Microbiology Vocabulary

Microbes in Our Lives

• Microorganisms are too small to be seen without magnification.

• Microbes include bacteria, fungi, protozoa, microscopic algae, viruses, and prions.

Roles of Microbes

• Pathogenic microbes cause disease.

• Some microbes cause food spoilage.

• Microbes are the basis of the food chain in aquatic environments.

• Microbes decompose organic waste.

• Microbes incorporate nitrogen gas from the air into organic compounds.

• Microbes generate oxygen through photosynthesis.

• Microbes produce chemical products like ethanol, acetone, and vitamins.

• Microbes produce fermented foods such as vinegar, cheese, yogurt, alcoholic beverages, and bread.

• Microbes produce products used in manufacturing (e.g., cellulose) and disease treatment (e.g., insulin).

The Microbiome

• The microbiome (microbiota) is a group of microbes that live stably on/in the human body.

  • Helps maintain good health.

  • Can prevent the growth of pathogenic microbes.

  • May help train the immune system to discriminate threats.

• Resident microbiota:

  • Acquired before birth.

  • May colonize the body indefinitely.

• Transient microbiota: May colonize the body fleetingly.

Human Microbiota

• Window of opportunity for microbiota modulation:

  • Prenatal factors: Placenta, maternal diet, gestation.

  • Neonatal factors: Mode of delivery, gestational age.

  • Postnatal factors: Feeding (breast milk vs. formula), weaning, geographical location, family members, host interactions.

Gut Microbiome and Health

• Gut microbiome is associated with Parkinson’s Disease and autism.

Types of Microorganisms

• Bacteria

• Archaea

• Fungi

• Protozoa

• Algae

• Viruses

• Multicellular Animal Parasites (helminths)

Taxonomy

• Taxonomy is the science of classifying organisms to show the degree of similarity among them.

• Organisms are assigned to categories (taxa).

The Three Domains

• Developed by Carl Woese in 1978.

• Three domains based on cellular organization:

  • Bacteria

  • Archaea

  • Eukarya:

    • Protists

    • Fungi

    • Plants

    • Animals

Taxonomic Hierarchy

• A series of subdivisions developed by Linnaeus to classify plants and animals.

Scientific Nomenclature

• Carolus Linnaeus established the system of scientific nomenclature in 1735.

• Binomial nomenclature: genus and species.

  • Italicized or underlined, e.g., Escherichia coli, Staphylococcus aureus.

Bacteria

• Prokaryotes (“Prenucleus”).

• Single-celled (unicellular).

• Peptidoglycan cell walls.

• Divide via binary fission.

• Derive nutrition from organic or inorganic chemicals or photosynthesis.

• May “swim” using flagella.

Archaea

• Prokaryotes.

• Lack peptidoglycan cell walls (or may lack a cell wall entirely).

• Often live in extreme environments.

  • Methanogens

  • Extreme halophiles

  • Extreme thermophiles

• Not known to cause disease in humans.

Fungi

• Eukaryotes.

• Chitin cell walls.

• Absorb organic chemicals for energy.

• Yeasts are unicellular.

• Molds and mushrooms are multicellular.

• Metabolize complex carbohydrates.

Protozoa

• Eukaryotes.

• Absorb or ingest organic chemicals.

• May be motile via pseudopods, cilia, or flagella.

• Free-living or parasitic.

• Some are photosynthetic.

• Reproduce sexually or asexually.

Algae

• Eukaryotes.

• Cellulose cell walls.

• Found in freshwater, saltwater, and soil.

• Use photosynthesis for energy; produce oxygen and carbohydrates.

• Sexual and asexual reproduction possible.

Multicellular Animal Parasites

• Eukaryotes.

• Multicellular animals.

• Not strictly microorganisms.

• Parasitic flatworms and roundworms are called helminths.

Viruses

• Acellular.

• Consist of DNA or RNA core.

• Core is surrounded by a protein coat.

• Replicated only within a living host cell.

Microbial Diversity and Habitats

• Microbial populations are diverse, taking advantage of niches and competing with other organisms.

• Extremophiles live in extreme conditions (pH, temperature, salinity); most are members of the Archaea.

Microbial Ecology

• Microbial ecology studies the relationship between microorganisms and their environment.

• Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus into forms used by plants and animals.

• The Carbon Cycle

• The Nitrogen Cycle

Degradation of Synthetic Chemicals in Soil and Water

• Bioremediation: Use of microbes to detoxify or degrade pollutants, enhanced by nitrogen and phosphorus fertilizer.

• Composting: Arranging organic waste to promote microbial degradation by thermophiles, converting plant remains into humus.

The First Observations

• 1665: Robert Hooke reported that living things are composed of little boxes, or “cells.” Cell theory: All living things are composed of cells.

• 1673–1723: Anton van Leeuwenhoek observed and documented the first microbes with detailed drawings, calling them “Animalcules”.

The Debate over Spontaneous Generation

• Spontaneous generation: Life arises from nonliving matter; a “vital force” is necessary.

• Biogenesis: Living cells arise only from preexisting living cells.

Experiments

• 1668: Francesco Redi's experiment with decaying meat in covered, open, and sealed jars.

• 1765: Lazzaro Spallanzani boiled nutrient solutions in sealed flasks, showing no microbial growth.

