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Fundamentals of Microbiology and Microbiome

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  • What is a microbe?

    A microbe or microorganism is a tiny living organism too small to be seen with the unaided eye.
  • Relative size of viruses and bacteria

    A typical virus measures about 100 nm, which is 10 times smaller than a typical bacterium (~1 μm).
  • Roles of microbes in the environment

    Microbes decompose organic waste, generate oxygen by photosynthesis, incorporate nitrogen gas into organic compounds, and produce food and chemical products.
  • Definition of microbiome

    A microbiome is a characteristic microbial community occupying a defined habitat, including the microorganisms and their environment.
  • Difference between microbiome and microbiota

    Microbiota refers to all microorganisms living stably on/in a habitat, while microbiome includes the community plus their environment and activity.
  • Resident vs transient microbiota

    Resident microbiota colonize the body indefinitely; transient microbiota colonize temporarily.
  • Importance of the human microbiome

    The microbiome aids immune development, pathogen resistance, nutrition (e.g., vitamin K2 production), and influences behavior and mental health.
  • Taxonomy and classification

    Taxonomy is the classification, description, identification, and naming of living organisms, established by Carolus Linnaeus with hierarchical ranks.
  • Three domains of life

    The three domains are Bacteria, Archaea, and Eukarya, distinguished by rRNA sequences and cellular features.
  • Characteristics of prokaryotes

    Prokaryotes are single-celled organisms without a nuclear membrane, including bacteria and archaea, with simpler cell structures.
  • Differences between Bacteria and Archaea

    Bacteria have ester-linked membrane lipids and bacterial rRNA; Archaea have ether-linked lipids and unique rRNA sequences.
  • Viruses and the tree of life

    Viruses are not considered alive, have independent genetic lineages, and do not fit into the traditional tree of life.
  • Binomial naming system

    Organisms are named by genus (capitalized) and species (lowercase), italicized in print, e.g., Escherichia coli.
  • Examples of binomial names

    Names can be descriptive (e.g., Staphylococcus aureus), honor scientists (e.g., Escherichia coli), or reference geographic locations.
  • Microbial roles in food production

    Microbes like Lactobacillus and Penicillium species are used in yogurt, cheese, soy sauce, bread, and beer production.
  • Theory of spontaneous generation

    The disproven idea that living organisms arise from nonliving matter; replaced by germ theory and cell theory.
  • Germ theory of disease

    Diseases are caused by microbes; established by scientists like Pasteur and Koch through experiments and postulates.
  • Koch's postulates

    A set of criteria to link a specific microbe to a specific disease.
  • Microbial ecology and human welfare

    Microbes recycle vital elements, treat sewage, clean pollutants, control insect pests, and are used in biotechnology.
  • Biofilms

    Complex microbial communities attached to surfaces; can be beneficial (protect mucous membranes) or harmful (cause infections, resist antibiotics).
  • Emerging infectious diseases

    New or increasing diseases caused by factors like antibiotic resistance, global travel, and environmental changes.