1. Introduction to Microbial World

• Microbiology


  An advanced biology course that is the study of microbes, which are extremely small (microscopic) living organisms and certain non-living entities

  
• Living microbes (cellular microbes or microorganisms)

  • Bacteria
  • Archaea
  • Some algae
  • Protozoa
  • Some fungi

  
• Non-living microbes (acellular microbes or infectious particles)

  • Viroids
  • Prions
  • Viruses
• Microbes are ubiquitous (i.e., they are found virtually everywhere)

  
• Microorganisms


  • They are ubiquitous organisms that are too small to be seen by the unaided eye
  • They represent the major fraction of the Earth's biomass
  • Plants and animals are engaged in the world of microbes, their evolution and survival are influenced by microbial activities

  
• Germs


  The microbes that cause disease
• Pathogens


  The scientific term for disease-causing microbes
• Non-pathogens


  Microbes that do not cause disease; the vast majority of microbes are non-pathogens
• Indigenous microbiota


  Microbes that live on and in our bodies

  
• Opportunistic pathogens


  Microbes that can cause disease, but usually do not; they can be thought of as microbes that are awaiting the opportunity to cause disease
• Categories of diseases caused by pathogens

  • Infectious diseases
  • Microbial intoxications
• Microbial cells first appeared

  Between 3.8 and 4.3 billion years ago

  
• For the first 2 billion years of Earth's existence, microorganisms are capable to survive without oxygen in the atmosphere
• Candidates for the first microorganisms on Earth

  • Archaea
  • Cyanobacteria
• Phototrophic microorganisms (organisms that harvest energy from sunlight) occurred


  1 billion years ago
• First phototrophs


  • Purple sulfur bacteria
  • Green sulfur bacteria
• Cyanobacteria (oxygenic phototrophs) evolved and began the slow process of oxygenating Earth's atmosphere, multicellular life forms eventually evolved

  
• Infectious diseases of humans and animals have existed for as long as humans and animals have inhabited the planet
• Sumerians and Egyptians produced many foods using fermentation, such as bread, wine, and beer


  Around 5,000 B.C.E.
• They did not have the knowledge to explain exactly how those products were made, nor why fermentation happened. Therefore, they commonly viewed fermentation as a miracle provided by their gods
• During The Dark Ages in Medieval Europe, the pandemic plague has killed as much as one-third of the continent's population in individual pandemics in the Middle Ages
• Yersinia pestis


  The zoonotic disease from domestic and wild rats that caused the plague
• Robert Hooke


  Illustrated the first known image of microscope and fruiting molds, and started to formulate the "Cell Theory"

  
• Theodore Schwann and Matthias Jakob Schleiden


  Proposed the Cell Theory in 1838, which states that all plants and animals are made up of cells

  
• Antoine Van Leeuwenhoek


  The "Father of Microbiology" who made many simple single-lens microscopes and observed "animalcules" (bacteria and protozoa)

  
• Spontaneous generation


  A body of thought on the ordinary formation of living organisms without descent from similar organisms
• Francesco Redi


  An Italian physician who first challenged to disprove the theory of spontaneous generation in 1668 through a controlled experiment
• John Needham


  Defended the theory of spontaneous generation after observing that a heated uncovered flask containing broth still developed microorganisms after cooling the broth in open air

  
• Lazzaro Spallanzani


  An Italian Catholic priest who disproven Needham's claim by suggesting that microorganisms from the air probably entered Needham's solutions after they were boiled

  
• Rudolf Virchow


  A famous German physician and cellular pathologist who introduced the theory of biogenesis in 1858, which claims that living cells arise only from preexisting living cells

  
• Louis Pasteur


  A French chemist who made numerous contributions to microbiology including the resolution of the debate over spontaneous generation in 1861
• Edward Jenner


  A young British physician who pioneered the concept of vaccination by inoculating a healthy 8-year-old boy with scrapings of cowpox blisters from a previously cowpox-infected milkmaid, and developed a vaccine for smallpox
• Ignaz Sammelweiz


  A Hungarian physician who pioneered the antiseptic procedures through the development of the proper handwashing technique, which lowered the death rate of newly delivered mothers by decreasing the incidence of bacterial infections during childbirth

  
• Other contributions of Pasteur

  • Investigated different fermentation products
  • Developed the pasteurization process
  • Discovered life forms that could exist without oxygen (anaerobes)
  • Developed several vaccines, including rabies and anthrax vaccines
• Joseph Lister


  A British surgeon and medical scientist who introduced the aseptic technique in order to kill and prevent from microbial infection of surgical patients, and proved that microbes caused surgical wound infections
• Robert Koch

  Discovered that Bacillus anthracis produced spores, developed methods of fixing and staining bacteria, developed methods to cultivate bacteria, and made significant contributions to the germ theory of disease

  
• Koch's Postulates


  If an organism fulfills Koch's Postulates, it has been proven to be the cause of that particular infectious disease. Koch's Postulates helped prove the germ theory of disease.

  
• Circumstances do exist in which Koch's Postulates cannot be fulfilled (e.g. viruses, Mycobacterium tuberculosis, Treponema pallidum)

  
• Other highlights of the First Golden Age

  • Hans Christian Joachim Gram developed Gram staining technique in 1884
  • Richard Petri developed a transparent double-sided dish known as "Petri dish" in 1887
  • Paul Ehrlich proposed the theory of immunity in 1890 and developed salvarsan – a drug that can treat syphilis in 1910
  • Sergei Winogradsky isolated and characterized nitrogen- and sulfur-fixing bacteria from soil sediments in the mid to late 1800s

  
• Highlights of the Second and Third Golden Age

  • Alexander Fleming accidentally discovered the first antibiotic drug, penicillin, from Penicillium chrysogenum in 1928
  • Walter Gilbert and Frederick Sanger developed the Maxam-Gilbert method - the first generation of DNA sequencing methods in 1980
  • Kary Mullis developed the polymerase chain reaction (PCR) – a useful method in the molecular identification of microorganisms in the 1990s
  • Françoise Barré-Sinoussi discovered the human immunodeficiency virus (HIV) in the 2000s