Chapter 1. Scope & History

Why Study Microbiology

• Ecological Significance: Microorganisms are the most abundant primary producers and the ultimate decomposers of biomass on Earth. As such, microorganisms drive the energy and nutrient flows of the whole ecosystem, on which human life depends. 
• Beneficial Microbes: 
• Microbial inhabitants out-number human cells by 10-fold on an average body.  They are mostly harmless, normal residents, existing on body parts exposed to the outside environment (such as skin and digestive tract). Many of them are beneficial to human  health, providing necessary nutrients. 
• Microorganisms are used extensively in the production of food (e.g., cheese, yogurt, bread, wine, beer, vinegar) and pharmaceuticals (e.g., antibiotics, genetically-engineered human insulin)
• Pathogenic ("disease-causing") Microbes: Less than 1% of known microbes are pathogens. Most pathogens belong to groups like bacteria, viruses, and fungi. Many normally harmless microbe become "opportunistic" pathogens in immune-comprised human hosts. 
• Microbes are indispensable research tools.  They have simpler structures, reproduce quickly, and can be obtained in a large quantity.  Most crucially, knowledge learned from model microorganisms (e.g., E. coil and yeast) help understandings of basic human biology, because of the common ancestry (therefore, basic structure) of all life on earth.

Scope of Microbiology

• Tree of Life: 
• The traditional 5-kingdom classification exaggerate the biodiversity visible to human eyes (plans, animal). Contemporary classification is more objectively based on genes shared by all organisms. For example, a tree of life based on 16S ribosomal RNA showed three domains of life, including Eukarya, Bacteria, and Archaea.
• Distance between organisms on the three-domain tree of life is proportional to their evolutionary and genetic distances.  The visible biodiversity is only a tiny part of the overall phylogenetic diversity, which consists mostly of microorganisms.  
• Scientific nomenclature of microbes: binomial naming system, e.g. Bacillus anthracis (first part genus name, capitalized, may be initialized; second part species name, all lower case; both italicized or underlined)
• Organisms studied in Microbiology
• Bacteria: Single-celled prokaryotes ("lack of a nucleus").  Bacteriology is the study of bacteria.
• Algae: Single-celled, photosynthetic eukaryotes ("having a nucleus"). Phycology is the study of algae.
• Fungi: Heterotrophic ("living on organic matters"), often microscopic eukaryotes. Mycology is the study of fungi.
• Viruses: Non-cellular (acellular), obligate ("non-free-living") parasites
• Protozoa: Single-celled, mobile eukaryotes. Protozoology is the study of protozoa.
• Helminths & arthropods: Parasitic worms. Mosquitoes, ticks, mites, and lice often serve as vectors of infectious diseases. 
• Other fields of microbiology: e.g., 
• Immunology (study of host response to infection)
• Epidemiology (study of the frequency and geographic distributions of diseases)

History of Microbiology

• Historical roots
• 1665, Robert Hooke, first observed cellular structures of a slice of cork and named them "cells"
• Antoi van Leeuwenhoek was the first to observe live microorganisms
• The cell theory: all living organisms are composed of cell
• The Golden Age of Microbiology and the development of the "Germ Theory of Disease"
• Debate over "spontaneous generation"(a belief that life arises spontaneously from nonliving matters)
  
• Lewis Pasteur's experiment using swan-necked flasks disproved spontaneous generation, proved the ubiquity of microorganisms around us
• Pasteur's other signficant contributions include the discovery of microbial sources of fermentation and invention of "pasteurization" (killing of microbes using low heat), and the development of the first vaccine against Rabies.
• Robert Koch's contributions: Invented techniques for obtaining "pure cultures" of bacteria; Proposed "Koch's Postulates", a series of experimental protocols for establishing microbial agents of a disease; Identified important pathgenssuch as Bacillus anthracis.
• Development of "aseptic techniques" (techniques of preventing contamination by unwanted microorganisms) by Semmelweis (importance of hand-washing in clinics) and Lister (first aseptic surgery)
• Discovery of vaccination and immunity by Edward Jenner
• Development of Specialized fields:
• Discovery of viruses by Beijerinck
• The rise of chemotherapy: Paul Ehlich's discovery of anti-microbial compounds; Discovery of the first antibiotics (Penicillin) by Alexander Flemming; Selman Waksman coined the term "antibiotics".
• Modern developments: Discovery of DNA as the genetic material; Discovery of DNA structure of Watson and Crick; Discovery of antibody and adaptive immunity; Developemnt DNA technologies and genetic engineering; Genomics 
• New Emerging Infectious Diseases
• The claim of eliminating infectious disease proved to be overly optimistic and premature
• Some pathogens are newly discovered (e.g., Heliobacter pylori as the cause of peptic ulcer)
• The rise of antibiotic-resistance bacteria (e.g., hospital-acquired multi-drug resistant bacteria)
• New infectious diseases due to changing human behavior, e.g., HIV, avian flu, SARS, and Lyme disease.

Summary

1. All organisms (include human and microorganisms) share basic biological structures and mechanisms.
2. Microbial genetic and ecological diversities far exceed those of the macro-organisms.
3. Microorganisms adapt quickly to changing human behavior and ecology (e.g., global travel, climate change, and overuse of antibiotics), causing new infectious diseases.