Chapter 1


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Chapter 1

  1. 1. Foundations in Microbiology Sixth Edition Chapter 1 The Main Themes of Microbiology Lecture PowerPoint to accompany Talaro Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
  2. 2. Learning Objectives A student should learn the following concepts: 1. The study of microbiology includes bacteria, viruses, fungi, protozoa and algae. 2. Studies in microbiology have contributed significantly to the fields of chemistry, genetics, and ecology. 3. Microorganisms play a crucial role in the biosphere . 4. Microorganisms are continually adapting to the biosphere. 5. Microorganisms can be genetically modified to help the environment as well as to directly help humans. 6. Although the majority of microorganisms are not pathogenic , infectious diseases caused by microorganisms are still a common cause of death. 7. There are two types of cellular microorganisms ( prokaryotes and eukaryotes ). 8. All prokaryotes are microorganisms, but only some eucaryotes are microorganisms.
  3. 3. 9. Viruses are microorganisms that are noncellular ; they are much simpler than cells. 10. The general characteristics of microorganisms are organization, size, lifestyle. 11. Our current understanding of microbiology is the result of hundreds of years of work by thousands of microbiologists. 12. The advent of the microscope allowed scientists to see microorganisms and then begin to identify them as agents of disease. 13. The scientific method is a process in which scientists develop and test hypotheses . 14. The germ theory of disease states microorganisms can be the cause of diseases. 15. Taxonomy involves classifying, organizing and naming living organisms. 16. Taxonomy groups organisms based on their evolutionary history.
  4. 4. Key Terms emerging diseases pathogens bioremediation genetic engineering microbiology microscopic microorganisms microbes bacteria viruses fungi protozoa algae macroscopic adaptability immunology epidemiology biotechnology infectious procaryote eucaryote parasites hosts spontaneous generation abiogenesis biogenesis scientific methods hypotheses induction deduction inductive deductive theories law sterilization aseptic techniques
  5. 5. Key Terms morphology physiology genetics eubacteria archaebacteria Kingdom Procaryotae Kingdom Protista Kingdom Myceteae Kingdom Animalia Kingdom Plantae nomenclature taxonomy taxa classification identification domain kingdom phylum division class order family genus hierarchies scientific method species scientific names evolutionary
  6. 6. Microbiology <ul><li>Microorganisms are ubiquitous. </li></ul><ul><li>The study of organisms too small to be seen without magnification </li></ul><ul><li>Microscopic – Gr. mikros, small, and scopion, to see </li></ul><ul><li>Microbe – Gr. bios, life </li></ul><ul><li>Microorganisms include: </li></ul><ul><ul><li>bacteria </li></ul></ul><ul><ul><li>viruses </li></ul></ul><ul><ul><li>fungi </li></ul></ul><ul><ul><li>protozoa </li></ul></ul><ul><ul><li>helminths (worms) </li></ul></ul><ul><ul><li>algae </li></ul></ul>
  7. 7. Branches of Study Within Microbiology <ul><li>Immunology </li></ul><ul><li>Public health microbiology and epidemiology </li></ul><ul><li>Food, dairy and aquatic microbiology </li></ul><ul><li>Biotechnology </li></ul><ul><li>Genetic engineering and recombinant DNA technology </li></ul>
  8. 11. Microbes are Involved in <ul><li>Nutrient production and energy flow </li></ul><ul><li>Decomposition </li></ul><ul><li>Biotechnology </li></ul><ul><ul><li>production of foods, drugs and vaccines </li></ul></ul><ul><li>Genetic engineering </li></ul><ul><li>Bioremediation </li></ul><ul><li>Infectious disease </li></ul>
  9. 12. Infectious Diseases <ul><li>Nearly 2,000 different microbes cause diseases. </li></ul><ul><li>10 B new infections/year worldwide </li></ul><ul><li>13 M deaths from infections/year worldwide </li></ul>
  10. 13. Worldwide infectious disease statistics <ul><li>Depicts the 10 most common infectious causes of disease </li></ul>
