DNA barcoding in diet assessment
DNA barcoding in diet assessment is the use of DNA barcoding to analyse the diet of organisms. and further detect and describe their trophic interactions. This approach is based on the identification of consumed species by characterization of DNA present in dietary samples, e.g. individual food remains, regurgitates, gut and fecal samples, homogenized body of the host organism, target of the diet study.
Faeces of wolf (Canis lupus) collected in Sweden
Food web reconstruction by DNA barcodes at the coral reef of Moorea, French Polynesia. Dietary partitioning among three predatory fish species as detected using metabarcoding dietary analysis. The taxonomic resolution provided by the metabarcoding approach highlights a complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated.
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections, an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries.
HiSeq sequencers at SciLIfeLab in Uppsala, Sweden. The photo was taken during the excursion of SLU course PNS0169 in March 2019.
A schematic view of primers and target region, demonstrated on 16S rRNA gene in Pseudomonas. As primers, one typically selects short conserved sequences with low variability, which can thus amplify most or all species in the chosen target group. The primers are used to amplify a highly variable target region in between the two primers, which is then used for species discrimination. Modified from »Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas« by Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent, used under CC BY, available from: https://www.researchgate.net/figure/Hypervariable-regions-within-the-16S-rRNA-gene-in-Pseudomonas-The-plotted-line-reflects_fig2_224832532.
Barcoding is a tool to vouch for food quality. Here, DNA from traditional Norwegian Christmas food is extracted at the molecular systematic lab at NTNU University Museum.
Differences in the standard methods for DNA barcoding and metabarcoding. While DNA barcoding points to find a specific species, metabarcoding looks for the whole community.
