Microbiology Learning Objectives: Key Concepts and Study Guide

Microorganisms and Their Classification

Definition and Major Groups

Microorganisms, or microbes, are living organisms (or infectious biological entities) too small to be seen clearly with the naked eye, typically requiring a microscope. They are classified into several major groups:

• Bacteria (e.g., Escherichia coli, Staphylococcus aureus)

• Archaea (e.g., methanogens, halophiles)

• Fungi (e.g., yeasts like Saccharomyces cerevisiae; molds like Aspergillus)

• Protozoa (e.g., Giardia lamblia, Plasmodium falciparum)

• Algae (e.g., diatoms, Chlamydomonas)

• Helminths (microscopic stages of parasitic worms, e.g., schistosome larvae)

• Viruses (e.g., influenza virus, bacteriophages)

• Prions/Viroids (infectious proteins or small infectious RNAs)

Pathogens and Opportunistic Pathogens

Definitions and Examples

• Pathogen: A microbe capable of causing disease in a host with normal defenses (e.g., Mycobacterium tuberculosis).

• Opportunistic pathogen: Normally harmless or environmental flora that cause disease when host defenses are compromised or when they enter atypical sites (e.g., Pseudomonas aeruginosa in burns).

Biogenesis and Spontaneous Generation

Historical Experiments and Concepts

• Spontaneous generation: Disproven idea that life arises from nonliving matter.

• Biogenesis: All life arises from preexisting life.

• Pasteur's swan-neck flask experiment: Broth boiled in flasks with long, curved necks remained sterile because airborne microbes were trapped in the bend. When tilted/broken, contamination occurred, supporting biogenesis and linking microbes to contamination.

Koch's Postulates and the Germ Theory of Disease

Key Principles and Limitations

• Koch linked specific microbes to specific diseases (e.g., Bacillus anthracis to anthrax).

• Koch's Postulates:

  1. The suspected pathogen is present in all cases of the disease and absent from healthy organisms.

  2. The pathogen can be isolated and grown in pure culture.

  3. Inoculation of the pure culture into a healthy, susceptible host causes the same disease.

  4. The same pathogen can be re-isolated from the experimentally infected host.

• Limitations: Some pathogens cannot be cultured, some diseases are polymicrobial, and ethical constraints prevent human testing.

Aseptic Technique and Laboratory Safety

Goals and Importance

• Goals: Prevent contamination of cultures, the environment, and the experimenter.

• Importance: Ensures accurate results, maintains pure cultures, protects patient samples and lab staff, and prevents spread of pathogens.

Historical Contributions to Infection Control

Semmelweis, Lister, and Nightingale

• Ignaz Semmelweis: Introduced handwashing with chlorinated lime, reducing puerperal fever in maternity wards.

• Joseph Lister: Applied antiseptics (carbolic acid/phenol) to surgical wounds and instruments, reducing postoperative infections.

• Florence Nightingale: Instituted sanitation, ventilation, nutrition, and data-driven hospital reforms, dramatically lowering mortality in military hospitals.

Scientific Method in Microbiology

Steps and Distinctions

• Steps: Observation → Question → Hypothesis → Experiment → Analyze → Conclusion → Communicate/Revise.

• Observation vs. Conclusion:

  • Observation: What you directly detect (e.g., "broth becomes cloudy after 24 hr").

  • Conclusion: Interpretation based on data (e.g., "microbial growth caused turbidity").

• Law vs. Theory:

  • Scientific law: Descriptive generalization about how nature behaves (often mathematical; e.g., gas laws).

  • Theory: Well-substantiated explanation of some aspect of the natural world (e.g., theory of evolution).

Binomial Nomenclature and Taxonomy

System and Hierarchy

• Format: Genus species (italicized; Genus capitalized, species lowercase), e.g., Staphylococcus aureus.

• Information: Indicates taxonomic placement and sometimes morphology/traits (e.g., "aureus" = "golden").

• Taxonomic hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species (→ Strain).

• Domains: Bacteria, Archaea, Eukarya.

Strains and Species Naming

Definitions and Formatting

• Strain: A genetic variant or subtype within a species, often with distinct traits (e.g., E. coli O157:H7 vs. lab K-12).

