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Comprehensive Microbiology Study Notes (from Transcript)

Introduction to Microbiology

  • Microbiology: the study of life forms that are too small to be seen with the naked eye. Prefixes: micro- “small”, bio- “life”, ology- “study of.”
  • Microorganisms (microbes) are the most abundant organisms on earth and are extremely diverse; they are the smallest, simplest, and most numerous life forms.
  • Microorganisms are the most abundant on earth in terms of numbers and biomass; they exist in nearly every environment and are found in vast concentrations (e.g., tens of thousands of types in one liter of seawater).
  • Abundance can be described as: numbers, diversity, and biomass; they live in virtually all environments and are extremely adaptable.
  • Structurally simple: most microbes are prokaryotic; All life is made up of one of two cell types: ext{Prokaryotic} ext{ or } ext{Eukaryotic}
  • Functionally, microbes are not necessarily simple: they have evolved to overcome environmental challenges, survive extreme conditions, utilize host systems, and continuously adapt.

Types of Microorganisms (9 categories)

  • The 9 categories of microorganisms are:
    1. Bacteria
    2. Archaea
    3. Algae
    4. Protozoa
    5. Fungi
    6. Helminths
    7. Viruses
    8. Prions
    9. Arthropods (as vectors for microorganisms)

Bacteria

  • Type: Prokaryotes; unicellular; cell walls made of peptidoglycan.
  • Reproduction: binary fission (asexual).
  • Study: bacteriology.
  • Examples: Escherichia coli (E. coli), Listeria monocytogenes.

Archaea

  • Type: Prokaryotic cells; some lack cell walls, others have cell walls made of pseudomurein.
  • Habitat: live in extreme environments (hot springs, high salt, etc.).
  • Metabolism: carry out unusual metabolic processes; methanogens produce methane; extreme halophiles in salty environments; extreme thermophiles in hot, sulfurous waters.
  • Reproduction: binary fission (asexual).
  • Do not rely on peptidoglycan in their cell walls (cell wall composition differs from bacteria).

Algae

  • Type: Photosynthetic organisms; unicellular and multicellular (visible to naked eye).
  • Cell walls: often cellulose.
  • Primary role: perform photosynthesis; produce oxygen and carbohydrates; vital to ecosystems.
  • Some algae produce toxins (dinoflagellates) that cause harmful algal blooms; Alexandrium genus produces neurotoxins causing paralytic shellfish poisoning; red tides related to toxin production.

Protozoa

  • Type: Eukaryotes; unicellular; lack rigid cell walls.
  • Motility: many are motile via flagella, cilia, or pseudopodia.
  • Lifestyle: can be free-living or parasitic; parasites live on or within a host and produce disease in the host.
  • Reproduction: can be sexual or asexual.
  • Examples: Amoeba, Paramecium; Cryptosporidium (causes diarrhea).

Fungi

  • Type: Eukaryotes; unicellular (yeasts) or multicellular (molds, mushrooms).
  • Cell walls: made of chitin.
  • Reproduction: sexual or asexual.
  • Examples: Penicillium, Aspergillus; Candida albicans (yeast).
  • The study of fungi is mycology.

Helminths

  • Type: Eukaryotic, multicellular animal parasites.
  • Includes: flatworms (e.g., tapeworms) and roundworms (nematodes); range widely in size (tapeworms can reach meters, e.g., up to ~25 meters).
  • Reproduction: sexual and asexual.
  • Study: parasitology.

Viruses

  • Not technically living and not a real cell; not made of cells.
  • Structure: regular virion structures; genome is surrounded by a protein coat (capsid); capsid may be enclosed in a lipid envelope.
  • Size: virions are typically 10–100× smaller than bacterial cells.
  • Replication: can be visualized with an electron microscope but not with a light microscope; Viruses are only active when inside a living host cell (obligate intracellular parasites).
  • Study: virology.

Prions

  • Definition: Proteinaceous infectious particles.
  • Prions are misfolded proteins; they contain no nucleic acids and are not living or cellular.
  • Cause diseases known as transmissible spongiform encephalopathies (TSEs) (e.g., bovine spongiform encephalopathy, Creutzfeldt–Jakob disease, kuru).

Arthropods

  • Role: vectors of microorganisms; arthropods themselves are multicellular invertebrates.
  • They feed on blood or tissue fluids and can transmit pathogens (e.g., mosquitoes transmit the protozoan that causes malaria and various viruses such as yellow fever, West Nile, Zika; ticks transmit bacteria causing Lyme disease and Rocky Mountain spotted fever).

