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.