Shotgun Metagenomics
Definition
Sequencing all DNA in a sample rather than just the 16S amplicon. Provides taxonomic resolution beyond 16S and can characterise viruses and fungi, but requires more input material and computational processing, making it less practical for degraded forensic samples.
- Scope
- Sequences all DNA present, not a single targeted amplicon
- Advantage over 16S
- Finer taxonomic resolution, plus detection of viruses and fungi
- Cost
- Requires more input DNA and heavier computational processing
- Forensic limitation
- Less practical for degraded, low-quantity forensic samples
Common questions
Why is 16S amplicon sequencing still preferred over shotgun metagenomics for most body fluid identification casework?+
16S sequencing targets one short, well-conserved gene region, so it works reliably from the small, often degraded DNA quantities typical of forensic swabs and stains, whereas shotgun metagenomics needs substantially more intact starting material and far more sequencing and analysis capacity, making it impractical for routine casework volumes.
What can shotgun metagenomics reveal that 16S sequencing cannot?+
Because it sequences all DNA rather than one bacterial marker gene, it can also detect and characterise viral and fungal community members and can resolve bacterial identifications to a finer level than 16S alone typically allows, which matters in research settings or complex cases needing that extra resolution.
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)...
- Amplicon Sequencing
- A sequencing approach where a specific locus (here the 16S hypervariable region) is amplified from all members of a microbial community and...
- 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...