• 1861: Louis Pasteur demonstrated that microorganisms are present in the air using nutrient broth in flasks, either sealed or left open.

Disproving Spontaneous Generation

• Pasteur demonstrated that microbes are present in nonliving matter.

• Aseptic techniques prevent microbial contamination.

Milestones in the First Golden Age of Microbiology (1857–1914)

• Pasteur:

  • Fermentation

  • Disproved spontaneous generation

  • Pasteurization

• Lister: Aseptic surgery

• Koch: Germ theory of disease, pure cultures, Mycobacterium tuberculosis, Vibrio cholerae

• Neisser: Neisseria gonorrhoeae

• Finlay: Yellow fever

• Hess: Agar (solid) media

• Metchnikoff: Phagocytosis

• Gram: Gram-staining procedure

• Escherich: Escherichia coli

• Petri: Petri dish

• Kitasato: Clostridium tetani

• von Bering: Diphtheria antitoxin

• Ehrlich: Theory of immunity

• Winogradsky: Sulfur cycle

• Shiga: Shigella dysenteriae

• Ehrlich: Syphilis treatment

• Chagas: Trypanosoma cruzi

• Rous: Tumor-causing virus (1966 Nobel Prize)

The First Golden Age of Microbiology

• 1857–1914

• Fermentation: Microbial conversion of sugar to alcohol in the absence of air.

• Pasteurization: Application of high heat for a short time to kill harmful bacteria in beverages.

The Germ Theory of Disease

• 1840s: Ignaz Semmelweis advocated handwashing to prevent the transmission of puerperal fever.

• 1876: Robert Koch discovered that a bacterium causes anthrax and provided Koch’s postulates to demonstrate that a specific microbe causes a specific disease.

Vaccination

• 1796: Edward Jenner inoculated a person with cowpox virus, who then became immune to smallpox.

• The protection is called immunity.

The Second Golden Age of Microbiology

• Focus on treating diseases caused by microbes.

• Chemotherapy: Treatment of disease with chemicals; can involve synthetic drugs or antibiotics.

• Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes.

The First Synthetic Drugs

• Paul Ehrlich speculated about a “magic bullet”.

  • 1910: Ehrlich developed salvarsan, a synthetic arsenic-based drug, to treat syphilis.

  • 1930s: Sulfonamides were synthesized.

A Fortunate Accident—Antibiotics

• 1928: Alexander Fleming discovered the first antibiotic (by accident).

• Fleming observed that Penicillium fungus made penicillin, which killed Staphylococcus aureus.

• 1940s: Penicillin was tested clinically and mass-produced.

Second and Third Golden Ages of Microbiology

• Fleming, Chain, and Florey: Penicillin

• Waksman: Streptomycin

• H. Krebs: Chemical steps of the Krebs cycle

• Enders, Weller, and Robbins: Poliovirus cultured in cell cultures

• Beadle and Tatum: Genetic control of biochemical reactions

• Medawar: Acquired immune tolerance

• Sanger and Gilbert: Techniques for sequencing DNA

• Jerne, Köhler, and Milstein: Technique for producing monoclonal antibodies

• Tonegawa: Genetics of antibody production

• Bishop and Varmus: Cancer-causing genes (oncogenes)

• Murray and Thomas: First successful transplants using immunosuppressive drugs

• Fischer and E. Krebs: Enzymes that regulate cell growth (protein kinases)

• Roberts and Sharp: Split genes

• Mullis: Polymerase chain reaction (PCR)

• Doherty and Zinkernagel: Cell-mediated immunity

• Agre and MacKinnon: Water and ion channels in plasma membranes

• Marshall and Warren: Helicobacter pylori as the cause of peptic ulcers

• Barré-Sinoussi and Montagnier: Discovery of HIV

• Ramakrishnan, Steitz, and Yonath: Structure and function of ribosomes

• Beutler, Hoffmann, and Steinman: Innate immunity; dendritic cells in adaptive immunity

• Tu: Treatment for malaria

• Campbell and Omura: Discovery of ivermectin

• Charpentier and Doudna: Genome editing

• Alter, Houghton, and Rice: Discovery of hepatitis C virus

Bacteriology, Mycology, and Parasitology

• Bacteriology is the study of bacteria.

• Mycology is the study of fungi.

• Parasitology is the study of protozoa and parasitic worms.

Immunology and Virology

• Virology is the study of viruses.

• Immunology is the study of immunity.

• Vaccines and interferons are used to prevent and cure viral diseases.

Molecular Genetics

• Microbial genetics: Study of how microbes inherit traits.

• Molecular biology: Study of how DNA directs protein synthesis.

Important Concepts to Know

• Experiments and scientists involved in the debate over spontaneous generation.

• Taxonomic hierarchy and binomial nomenclature.

• Ignaz Semmelweis and the importance of handwashing.

• Antiseptics in medical facilities.

• Koch's postulates.

• Definitions: microbial ecology, immunology, bacteriology, virology, parasitology, microbial genetics.

• Differences between eukaryotes and prokaryotes.

• Bioremediation vs. composting.

• Definition of extremophiles.

• Types of human microbiota.

• Definition of an opportunistic pathogen.

• Types of microorganisms and their characteristics.

• Contributions to the Golden Age of Microbiology.