Classification of Microorganisms

Introduction to Microbial Classification

• Microbiology focuses on the classification of microorganisms.
• Historically, organisms were categorized as either plants or animals.
• In 1937, prokaryotic (no membrane-bound nucleus) and eukaryotic (organisms with a nucleus) cells were first distinguished.
• Various taxonomic systems have been proposed over time, with emphasis on phenotypic relationships (observable characteristics).

The Five Kingdom System

• Proposed by Robert Whittaker in 1969.
• Suggests that eukaryotes evolved from prokaryotes based on observable traits.
• Classifies organisms into five kingdoms:

1. Prokaryotae (Monera)
   • Includes all prokaryotic cells (Bacteria and Archaea).
2. Protista
   • Comprises unicellular eukaryotes such as algae and protozoa.
3. Fungi
   • Encompasses molds and yeasts.
4. Animalia
   • Represents all multicellular animals.
5. Plantae
   • Covers all plants.

The Three Domain System

• Proposed by Carl Woese in 1978, focusing on evolutionary (phylogenetic) relationships based on nucleotide sequences of rRNA (16S rRNA for prokaryotes and 18S rRNA for eukaryotes).
• Significance of rRNA:

1. Present in all living cells.
2. Functions similarly across life forms.
3. Highly conserved molecule.

• Molecular Phylogeny:
• Reveals three major domains, which differ from Whittaker's five kingdoms.
• Domains are higher than kingdoms in biological classification.
• The three domains are:
  1. Bacteria
  2. Archaea
  3. Eukarya

Comparison of Ribosomes

• Prokaryotic Ribosome (70S):
• 30S and 50S subunits
• Composed of 21 different proteins, mainly 16S rRNA.
• Eukaryotic Ribosome (80S):
• 40S and 60S subunits
• Approximately 30 proteins and 18S rRNA.

Bergey's Manual

• A resource that categorizes prokaryotes under two domains: Archaea and Bacteria using molecular phylogeny based on 16S rRNA.
• Organizes biological classifications into domains, phyla, classes, orders, families, etc.
• Provides identification schemes (e.g., dichotomous keys) based on various criteria:
• Cell wall structure, morphology, staining properties, oxygen requirements, and biochemical test results.

Traditional Classification Methods

• Morphological Characteristics:
• Size, shape, and structural features of organisms.
• Ecological Niche:
• Environment or habitat where organisms are typically found.
• Biochemistry:
• Differences in metabolic processes; includes differential and selective growth conditions.
• Differential Staining:
• Techniques like Gram staining to identify cellular structures.

Molecular Classification Methods

• Involves biochemical analysis and DNA analysis techniques:
• G/C Ratios: Measure DNA base composition.
• DNA Sequencing/Fingerprinting:
  • Techniques like ribotyping (16S & 18S rRNA).
• Polymerase Chain Reaction (PCR): A method to amplify DNA segments.
• Microarray Technology:
  • Involves screens for thousands of gene expressions.
• Southern Blotting & FISH: Other molecular methods for identifying genetic material.

### Molecular Identification Methods

• Serological Techniques:
• Measure antibodies or cytokine production in response to microbial antigens (e.g., ELISA).
• Enzyme Assays:
• Assessing enzyme activities such as reverse transcriptase for HIV.
• Soft-Ionization Mass Spectroscopy (MALDI): Used for detailed microbial identification.
• Phage Typing & Fatty Acid Profiles: Emerging methods for identifying and classifying bacteria.