  11. 15. The More Things Change <ul><li>Antibiotics introduced 1940s; vaccination widespread </li></ul><ul><li>1964 – Surgeon General states “Its time to close the book on infectious diseases. The war against pestilence is over.” </li></ul><ul><li>1980 – thirty-five years later Surgeon General reports “Infectious diseases a rising peril; death rates in US up 58% since 1980. Organisms changed and people changed.” </li></ul>
  12. 16. What changed? <ul><li>Due to advances in medicine people live longer and are sicker; heightened susceptibility to “garden-variety organisms.” </li></ul><ul><li>Highly mobile populations with introduction of diseases into naïve populations. </li></ul><ul><li>↑ emerging (newly recognized pathogens ) and re-emerging infectious diseases. </li></ul><ul><ul><ul><li>SARS , avian and swine flu </li></ul></ul></ul><ul><ul><ul><li>Change in agricultural practices </li></ul></ul></ul><ul><ul><ul><li>Encroachment on wild habitats </li></ul></ul></ul><ul><ul><ul><li>Mass production of foods – Escherichia coli O157:H7 </li></ul></ul></ul>
  13. 17. What Changed? <ul><li>Microorganisms’ adaptability, antibiotic resistance, and overuse of antibiotics – MSRA </li></ul><ul><li>Many conditions thought to be degenerative associated with microorganisms </li></ul><ul><ul><li>Cervical cancer and HPV </li></ul></ul><ul><ul><li>Gastric ulcers and gastric cancer (carcinoma and lymphoma) with Helicobacter pylori </li></ul></ul><ul><ul><li>Hepatic carcinoma and viral hepatitis </li></ul></ul><ul><ul><li>Cardiovascular disease </li></ul></ul>
  14. 18. Emerging infectious disease <ul><li>An emerging infectious disease (EID) is an infectious disease whose incidence has increased in the past 20 years and threatens to increase in the near future. </li></ul><ul><li>EIDs include diseases: </li></ul><ul><ul><li>caused by a newly identified microorganism or newly identified strain of a known microorganism (e.g. SARS , AIDS ) </li></ul></ul><ul><ul><li>new infections resulting from change or evolution of an existing organism (e.g. influenza ) </li></ul></ul><ul><ul><li>a known infection which spreads to a new geographic area or population (e.g. West Nile virus ) </li></ul></ul><ul><ul><li>newly recognized infection in an area undergoing ecologic transformation (e.g. Lyme disease ) </li></ul></ul><ul><ul><li>pre-existing and recognized infections reemerging due to drug resistance or a breakdown in public health (e.g. tuberculosis ) </li></ul></ul><ul><ul><li>adverse synergistic interaction among emerging diseases as well as interaction with other infectious and non-infectious conditions that leads to the development of novel syndemics . </li></ul></ul>
  15. 19. Syndemic <ul><li>refers to the concentration of two or more diseases or other health conditions in a population in which there is some level of biological interaction among the diseases and health conditions that magnifies the negative health effects of one or more of the co-present diseases or health conditions. </li></ul>
  16. 20. Mechanisms of emergence and reemergence <ul><li>Microbial adaption; e.g. genetic drift and genetic shift in Influenza A </li></ul><ul><li>Changing human susceptibility; e.g. immunocompromise with HIV/AIDS </li></ul><ul><li>Climate and weather; e.g. diseases with zoonotic vectors such as West Nile Disease (transmitted by mosquitoes ) are moving further from the tropics as the climate warms </li></ul><ul><li>Change in human demographics and trade; e.g. rapid travel enabled SARS to rapidly propagate around the globe </li></ul><ul><li>Economic development; e.g. use of antibiotics to increase meat yield of farmed cows leads to antibiotic resistance </li></ul><ul><li>Breakdown of public health; e.g. the current situation in Zimbabwe </li></ul><ul><li>Poverty and social inequality; e.g. tuberculosis is primarily a problem in low-income areas </li></ul><ul><li>War and famine </li></ul><ul><li>Bioterrorism ; e.g. 2001 Anthrax attacks </li></ul><ul><li>Dam and irrigation system construction; e.g. malaria and other mosquito borne diseases </li></ul>
  17. 21. <ul><li>Constant mutation is called, antigenic drift - gradually change their amino acid composition </li></ul><ul><li>Antigenic shift – one of the genes or RNA strands is substituted with a gene or strand from another influenza virus from a different animal host </li></ul>
