Microbiology – Lecture Notes

Fundamental Characteristics of Microorganisms

• Visibility

  • Require specialized instrumentation (light or electron microscopes) because individual cells/particles are below the resolution limit of the naked eye (≈0.2 mm).

• Basic Groupings

  • Cellularity
  • Acellular / non-living agents: viruses, viroids, prions.
  • Cellular / living microbes: bacteria, archaea, fungi, protozoa, some algae, helminths (parasitic worms during egg/larval stages).
  • Presence/absence of a nucleus
  • Prokaryotic: no true nucleus, no membrane-bound organelles (bacteria, archaea).
  • Eukaryotic: true nucleus, membrane-bound organelles (fungi, protozoa, helminths, algae).

• Five (plus one) classic categories shown on slide

  1. Bacterium – example: Escherichia coli (lower-left image).
  2. Fungus – pictured top-centre.
  3. Protozoan – pictured upper-right.
  4. Viruses – example: Herpes simplex (below fungus).
  5. Prions – far right; infectious proteins only (no nucleic acid).
  6. Helminths (parasitic worms) – eggs, not adult worms, initiate host infection.

• Pathogen definition

  • Any microorganism/agent that causes disease when it invades the host.

• Opportunistic behaviour of normal flora

  • Beneficial gut microbes become pathogenic if:
  • Overgrow (excessive numbers).
  • Are depleted (leave ecological niche vacant for pathogens).
  • Relocate (e.g.
    GI bacteria entering urinary tract → UTI).

Prokaryotes vs. Eukaryotes (Venn Diagram Walk-through)

• Prokaryote keywords students shouted:
  • “No nucleus”, “no membrane bound organelles”, “DNA is circular”, “microscopic”.
• Helpful mnemonic: “Pro-No” (prokaryotes: no nucleus, no organelles).

Branches of Microbiology ("Six branches" slide)

1. Medical microbiology – study of pathogens, diagnosis, therapy.
2. Agricultural microbiology – microbe–plant/soil interactions; crop diseases.
3. Industrial microbiology & Biotechnology
   • Fermentation, antibiotics, vitamins, food processing.
   • DNA “fingerprint” analysis (whole-genome commonalities/mutations).
   • Engineering microbes/plants for food scarcity alleviation.
4. Immunology – host immune response (T cells, B cells, memory formation).
5. Environmental microbiology – microbial ecology, bioremediation.
6. Food microbiology & Safety – microbial limits in food, spoilage testing.

Immunology & Vaccination (class dialogue)

• Vaccines act as controlled antigen exposure → adaptive immunity.
• Possible mild post-vaccination malaise = immune activation.
• Sensitivity varies among individuals.

Microbes & the Environment (Salt, pH, Survival)

• Door-handle example: many species present, but few infect because
  • Human skin’s high-salt, low-water milieu inhibits salt-intolerant species.
  • Only organisms possessing salt-metabolizing enzymes can persist.
• High salt = first-line innate defense (chemical barrier).

Demonstration: "Microorganisms are Everywhere"

1. Obtain sterile cotton ball.
2. Insert into sterile growth medium ("media").
3. Incubate.
4. Outcomes
   • No growth → sterility maintained.
   • Growth indicators: turbidity (cloudiness), colour shift (red → orange/yellow, pH drop), foul odour.
5. Potential contamination sources: non-sterile cotton, poor aseptic technique, non-sterile lab air.

Growth Media Essentials

• Media = nutrient preparation that supports microbial growth.
• Physical forms
  • Liquid (broth)
  • Semisolid (soft agar; appears solid but flows when tube tilted)
  • Solid (agar plates/slants; “hard Jell-O” texture)
• Functional categories
  • General-purpose (nutrient agar) – broad growth.
  • Selective (high salt, bile salts, antibiotics) – suppress unwanted, allow target.
  • Differential (pH dyes, indicators) – colony colour change reveals metabolic traits.
  • Some plates combine both (selective & differential).

Historical Experiments & Key Scientists

• Louis Pasteur – Swan-Neck Flask

  • Heat-sterilised broth in flasks.
  • One neck left intact (dust trapped), one neck broken (direct air access).
  • Only broken flask became turbid → disproved spontaneous generation; contamination originates from environment.
  • Suggested improvements discussed in class: UV sterilisation, autoclave (121\,^{\circ}\text{C},\ 15\,\text{psi},\ 15\,\text{min}).

• Robert Koch – Koch’s Postulates

  1. Suspected pathogen found in every case of disease, absent in healthy.
  2. Isolate and grow pathogen in pure culture.
  3. Inoculate healthy host → same disease appears.
  4. Re-isolate identical pathogen from experimentally infected host.
  • Foundation for linking microbes to specific diseases and for mutation studies/resistance tracking.

• Ignaz Semmelweis – Introduced mandatory hand-washing in maternity wards → drastic drop in puerperal fever.

• Joseph Lister – Pioneered antiseptic surgery using phenol on instruments/wounds (chemical antisepsis).

• Carl von Linné (Linnaeus) – Developed hierarchical taxonomy & binomial nomenclature.

  • Scientific name: Genus species (italicised; Genus capitalised, species lowercase).
  • Hierarchy mnemonic: “Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species”.

Microscopy Basics

• Compound light microscope parts referenced
  • Ocular lens M_{ocular}=10\,\times (fixed).
  • Objective lenses: 4× (scanning), 10× (low), 40× (high dry), 100× (oil-immersion).
  • Coarse focus (large knob) – major stage movement; fine focus – precise clarity.
  • Stage, condenser, iris diaphragm, light source.
• Total magnification
  M{total}=M{ocular}\times M_{objective}
  Example: 10× ocular × 40× objective = 400×.
• Resolution (d) / Resolving power d=\frac{0.5\,\lambda}{NA}
  • Need high numerical aperture (NA) + short wavelength (blue light) for small d (better resolution).

Staining Techniques Discussed

• Simple stains (one dye)
  • Crystal violet, methylene blue.
  • Highlight morphology only (coccus, bacillus, spirillum).
• Differential stains
  • Gram stain (not fully covered in audio but implied).
  • Acid-fast stain: red = acid-fast (e.g.
    Mycobacterium), blue = non-acid-fast.
• Stains improve contrast so transparent cells become visible.

Genetics, Mutations & Antibiotic Resistance (preview)

• Microbiologists analyse microbial genomes (“fingerprints”) to pinpoint mutations enabling:
  • Antibiotic resistance.
  • Environmental adaptation.
  • Immune evasion.
• Understanding mutation pathways helps design next-generation therapeutics.

Practical/ethical implications highlighted

• Proper hand-washing & antisepsis save lives.
• Vaccination builds population immunity with minimal risk.
• Misuse of antibiotics fosters resistance; genomic surveillance is essential.
• Engineered microbes & crops hold promise for food security but require safety oversight.