Using rRNA gene sequences in microbiology Sequencing of rRNA genes (such as 16S rRNA in bacteria or 18S rRNA in eukaryotes) can be used to:

Introduction / Context:
Ribosomal RNA (rRNA) genes are highly conserved across all domains of life, with variable regions that enable discrimination among taxa. Sequencing these genes underpins molecular taxonomy, microbial ecology surveys, and the initial identification of unknown isolates.

Given Data / Assumptions:

• 16S rRNA (bacteria/archaea) and 18S rRNA (eukaryotes) contain conserved and variable regions.
• Comparison to curated databases supports identification and phylogeny.
• Phenotypic traits (e.g., Gram reaction) are not predicted solely from rRNA sequence.

Concept / Approach:
By aligning an unknown rRNA gene sequence with reference sequences, one can determine its closest relatives and place the organism on a phylogenetic tree. This provides a tentative identification (often to genus, sometimes species) and evolutionary context, but does not directly yield phenotypic characteristics such as cell wall architecture, PFGE banding patterns, or drug susceptibility.

Step-by-Step Solution:
Amplify rRNA gene (e.g., 16S) using universal primers.Sequence and compare to databases to find nearest neighbors.Use phylogenetic analysis to infer relatedness and tentative identity.

Verification / Alternative check:
Metagenomic surveys and clinical diagnostics routinely rely on 16S/18S sequencing for culture-independent identification, confirming this application.

Why Other Options Are Wrong:

• Eukaryotes only: incorrect—prokaryotes are a primary use case.
• PFGE pattern prediction: banding depends on genome restriction sites, not rRNA sequences.
• Gram reaction prediction: not reliably deduced from rRNA alone.
• Antibiotic susceptibility: requires phenotypic testing or specific resistance gene detection.

Common Pitfalls:
Overinterpreting rRNA data as predictive of phenotype; it is primarily taxonomic/phylogenetic.

Final Answer:
Obtain a tentative identification of a new microorganism and infer its phylogenetic relatedness.