• Species (specific epithet): Second word, lowercase (e.g., coli).

• Both italicized (or underlined when handwritten).

Normal Microbiota (Flora)

Establishment and Roles

• Normal microbiota: Microbes that colonize healthy body sites (skin, gut, mouth, etc.) without causing disease.

• Establishment: Begins at birth (delivery mode, breast milk/formula, environment), evolves with diet, antibiotics, age.

• Roles:

  • Colonization resistance against pathogens (competition, bacteriocins).

  • Metabolic functions (vitamins K, B; SCFAs).

  • Immune system development and modulation.

  • Impacts drug metabolism and disease risk.

Symbiosis: Parasitism, Mutualism, and Commensalism

Definitions and Examples

• Parasitism: One benefits, host harmed (e.g., Plasmodium in humans).

• Mutualism: Both benefit (e.g., gut bacteria producing vitamins).

• Commensalism: One benefits, other unaffected (e.g., skin Staphylococcus epidermidis).

Microbial Impact on Industry and Environment

Applications and Examples

• Industry: Fermentation (bread, cheese, yogurt, beer), pharmaceuticals (antibiotics, insulin via recombinant DNA), bioplastics, enzymes.

• Environment: Biogeochemical cycles (C, N, S), bioremediation (soil spill cleanup), wastewater treatment, biofuel production (algae).

Biofilms

Formation and Healthcare Implications

• Formation (stages):

  1. Reversible attachment to surface.

  2. Irreversible attachment via adhesins/extracellular polymeric substances (EPS).

  3. Maturation (3-D structure, channels, quorum sensing).

  4. Dispersion (cells detach to colonize new sites).

• Healthcare implications:

  • Increased antibiotic tolerance and immune evasion.

  • Chronic/recurrent infections (e.g., catheters, prosthetics, cystic fibrosis lungs).

  • Source control (device removal) often required in addition to antimicrobials.

Culture Media in the Laboratory

Formats and Functions

• Physical form: Liquid (broth), semisolid, solid (agar plates/slants).

• Function/types:

  • General purpose: Nutrient agar, tryptic soy agar.

  • Enriched: Blood or chocolate agar (fastidious organisms).

  • Selective: Inhibits some, permits others (e.g., MacConkey selects Gram-negatives).

  • Differential: Shows metabolic differences (e.g., lactose fermenters pink on MacConkey).

  • Selective/differential: MSA (selects staphylococci; differentiates mannitol fermenters).

  • Defined vs. complex: Exact chemical composition known vs. unknown (e.g., peptones).

Aseptic Technique: Core Elements

• Hand hygiene, PPE.

• Flame sterilization (loops/needles), disinfecting surfaces.

• Minimizing exposure (keep lids closed, work near flame/hood).

• Proper transfer methods; labeling; waste disposal.

Streak Plate Technique

Goal and Importance

• Goal: Mechanically dilute a mixed culture across an agar surface to obtain isolated colonies derived from single cells.

• Importance: Isolation enables pure culture establishment, accurate identification, antimicrobial testing, and study of colony morphology.

Staining Techniques

Simple vs. Structural Stains

• Simple stains: Use one basic dye (e.g., methylene blue, crystal violet) to increase contrast and reveal cell shape, size, and arrangement.

• Structural (special) stains: Target specific cell structures and provide localization/visibility of features:

  • Capsule stain: Negative stain with India ink or nigrosin + counterstain; detects capsules.

  • Endospore stain: (Schaeffer-Fulton: malachite green + heat; safranin counterstain) distinguishes spores vs. vegetative cells.

  • Flagella stain: Increases flagella diameter to visualize distribution/arrangement.

Prokaryotic vs. Eukaryotic Cells

Comparison Table

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	No true nucleus	True nucleus (membrane-bound)
DNA	Circular, free-floating	Linear, organized into chromosomes
Organelles	No membrane-bound organelles	Membrane-bound organelles (e.g., mitochondria, ER, Golgi)
Size	Smaller (1–10 μm)	Larger (10–100 μm)
Examples	Bacteria, Archaea	Fungi, protozoa, algae, plants, animals