  18. 22. Article Sources and Contributors <ul><li>Emerging infectious disease Source: Contributors: Amphytrite, Anders Sandberg, Arch dude, BSquared04, Chiko032, Hans999, Happy </li></ul><ul><li>B., Johnmorrow, Joshfinnie, K-BO, Kanook, Luis Fernández García, MarcoTolo, Mawijk, Neg, Nihiltres, NiteSensor23, Parkway04, Pearle, Pgan002, PhilMacD, Rohitsingh, Sabedon, Wervo, </li></ul><ul><li>Zvika, 14 anonymous edits </li></ul>
  19. 23. <ul><li>Bibliographic details for &quot;Syndemic&quot; </li></ul><ul><li>Page name: Syndemic </li></ul><ul><li>Author: Wikipedia contributors </li></ul><ul><li>Publisher: Wikipedia, The Free Encyclopedia . </li></ul><ul><li>Date of last revision: 16 April 2010 16:06 UTC </li></ul><ul><li>Date retrieved: 1 June 2010 10:50 UTC </li></ul><ul><li>Permanent link: </li></ul>
  20. 24. <ul><li>Wikipedia, The Free Encyclopedia. July 22, 2004, at 10:55 UTC. Available at: . accessed June 1, 2010. </li></ul>
  21. 25. <ul><li>Page name: Emerging infectious diseases </li></ul><ul><li>Author: Wikipedia contributors </li></ul><ul><li>Publisher: Wikipedia, The Free Encyclopedia . </li></ul><ul><li>Date of last revision: 10 May 2008 14:24 UTC </li></ul><ul><li>Date retrieved: 1 June 2010 10:52 UTC </li></ul><ul><li>Permanent link: </li></ul>
  22. 26. Characteristics of Microbes <ul><li>Prokaryotes and eukaryotes </li></ul><ul><ul><li>prokaryote – microscopic, unicellular organisms, lack nuclei and membrane-bound organelles </li></ul></ul><ul><ul><li>eukaryote – unicellular (microscopic) and multicellular, nucleus and membrane-bound organelles </li></ul></ul><ul><li>Viruses </li></ul><ul><ul><li>acellular, parasitic particles composed of a nucleic acid and protein </li></ul></ul>
  23. 27. Insert figure 1.5 basic cell and virus structures
  24. 28. Microbial Dimensions <ul><li>Prokaryotes are measured in micrometers. </li></ul><ul><li>Viruses in nanometers </li></ul><ul><li>Helminths are measured in millimeters. </li></ul>
  25. 29. Insert figure 1.7 measurements
  26. 30. Historical Foundations of Microbiology <ul><li>300 years of contributions by many </li></ul><ul><li>Prominent discoveries include: </li></ul><ul><ul><li>microscopy </li></ul></ul><ul><ul><li>scientific method </li></ul></ul><ul><ul><li>development of medical microbiology </li></ul></ul><ul><ul><li>microbiology techniques </li></ul></ul>
  27. 31. Antonie van Leeuwenhoek (1632-1723) <ul><li>Dutch linen merchant </li></ul><ul><li>First to observe living microbes </li></ul><ul><li>Single-lens magnified up to 300X </li></ul>Insert figure 1.8
  28. 32. Insert figure 1.9 (a) microscope
  29. 33. Spontaneous Generation Abiogenesis: early belief that some forms of life could arise from vital forces present in nonliving or decomposing matter (flies from manure, etc) {Biogenesis: as opposed to abiogenesis }
  30. 34. Scientific Method <ul><li>A general approach to explain a natural phenomenon </li></ul><ul><li>Form a hypothesis - a tentative explanation that can be supported or refuted by observation and experimentation </li></ul><ul><li>A lengthy process of experimentation, analysis and testing either supports or refutes the hypothesis. </li></ul>
  31. 35. <ul><li>Results must be published and repeated by other investigators. </li></ul><ul><li>If hypothesis is supported by a growing body of evidence and survives rigorous scrutiny, it moves to the next level of confidence - it becomes a theory. </li></ul><ul><li>If evidence of a theory is so compelling that the next level of confidence is reached - it becomes a Law or principle. </li></ul>
  32. 36. Fig. 10
  33. 37. Discovery of Spores and Sterilization <ul><li>John Tyndall and Ferdinand Cohn each demonstrated the presence of heat resistant forms of some microbes. </li></ul><ul><ul><li>Cohn determined these forms to be endospores. </li></ul></ul><ul><li>Sterility requires the elimination of all life forms including endospores and viruses. </li></ul>
  34. 38. Development of Aseptic Techniques <ul><li>Dr. Oliver Wendell Holmes – observed that mothers of home births had fewer infections than those who gave birth in hospital </li></ul><ul><li>Dr. Ignaz Semmelweis – correlated infections with physicians coming directly from autopsy room to maternity ward </li></ul>
