Metagenomics
Definition
The direct sequencing of all DNA extracted from an environmental sample, bypassing the need to culture individual organisms. It produces a community-wide genetic profile that can be searched against reference databases to identify constituent species and their relative abundances.
- Method
- Direct sequencing of all DNA in an environmental sample
- Bypasses
- Need to culture individual organisms
- Output
- Community-wide genetic profile
- Used against
- Reference sequence databases
Common questions
Why is bypassing culturing an advantage in forensic metagenomics?+
Many microorganisms found in soil, water, or decomposition sites cannot be cultured in a laboratory at all, or grow too slowly to be useful for time-sensitive casework. Sequencing DNA directly from the sample captures organisms that culturing would simply miss, giving a more complete picture of what is actually present.
What limits how confidently a metagenomic result can identify species present in a sample?+
The result is only as good as the reference database it is compared against, so poorly represented or novel organisms may be misidentified or missed entirely. Contamination during sample collection or sequencing can also introduce sequences that did not originate from the scene, requiring careful controls to rule out.
Related terms
- 16S rRNA Amplicon Sequencing
- A targeted sequencing approach that amplifies a variable region of the bacterial 16S ribosomal RNA gene, which acts as a universal phylogenetic...
- Cadaver Decomposition Island (CDI)
- The localised area of soil and vegetation altered by the decomposition fluids and gases released from a body. A CDI has a...
- Collagen Peptide Barcoding
- Species identification from trypsin-digested collagen analysed by mass spectrometry. Peptide sequences differ between species at diagnostic positions that survive tanning and heat...
- DNA Fragmentation
- Physical breakage of the DNA backbone into short pieces. In degraded samples the average fragment length may be 50-200 bp, making long...
- Library Preparation (aDNA)
- Enzymatic end-repair, adapter ligation, and amplification of all DNA fragments in a sample regardless of length, used in ancient-DNA and degraded-sample workflows....
- PCR Inhibitor
- A co-extracted substance that interferes with Taq polymerase activity or primer annealing. Common inhibitors in forensic samples include haemoglobin (from blood on...
- Post-Mortem Interval (PMI)
- The time elapsed between death and discovery or examination of remains. PMI estimation draws on multiple disciplines: soft tissue decomposition stage, insect...
- Short-Amplicon Strategy
- A PCR design that targets the shortest possible fragment length: often 80-150 bp: within a diagnostic locus such as COI. Shorter targets...
- Soil Microbiome
- The total community of microorganisms inhabiting a soil sample. Each location has a characteristic baseline community shaped by climate, vegetation, and soil...
- Thanatomicrobiome
- The community of microorganisms that colonise a body after death, arising primarily from gut bacteria that breach the intestinal wall and spread...
Explained in these topics
- DNA from Degraded and Processed Wildlife ProductsShotgun sequencing of all DNA in a sample followed by bioinformatic assignment of reads to taxa. Does not require prior knowledge of which species are present;...
- Microbial and Microbiome Evidence in Forensic Cases