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DNA metabarcoding and its applications

DNA metabarcoding is a process that enables the characterisation of DNA samples, including eDNA from environmental sources, using sequencing technologies. This approach involves the simultaneous sequencing of short, standardised DNA sequences, known as DNA barcodes, from various environmental samples.


What are DNA barcodes? A DNA barcode is a highly variable portion of a DNA sequence that differs significantly between taxa (Figure 1), enabling the delineation of species or strains. It must be present in all target taxa and include conserved regions, which are identical segments of the sequence, to facilitate targeting by PCR amplification.

Image explaining the DNA barcode, showing conserved regions at both ends of a nucleotide sequence where forward and reverse primers align. The middle section, represented by dotted lines, illustrates the variable region, which serves as the DNA barcode used for species identification. The height of each nucleotide letter (0-100%) in the image represents the relative abundance of taxa in the reference library with that base at that specific position.
Figure 1 Visual representation of a DNA metabarcode showing the position of each base and its corresponding letter. The height of each letter (0-100%) represents the relative abundance of taxa in the reference library with that base at that specific position. The figure highlights conserved regions (100% of all taxa) used for primer design, along with the variable region showing bases present in different percentages of taxa. (Image credit: Joe Taylor, UKCEH; This image is licensed under a Creative Commons Attribution 4.0 International (CC BY-NC-SA 4.0) license)

The table below shows examples of taxonomic genes commonly used as DNA barcodes:

OrganismTaxonomic genes for DNA barcodes
Animalsmitochondria COI, 12S Cytb, 16S
Plants chloroplast plastid matK, rbcL, psbA-trnH, ITS
Bacteria/Archaea16S rRNA gene, COI, rpoB, cpn60, tuf, RIF
FungiITS, 18S (SSU) (RPB1 (LSU), RPB2 (LSU)
Protists/all eukaryotes18S, 28S rRNA genes, ITS, COI, rbcL

In the following pages, you will explore the applications of metabarcoding in eDNA analysis by reviewing selected research articles as case studies. These studies demonstrate the effectiveness of eDNA metabarcoding in assessing biodiversity across various habitats and ecosystems.