  35. 39. Development of Aseptic Techniques <ul><li>Joseph Lister – introduced aseptic techniques reducing microbes in medical settings to prevent infections </li></ul><ul><ul><li>involved disinfection of hands using chemicals prior to surgery </li></ul></ul><ul><ul><li>use of heat for sterilization </li></ul></ul>
  36. 40. Aseptic Technique <ul><li>Methods of handling microbial cultures, patient specimens, and other sources of microbes in a way that prevents infection of the handler and others who may be exposed. </li></ul>
  37. 41. Pathogens and Germ Theory of Disease <ul><li>Many diseases are caused by the growth of microbes in the body and not by sins, bad character, or poverty, etc. </li></ul><ul><li>Two major contributors: </li></ul><ul><li>Louis Pasteur and Robert Koch </li></ul>
  38. 42. Louis Pasteur (1822-1895) <ul><li>Showed microbes caused fermentation and spoilage </li></ul><ul><li>Disproved spontaneous generation of microorganisms </li></ul><ul><li>Developed pasteurization </li></ul><ul><li>Demonstrated what is now known as Germ Theory of Disease </li></ul><ul><li>Developed a rabies vaccine </li></ul>Insert figure 1.11
  39. 43. Page 14.d
  40. 44. Robert Koch (1843-1910) <ul><li>Established Koch’s postulates - a sequence of experimental steps that verified the germ theory </li></ul><ul><li>Identified cause of anthrax, TB, and cholera </li></ul><ul><li>Developed pure culture methods </li></ul>Insert figure 1.12
  41. 45. Koch’s Postulates <ul><li>Determining the causative or etiologic agent of infectious disease: </li></ul><ul><li>Find evidence of a particular microbe in every case of a disease. </li></ul><ul><li>Isolate that microbe from an infected subject and cultivate it artificially in the laboratory. </li></ul><ul><li>Inoculate a susceptible healthy subject with the laboratory isolate and observe the resultant disease. </li></ul><ul><li>Reisolate the agent from this subject. </li></ul>
  42. 47. Taxonomy : Organizing, Classifying and Naming Living Things <ul><li>Formal system originated by Carl von Linn é </li></ul><ul><li>(1701-1778) </li></ul><ul><li>Concerned with: </li></ul><ul><ul><li>classification – orderly arrangement of organisms into groups </li></ul></ul><ul><ul><li>nomenclature – assigning names </li></ul></ul><ul><ul><li>identification – discovering and recording traits of organisms for placement into taxonomic schemes </li></ul></ul>
  43. 48. Levels of Classification <ul><li>Domain - Archaea, Bacteria & Eukarya </li></ul><ul><li>Kingdom – 5 </li></ul><ul><ul><li>Monera </li></ul></ul><ul><ul><li>Plantae </li></ul></ul><ul><ul><li>Protista </li></ul></ul><ul><ul><li>Animalia </li></ul></ul><ul><ul><li>Fungi </li></ul></ul><ul><li>Phylum or Division </li></ul><ul><li>Class </li></ul><ul><li>Order </li></ul><ul><li>Family </li></ul><ul><li>Genus </li></ul><ul><li>species </li></ul>
  44. 49. Fig. 1.14
  45. 50. Fig. 1.13.a
  46. 51. Naming Micoorganisms <ul><li>Binomial (scientific) nomenclature </li></ul><ul><li>Gives each microbe 2 names: </li></ul><ul><ul><li>Genus - noun, always capitalized </li></ul></ul><ul><ul><li>species - adjective, lowercase </li></ul></ul><ul><li>Both italicized or underlined </li></ul><ul><ul><li>Staphylococcus aureus (S. aureus) </li></ul></ul><ul><ul><li>Bacillus subtilis (B. subtilis) </li></ul></ul><ul><ul><li>Escherichia coli (E. coli) </li></ul></ul>
  47. 52. Evolution - living things change gradually over millions of years <ul><li>Changes favoring survival are retained and less beneficial changes are lost. </li></ul><ul><li>All new species originate from preexisting species. </li></ul><ul><li>Closely related organism have similar features because they evolved from common ancestral forms. </li></ul><ul><li>Evolution usually progresses toward greater complexity. </li></ul>
  48. 53. Fig. 1.1
  49. 54. 3 Domains <ul><li>Eubacteria - true bacteria, peptidoglycan </li></ul><ul><li>Archaea - odd bacteria that live in extreme environments, high salt, heat, etc. </li></ul><ul><li>Eukarya- have a nucleus and organelles </li></ul>
  50. 55. Insert figure 1.15 Woese-Fox System