Resilience of gut microbial assemblages in farmed fish revealed by long-term dietary changes

Abstract

Changes in the gut microbial assemblages associated with dietary changes are still poorly explored, but may have profound effects in the life-history and physiology of fishes. Here, we have investigated the influence of the diet type on the autochthonous gut microbiomes of gilthead seabream (Sparus aurata). We conducted a 60-day assay in which a dietary shift from commercial to a diet based only on shrimp, followed by determination of gut microbial assemblages using 16S rRNA gene amplicon sequencing. The most prevalent species belonged to the genus Ralstonia, present in all samples, but was enhanced after the switch to shrimp diet. This seems to be a key genus whose functional relevance needs still to be unveiled given the wide distribution in samples with marine origin. Our results also pointed that nor the diet or the environmental microbiota (i.e. present in the water tanks) played a paramount role in the structure of the gut microbiome at the long-term. After 40 days, the gut microbial communities under both dietary treatments were very similar, being some species of the genera Ralstonia, Paraburkholderia, Fulvimonas, Pseudomonas and Cutibacteriumpart of the core-microbiome conserved at similar abundances over time. These results may challenge the common wisdom that diet is the primary determinant of gut microbiome composition in the long-term. In the era of the search for alternatives to fish-based ingredients in the aquafeed sector, and considering the paramount role of the gut microbiota in the fish health, this work offers valuable information for feed manufacturers to explore different nutritional strategies for aquaculture production, as long as the impact of the feeds on the physiology and quality of the fish are also tested.