Amplicon Sequencing
Definition
A sequencing approach where a specific locus (here the 16S hypervariable region) is amplified from all members of a microbial community and the amplicons are sequenced to profile community composition.
- Target region
- 16S rRNA hypervariable region
- Input
- Mixed microbial community DNA
- Output
- Community composition profile
- Forensic application
- Body fluid identification
Common questions
Why is 16S rRNA used rather than sequencing the whole microbial genome?+
The 16S gene contains conserved regions that let a single primer pair amplify it across almost all bacteria, flanking variable regions specific enough to distinguish species. This lets one PCR and sequencing run profile an entire mixed community cheaply.
What makes a microbial profile useful for identifying body fluid type?+
Different fluids host characteristically different bacterial communities, for example vaginal secretions are dominated by Lactobacillus species that are largely absent from saliva or blood. Matching the amplicon-derived community profile against reference fluid signatures supports a fluid-type call.
Related terms
- 16S rRNA Gene
- The gene encoding the 16S ribosomal RNA subunit present in all bacteria and archaea. Conserved regions allow universal amplification; hypervariable regions (V1-V9)...
- Community State Type (CST)
- A classification of vaginal microbiome profiles into distinct clusters. Most CSTs are dominated by a single Lactobacillus species; one CST (often called...
- Microbiome
- The total community of microorganisms (bacteria, archaea, fungi, viruses) inhabiting a body site, along with their collective genetic material. Each body site...
- OTU / ASV
- Operational Taxonomic Unit (OTU) and Amplicon Sequence Variant (ASV) are the units of microbial diversity in 16S data. OTUs cluster reads at...
- Shotgun Metagenomics
- Sequencing all DNA in a sample rather than just the 16S amplicon. Provides taxonomic resolution beyond 16S and can characterise viruses and...