Microbiome and Human Health

  • Microbiome (microbiota, normal flora): trillions of microbes living on and in the human body.
  • The human body hosts more microbial cells than human cells overall; ratio commonly cited around 5:1.
  • Microbes are present on many body sites including skin, mouth, GI tract, lungs, urogenital tract, and other exposed surfaces.
  • Microbiota contributes immense genetic diversity: estimates suggest >2,000 microbial genes for every human gene (~2,000,000 microbial genes vs ~20,000 human genes).
  • Viruses outnumber bacteria by roughly 5:1.
  • The microbiome weighs about 2.5 pounds (≈1.1 kilograms) and occupies roughly 2.5 liters in volume.

Benefits of the microbiome

  • Provides energy and nutrients from the diet; helps extract energy and nutrients.
  • Crowds out or inhibits pathogens by occupying niches and producing antimicrobial substances.
  • Secretes vitamins (e.g., vitamin K and some B vitamins).
  • May inhibit or prevent certain diseases or conditions related to improper immune responses or dysbiosis.

Where are they and what are they doing?

  • Microbes reside wherever the body interfaces with the outside world: mouth, lungs, GI tract, urogenital tract, skin.
  • Microbiome helps extract energy and nutrients, and contributes to overall health by supporting digestion and immune function.
  • Key statistics:
    • Microbes contribute an enormous number of genes beyond the human genome: ≈ 2{,}000{,}000 microbial genes vs 20{,}000 human genes.
    • Bacteria outnumber human cells by roughly a factor of 5:1.
    • The human body contains roughly 2.5 ext{ lb} of microbial biomass and roughly 2.5 ext{ L} of microbial volume.

How is the microbiome acquired?

  • BIRTH: newborns acquire microbes from the mother’s birth canal and from care-givers’ skin.
  • BREAST MILK: provides nutrients, vitamins, antibodies, and a diverse microbial population to populate the baby’s gut.
  • ENVIRONMENT: continued exposure to soil, water, people, pets, plants, and diverse foods contributes to microbiome development over life.

Microbes, Disease, and Epidemiology

  • Opportunistic pathogens: infections caused by organisms that are normally harmless or beneficial; can cause disease when normal flora is disrupted, in immunocompromised individuals, or when the microbiota gains access to normally sterile sites.
  • Only a small fraction of microbes are pathogenic (roughly ~1%); about 2{,}000 microbes are pathogenic to humans.
  • The majority of microbes are harmless or beneficial.
  • Global burden of infectious diseases has shifted but remains significant in poorer nations; many infections are preventable with vaccines and treatable with drugs.
  • Notable infectious diseases contributing to global mortality include: pneumonia and influenza, HIV/AIDS, malaria, tuberculosis, among others.

Classification and Taxonomy

  • Classification reflects evolutionary relationships and functional similarities across organisms.
  • The 3 domains (and their cellular organization):
    • Bacteria: prokaryotes
    • Archaea: prokaryotes (often in extreme environments)
    • Eukarya (Eukaryota): eukaryotes
  • Binomial nomenclature: scientific name consists of genus and species; rules:
    • Genus name capitalized; species name lowercase; both italicized (e.g., Staphylococcus aureus).
    • The genus name can be abbreviated with the first letter after it has been stated (e.g., S. aureus).
  • Taxonomic ranks (from broad to specific): Domain, ext{Kingdom}, ext{Phylum}, ext{Class}, ext{Order}, ext{Family}, ext{Genus}, ext{Species}; 8 ranks in total.
  • Eukaryotes are more closely related to Archaea than to Bacteria.
  • Eukaryotic kingdoms include Plantae, Animalia, and Fungi; since advances in genetics, the Protista kingdom is no longer used as a single clade; organisms formerly in Protista are reorganized into multiple clades and higher taxonomic levels.

Example taxonomy (illustrative)

  • Domain: Eukarya

  • Kingdom: Fungi

  • Phylum: Ascomycota

  • Class: Hemiascomycetes

  • Order: Saccharomycetales

  • Family: Saccharomycetaceae

  • Genus: Saccharomyces

  • Species: S. cerevisiae

  • Notable bacterial examples in taxonomy tables include E. coli (Escherichia coli).

Characteristics of Living Organisms

1) Made of organic macromolecules
2) Composed of cells
3) Grow and reproduce
4) Use energy and raw materials (metabolism)
5) Respond to their environment
6) Maintain homeostasis
7) Evolve and adapt to environmental changes

History of Microbiology and Key Experiments

  • Spontaneous generation: the hypothesis that living organisms arise from nonliving matter.
  • Biogenesis: the hypothesis that living organisms arise from preexisting life.
  • Cell theory: all living things are composed of cells and arise from preexisting cells.

