Beaked redfish, dominated by Sebastes mentella, have recently reached record abundance levels in the Gulf of St. Lawrence (GSL) and knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of the visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, a total of 27 taxonomic sequence matches, 16 at the species level considered as primary prey, were obtained from 185 stomachs with DNA metabarcoding and compared to the 26 prey types, 16 at genus or species level, obtained with stomach content analysis (SCA). While both techniques pointed to a similar definition of diet composition, our results also revealed that the SCA and DNA metabarcoding perform differently among prey categories, both in terms of detectability and taxonomical resolution, as well as in estimated contribution to diet. The use of DNA metabarcoding along with SCA improves the taxonomical resolution of visually determined prey, which supports the concept that both techniques provide useful complementary information that is best used together to gain a maximum level of information on the predator’s diet.

Redfish stomachs were thawed for visual analysis at the Maurice-Lamontagne Institute (Mont-Joli, Canada) and each prey taxon found in the stomach contents was weighed and identified to the lowest taxonomic level possible under a dissecting microscope and using keys and identification guides. For metabarcoding, matched reads with equal quality scores for more than one species were assigned to a higher taxonomic level since it was impossible to discriminate species with certainty. Barque (https://github.com/enormandeau/barque) then produced a table of prey taxa counts (including the multiple hits) for each sample.

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