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.
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...
Explained in
- Microbiome-Based Body Fluid IdentificationSequencing all DNA in a sample rather than just the 16S amplicon. Provides taxonomic resolution beyond 16S and can characterise viruses and fungi, but requires...