’s most common bacterial infection • Legionellosis (Legionella sp.) in water pipes and misting stations • Endocarditis caused by bacteria on catheters

46. Emerging Infectious Diseases • New diseases that have “arisen” in recent years • Avian Influenza A (H5N1), or bird flu, came to the world’s attention in 2003 • As of 2008, 242 people have fallen ill (~50% mortality) • Methicillin-Resistant S. aureus(MRSA) began popping up in the 1980s leading to increased use of vancomycin • Vancomycin-Resistant S. aureus was reported in US in 2002

47. Emerging Infectious Diseases • Bovine Spongiform Encephalopathy (BSE or Mad Cow Disease) is caused by Prions, small protein particles • Result of cattle feed supplemented with protein • Causes madness and death • Creutzfeldt-Jakob Disease in humans • Hemorrhagic Fevers • Viral diseases causing weakening of capillaries and spontaneous clotting in blood vessels • Ebola and Marburg viruses

48. Acquired Immunodeficiency Syndrome (AIDS) • Caused by Human Immunodefieciency Virus (HIV) • Attacks CD4+ (helper) T cells responsible for coordinating the efforts of the immune system • Patients succumb to opportunist infections • Pneumocystis pneumonia and Kaposi’s sarcoma • By 2007, over 1 million Americans had been diagnosed with AIDS and over 50% had died as a result ~1.2 million Americans are suspected to be HIV-positive

49. Check Your Understanding • Differentiate between normal microbiota and infectious diseases. • What is a biofilm? How are biofilms important? • What is an emerging infectious disease? What factors contribute to the emergence of an infectious disease? Describe some of the more “recent” emerging diseases that have impacted human society.