Metabarcoding is a method of sequencing the DNA barcodes of many different organisms in parallel.
Classic DNA barcoding is of limited use for biodiversity surveys for two main reasons. First, it is too slow and expensive for generating large-scale data across diverse groups (e.g. arthropods other invertebrates) because it requires a separate sequencing reaction for each specimen. Second, it can’t be used on samples that contain DNA from a mixture of related species (e.g. environmental samples).
Metabarcoding solves this problem by using High Throughput Sequencing on community DNA to identify diverse taxa in a single reaction.
When metabarcoding is applied to environmental samples, such as water, it is known as 'eDNA metabarcoding'.
The principle steps in a metabarcoding pipeline are:
1. Extract community DNA from your sample. If you are working with bulk samples of invertebrates, this includes a homogenisation (blending) step prior to DNA extraction.
2. Amplify a barcode region using primers optimised for your target taxon group (e.g. fish / arthropods / molluscs). This makes millions of copies of the barcode gene in preparation for sequencing.
3. Sequence the amplified DNA on a high throughput sequencing platform such as the Illumina MiSeq, which generates around 30 million sequences in around 2.5 days.
4. Bioinformatically process the raw sequence data to obtain a species x sample table that can be used for ecological analysis