16S rRNA
Definition
The small-subunit ribosomal RNA gene in bacteria (~1,550 bp). The V3-V4 hypervariable region (~470 bp) is amplified with universal bacterial primers for species identification, microbiome profiling, and biothreat attribution.
- Gene length
- ~1,550 base pairs
- Amplified region
- V3-V4 hypervariable region, ~470 bp
- Found in
- Bacteria, not human DNA
- Uses
- Species ID, microbiome profiling, biothreat attribution
Common questions
Why sequence only the V3-V4 region instead of the full gene?+
The V3-V4 region is short enough to sequence cheaply and quickly with standard platforms while still sitting between conserved primer-binding sites, giving enough taxonomic variation to identify most bacterial species or genera without the cost of full-gene sequencing.
Can 16S rRNA always tell closely related bacterial species apart?+
Not reliably. Very closely related species or strains can share nearly identical 16S sequences, so results are sometimes reported only to genus level, and other markers are used alongside it when finer resolution is needed.
Related terms
- BOLD Systems
- Barcode of Life Data System (University of Guelph, Canada). Holds over 9 million COI reference barcodes linked to voucher specimens, with mandatory...
- COI (COX1)
- Cytochrome-c oxidase subunit I gene. The 658-base-pair Folmer fragment is the globally adopted barcode-of-life marker for animals, curated in BOLD Systems and...
- Cytochrome B (Cyt B)
- A mitochondrial protein-coding gene widely used in forensic species identification before COI barcoding was standardised. Still used because its reference database for...
- ITS Region
- Internal transcribed spacer region, flanking the 5.8S rRNA gene between the 18S and 28S subunits in fungi and plants. The ITS1-5.8S-ITS2 fragment...
- PCR-RFLP
- PCR followed by restriction fragment length polymorphism analysis. A restriction enzyme cuts the amplicon at species-specific recognition sites; the resulting fragment pattern...
- SILVA
- Curated ribosomal RNA sequence database (Max Planck Institute for Marine Microbiology, Bremen). Provides quality-filtered 16S, 18S, 23S, and 28S reference alignments for...