Biology Taxonomy and Classification

Taxonomy and Bacterial Classification

• Taxonomy: The science of classifying living organisms, derived from the Greek words "taxes" (arrangement) and "nomos" (law).
• Nomenclature: Assignment of scientific names to various taxonomic categories and individual organisms.
• Classification: Organizes organisms into a hierarchy of taxa (categories) to facilitate study.
• Identification: Process of discovering and recording traits of organisms for recognition and classification based on genotypic and phenotypic characteristics.

Key Figures in Taxonomy

• Carl von Linné (Linnaeus): Established fundamental classification rules and taxonomic categories.
• Robert Whittaker: Developed Whittaker's tree; classification based on structural similarities, distinguishing between prokaryotic and eukaryotic organisms.
• Carl R. Woese: Introduced the Three-Domain System of Classification, including Archaea, Bacteria, and Eucarya.

Bacterial Naming and Structure

• International Code of Nomenclature of Bacteria (ICNB or Bacteriological Code): Provides accepted labels for universal recognition of organisms.
• Binomial System: Each organism is assigned a Latin or Greek-derived genus and species name.
• Genotypic Characteristics: Focus on an organism's genetic makeup, including genes and nucleic acids.
• Phenotypic Characteristics: Relate to observable features of organisms, requiring varying degrees of analysis for detection.

Structural Components of Bacteria

• N-acetyl-D-glucosamine (NAG) and N-acetyl-D-muramic acid (NAM): Two alternating sugars forming part of bacterial cell walls.
• Bacterial Cell Wall: Known as the peptidoglycan or murein layer; provides shape, strength, and protection against osmotic pressure and mechanical disruption.

Gram Staining and Cell Wall Types

• Gram Positive Cell Wall: Thick peptidoglycan layer, teichoic and lipoteichoic acids providing rigidity and attracting cations.
• Gram Negative Cell Wall: Thin peptidoglycan layer, periplasmic space, and an outer membrane composed of proteins, phospholipids, and lipopolysaccharides (LPS).
• Crystal Violet: Primary stain in Gram staining procedure.
• Iodine: Acts as a mordant to strengthen primary stain affinity.
• Alcohol: Used for decolorization in the Gram staining process.
• Safranin Red: Counterstain used in Gram staining to visualize Gram-negative cells.

Variability and Specific Bacteria

• Gram Variability: Example organisms include Mobiluncus spp. and Gardnerella vaginalis, displaying natural variability in Gram reactions.
• Exceptions in Gram Reaction:
  • All cocci are Gram positive except for Neisseria and Branhamella/Moraxella, and Veilonella.
  • All bacilli are Gram negative except for Mycobacterium, Bacillus, Clostridium, and several others.
• Mycoplasma & Ureaplasma: Have a gram-negative reaction due to the absence of a cell wall.
• Mycobacterium and Nocardia spp.: Have gram-positive structures but include significant hydrophobic lipids that affect staining permeability.

Acid-Fast Organisms and Staining Techniques

• Acid-Fast Organisms: Contain a waxy layer with more than 60% of their cell wall being lipid, mainly mycolic acid, contributing to their unique staining properties.
• Acid-Fast Staining: A specialized staining method designed for bacteria with high lipid content in their cell walls, facilitating their identification.