Classification of Microorganisms

Foundations - Kingdoms & Domains Galore

• Traditional Systems:
  • Linnaeus: Two Kingdoms (Plantae, Animalia).
  • Whittaker (1969): Five Kingdoms, based on cell structure, mode of nutrition, body organization.
    • Monera (prokaryotic, unicellular)
    • Protista (eukaryotic, mostly unicellular)
    • Fungi (eukaryotic, saprophytic, chitin cell wall)
    • Plantae (eukaryotic, photosynthetic, cellulose cell wall)
    • Animalia (eukaryotic, heterotrophic, no cell wall)
• Modern System: Three Domains (Carl Woese, 1977):
  • Based on 16S rRNA (prokaryotes) & 18S rRNA (eukaryotes) gene sequencing.
  • Bacteria: Prokaryotic, peptidoglycan cell walls.
  • Archaea: Prokaryotic, distinct cell wall lipids, often extremophiles.
  • Eukarya: Eukaryotic cells; includes Protista, Fungi, Plantae, Animalia.

⭐ Carl Woese proposed the three-domain system (Bacteria, Archaea, Eukarya) based on differences in 16S rRNA sequences.

Bacteria - Gram's Colorful Crew

⭐ Gram-positive bacteria have a thick peptidoglycan layer and teichoic acids, while Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane containing Lipopolysaccharide (LPS).

• Gram Staining: Differentiates bacteria based on cell wall composition.
  • Gram-Positive (G+):
    • Thick peptidoglycan layer.
    • Teichoic & lipoteichoic acids.
    • Stain Purple/Blue.
    • Examples: Staphylococcus, Streptococcus, Clostridium.
  • Gram-Negative (G-):
    • Thin peptidoglycan layer.
    • Outer membrane with Lipopolysaccharide (LPS - Endotoxin).
    • Periplasmic space.
    • Stain Pink/Red.
    • Examples: E. coli, Salmonella, Pseudomonas.
• Atypical Bacteria: Poorly staining/non-staining.
  • Mycoplasma (no cell wall), Mycobacteria (acid-fast), Spirochetes (too thin), Chlamydia, Rickettsia (intracellular).
• 📌 Mnemonic: Positive Purple; Negative piNk.

Viruses - Not Quite Alive

• Acellular, obligate intracellular parasites; not truly living organisms.
• Lack metabolic machinery; hijack host cell for replication (protein synthesis, energy).
• Core components:
  • Nucleic acid: DNA or RNA (single-stranded (ss) or double-stranded (ds)).
  • Capsid: Protein shell; protects genome, aids in entry.
  • Envelope (optional): Lipid layer; derived from host cell membrane.
• Key classification criteria:
  • Genome type & strandedness (e.g., ssRNA, dsDNA).
  • Capsid morphology (e.g., icosahedral, helical, complex).
  • Presence/absence of envelope.

⭐ Baltimore Classification categorizes viruses based on their mRNA synthesis pathway. Key exceptions: Parvoviridae (ssDNA), Reoviridae (dsRNA).

Fungi & Parasites - Frenemies & Freeloaders

• Fungi: Eukaryotes; chitin cell wall, ergosterol in cell membrane. Often opportunistic.
  • Forms:
    • Yeasts: Unicellular, budding. Candida, Cryptococcus.
    • Molds: Multicellular, hyphae (septate/aseptate), spores. Aspergillus, Mucorales.
    • Dimorphic:

      ⭐ Dimorphic fungi exist as 'Mold in the Cold (environment, 25°C)' and 'Yeast in the Heat (host tissue, 37°C)'. Examples: Histoplasma, Blastomyces, Coccidioides, Sporothrix.

  • Mycoses: Superficial, cutaneous, subcutaneous, systemic infections.
• Parasites: Eukaryotes; host-dependent, complex life cycles.
  • Protozoa (unicellular):
    • Amoebae: E. histolytica (dysentery).
    • Flagellates: Giardia, Trichomonas, Trypanosoma, Leishmania (sandfly vector).
    • Apicomplexa: Plasmodium (malaria; mosquito vector), Toxoplasma, Cryptosporidium.
  • Helminths (worms):
    • Nematodes (round): Ascaris, Hookworms, Enterobius.
    • Cestodes (tape): Taenia spp. (cysticercosis), Echinococcus (hydatid).
    • Trematodes (flukes): Schistosoma, Fasciola. and Parasites (protozoa, helminth examples) microscopic views)

High‑Yield Points - ⚡ Biggest Takeaways

• Whittaker's five-kingdom classification (Monera, Protista, Fungi, Plantae, Animalia) is key.
• Carl Woese's three-domain system (Bacteria, Archaea, Eukarya) uses 16S rRNA sequences.
• Phenotypic classification: morphology, staining (Gram, ZN), biochemical tests.
• Genotypic methods (PCR, sequencing) offer precise identification and relatedness.
• Bergey's Manual is the standard reference for bacterial taxonomy.
• Viruses: acellular, obligate intracellular parasites; classified by nucleic acid, capsid, envelope.
• Prions (infectious proteins) and viroids (infectious RNA) are unique pathogens.