This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

This preliminary study used DNA metabarcoding to test whether the stomach content and gut microbiome of tuna could be a viable near real-time monitoring tool for detecting composition and change in oceanic ecosystems. The gut content of skipjack (Katsuwonus pelamis, n=55) and yellowfin tuna (Thunnus albacares, n=46) captured in the Pacific Ocean during El Niño Southern Oscillation events (ENSO) between 2015-2017 were examined by high throughput sequencing and complemented by morphological assessments to identify fishes, crustaceans and cephalopods in the stomach content. Gut microbiome was examined solely by high throughput sequencing. Stomach content and gut microbiome were compared between tuna species, ENSO events and capture location using generalised linear models. The full model (tuna species, capture location and interaction with ENSO) best explained fish prey composition, while capture location and ENSO weakly explained the composition of crustaceans and cephalopods. Skipjack and yellowfin tuna captured near coastal areas (Longitude<170°W) showed a greater diversity of prey compared to fish captured in oceanic regions of the Pacific, while Thunnus albacares showed a much more diverse stomach content than K. pelamis (21 fish, eight cephalopods and six crustaceans). Fish captured during La Niña events showed higher prey diversity compared to fish captured during El Niño. Tuna species best explained differences in gut microbiome to the Phylum level, while no model explained gut microbiome differences to the Order or Family level. This preliminary study shows that capture location and ENSO events explained differences in stomach content of K. pelamis and T. albacares, while tuna species best explained gut microbiome assemblages to the Phylum level.