Early Observations and Experiments

  • Anton van Leeuwenhoek (late 1600s–early 1700s): first to observe live cells (animalcules) with simple microscopes; described three shapes of bacteria: rods (bacilli), cocci, spirals.
  • Francesco Redi (1668): meat in jars experiment showing maggots arise from flies, challenging spontaneous generation.
  • John Needham (1748): nutrient broth experiments suggested spontaneous generation, later shown to involve contamination.
  • Lazzaro Spallanzani (1765): boiled broth in sealed flasks; no growth unless neck was broken, suggesting air or contaminants were involved.
  • Louis Pasteur (Golden Era, 1861): demonstrated air contains microorganisms with S-shaped flasks, refuting spontaneous generation; developed germ theory of fermentation and disease; pasteurization; vaccines.

Pasteur’s Experiments and Contributions

  • S-shaped flasks allowed air in but prevented microbial entry; showed that microorganisms came from the air, not spontaneous generation.
  • Fermentation: microorganisms known to cause fermentation; some bacteria convert sugar to alcohol; others convert alcohol to acetic acid (vinegar).
  • Pasteurization: heating liquids to roughly 50^ ext{o}C - 60^ ext{o}C to destroy contaminating bacteria.
  • Germ theory of disease: specific microorganisms cause specific diseases; vaccines developed for several diseases.
  • Pasteur is credited as the father of bacteriology and immunology.

The Germ Theory of Disease and Early Advocates

  • Ignaz Semmelweis (1840s): advocated handwashing with antiseptics to prevent puerperal fever; mortality dramatically reduced.
  • Joseph Lister (1860s): used antiseptics (carbolic acid) to prevent surgical wound infections; reduced infections and deaths.
  • Koch’s Postulates (1876): established a framework to prove a specific microbe causes a specific disease; applied to anthrax and other diseases (tuberculosis, diphtheria, typhoid fever, cholera, gonorrhea).
    1) The microorganism must be found in diseased animals but not in healthy ones.
    2) The microorganism must be isolated and grown in pure culture.
    3) The isolated microorganism must cause the original disease when inoculated into a susceptible animal.
    4) The microorganism must be reisolated from the experimentally infected animal.

Vaccination and Antibiotics

  • Edward Jenner (1796): observed cowpox protected against smallpox; inoculated a boy with cowpox material, then smallpox exposure, and the boy was protected—immunity and vaccination.
  • Alexander Fleming (1928): discovered penicillin from Penicillium mold inhibiting Staphylococcus aureus; penicillin mass produced in the 1940s.

Key Objectives Summary

  • Recognize the 9 categories of microorganisms and identify whether they are living or nonliving; if living, determine whether they are prokaryotic or eukaryotic and unicellular or multicellular; provide examples for each class.
  • Describe the microbiome, including sites on the human body where normal flora reside and their functions.
  • Define pathogens and opportunistic pathogens; discuss infectious diseases that kill the greatest number of people worldwide.
  • Understand the basic taxonomy system:
    • 3 domains: Bacteria, Archaea, Eukarya (prokaryotes vs eukaryotes)
    • 8 taxonomic ranks: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
    • Binomial nomenclature and abbreviation rules (e.g., S. aureus)
  • Appreciate the historical development of microbiology, including spontaneous generation, germ theory, Pasteur’s experiments, Koch’s postulates, Jenner’s vaccination, and Fleming’s antibiotic discovery.

Important Formulas and Notable Figures

  • Domain count: 3 domains.
  • Taxonomic ranks: 8 ranks from Domain to Species.
  • Pasteurization temperature range: 50^ ext{o}C ext{ to } 60^ ext{o}C.
  • Ratio of microbial to human cells: approximately 5:1 in favor of microbes.
  • Microbiome gene content vs human genome: ~2{,}000{,}000 microbial genes vs ~20{,}000 human genes.
  • Weight and volume of the microbiome: about 2.5 ext{ lb} and 2.5 ext{ L}.

References to Real-World Relevance and Ethics

  • Germ theory underpins modern medicine, vaccination programs, antisepsis, and sterilization practices; ethical considerations include equitable access to vaccines and antibiotics, responsible use to prevent resistance, and the importance of public health infrastructure.
  • The microbiome’s role in health and disease has implications for diet, probiotics/prebiotics, antibiotic stewardship, and personalized medicine.
  • Parasitic diseases and vectors (e.g., mosquitoes and ticks) highlight the importance of vector control, vaccination campaigns, and global health initiatives.