Classification of Microorganisms

1. Taxonomy Overview

• Definition: The science of classifying organisms to show relationships and identify them.

• Objective: To classify organisms, establish relationships, and provide a common reference for identifying species.

2. The Three Domains of Life

• Ribosomal RNA Comparison: Three distinct cell types based on ribosomal differences.

• Eukaryotes

• Bacteria (Prokaryotes)

• Archaea (Prokaryotes)

• Woese’s Contribution (1978): Proposed three domains based on rRNA sequences.

• Domain Eukarya: Kingdoms of animals, plants, fungi.

• Domain Bacteria: Includes pathogenic and non-pathogenic prokaryotes.

• Domain Archaea: Prokaryotes without peptidoglycan in cell walls; often live in extreme environments.

• Archaea Types:

1. Methanogens

2. Extreme Halophiles

3. Hyperthermophiles

3. Phylogenetic Trees

• Phylogeny: Evolutionary history of organisms.

• Molecular Clock: Mutation rates in genomes help track evolutionary divergence.

4. Scientific Nomenclature (Binomial Nomenclature)

• Every organism has a two-part scientific name (Genus + Species).

• Genus: Capitalized, noun.

• Species: Lowercase, often an adjective.

5. Taxonomic Hierarchy

• Hierarchy: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species.

• Classification of Prokaryotes: Based on similarities in rRNA, and prokaryotes are classified in two domains: Bacteria and Archaea.

• Prokaryotic Species: A population of cells with similar characteristics.

6. Classification of Eukaryotes

• Kingdoms:

• Fungi: Yeasts, molds, mushrooms.

• Plantae: Mosses, ferns, conifers, flowering plants.

• Animalia: Sponges, worms, insects, vertebrates.

• Protista: Unicellular eukaryotes.

7. Classification of Viruses

• Viruses aren’t classified within the three domains.

• Defined by their ecological niche, genetic characteristics, and morphology.

8. Methods of Classifying and Identifying Microorganisms

• Morphological Characteristics:

• Used for structural identification but not always reliable for classification.

• Differential Staining:

• Used to differentiate between gram-positive and gram-negative bacteria (e.g., Gram stain, acid-fast stain).

• Biochemical Tests:

• Enzymatic activities help differentiate species.

• Includes selective and differential media.

• Serology:

• Studies serum and immune responses.

• Antiserum: Used to identify microorganisms by matching antibodies to antigens.

• Slide Agglutination Test: Bacteria clump when mixed with specific antibodies.

• ELISA (Enzyme-Linked Immunosorbent Assay): Used to detect antigens or antibodies.

• Phage Typing:

• Determines susceptibility to specific bacteriophages (viruses that infect bacteria).

• DNA Fingerprinting:

• Uses restriction enzymes to cut DNA and compare the genetic similarities between organisms.

• Nucleic Acid Amplification Tests (NAATs):

• Amplifies microbial DNA for testing, useful when organisms can’t be cultured.

• Includes PCR (Polymerase Chain Reaction) and real-time PCR.

• DNA Chips:

• Detects pathogens by identifying unique genes using DNA probes.

• Fluorescent In Situ Hybridization (FISH):

• Uses fluorescent probes to detect microorganisms directly in samples (e.g., water, patient samples) without culturing.