Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

Ecological understanding of the role of consumer-resource interactions in
natural food webs is limited by the difficulty of accurately and
efficiently determining the complex variety of food types animals have
eaten in the field. We developed a method based on DNA metabarcoding
multiplexing and next-generation sequencing to uncover different taxonomic
groups of organisms from complex diet samples. We validated this approach
on 91 faeces of a large omnivorous mammal, the brown bear, using DNA
metabarcoding markers targeting the plant, vertebrate, and invertebrate
components of the diet. We included internal controls in the experiments
and performed PCR replication for accuracy validation in post-sequencing
data analysis. Using our multiplexing strategy, we significantly
simplified the experimental procedure and accurately and concurrently
identified different prey DNA corresponding to the targeted taxonomic
groups, with ≥60% of taxa of all diet components identified to
genus/species level. The systematic application of internal controls and
replication was a useful and simple way to evaluate the performance of our
experimental procedure, standardize the selection of sequence filtering
parameters for each marker data, and validate the accuracy of the results.
Our general approach can be adapted to the analysis of dietary samples of
various predator species in different ecosystems, for a number of
conservation and ecological applications entailing large-scale population
level diet assessment through cost effective screening of multiple DNA
metabarcodes, and the detection of fine dietary variation among samples or
individuals and of rare food items.