Identifying and Classifying Microorganisms Study Notes

Taxonomy

The science of classifying organisms into groups, or taxa, facilitating identification, classification, and nomenclature.

Hierarchical Order

The structure in taxonomy where species is the basic unit, with eukaryotes as groups capable of producing fertile offspring and prokaryotes as closely related strains.

Classification Basis

The development from general to specific characteristics, including microscopic examination, culture, biochemical tests, and nucleic acid analysis.

Phylogeny

The evolutionary relatedness among organisms, represented by the three-domain system introduced by Carl Woese et al., based on rRNA sequences.

Microscopic Morphology

Observation of size, shape, and staining (e.g., Gram stain, acid-fast, endospore, capsule) to aid in identifying microorganisms.

Serratia marcescens

A bacterium that produces red pigment at $22^\text{C}$.

Pseudomonas aeruginosa

A bacterium known for producing green pigment and a distinct fruity odor.

Differential Media

Media that distinguishes microorganisms based on their biochemical properties, e.g., Streptococcus pyogenes shows $\beta$-hemolytic colonies on blood agar.

Metabolic Capabilities

Capabilities that often utilize pH indicators to track sugar fermentation or urease production. The Catalase test is a primary biochemical diagnostic.

Commercial Tests

Systems like the Enterotube or API test strip enabling rapid, standardized identification via simultaneous tests.

Dichotomous Keys

Flowcharts with successive questions about morphological or biochemical traits used to differentiate species.

Serology

A method that uses commercial antibodies to detect specific antigens (proteins/polysaccharides) in microorganisms.

Nucleic Acid Amplification Tests (NAATs)

Techniques like Polymerase chain reaction (PCR) used to amplify specific sequences of DNA.

Polymerase chain reaction (PCR)

A method in NAATs that allows for rapid amplification of DNA sequences.

Mycobacterium tuberculosis

An example of a slow-growing organism that can be identified using PCR, taking $3-4$ hours compared to $6$ weeks for traditional culture.

Sequencing Ribosomal RNA Genes

A method that sequences highly conserved genes, such as $16S$ rDNA, to identify evolutionary relatives.

$16S$ rDNA

A specific type of ribosomal RNA gene sequenced to identify bacterial species.

$18S$ rDNA

The ribosomal RNA gene sequenced in eukaryotes to identify species relationships.

Serological Typing

Distinguishes organisms like $E. coli$ by antigenic types of flagella, capsules, or lipopolysaccharides (e.g., $E. coli O157:H7$ where 'O' is the lipopolysaccharide and 'H' is the flagella).

Molecular Typing

Uses DNA fingerprinting to distinguish phenotypically identical strains by comparing Restriction Fragment Length Polymorphisms (RFLPs) via gel electrophoresis, useful for tracing outbreaks.

Antibiograms

Identification based on antibiotic susceptibility; clearing zones around antimicrobial discs on an inoculated plate indicate susceptibility levels.