The intestinal holobiont: the key to optimizing carbohydrates utilization in rainbow trout fed with full plant-based diets? – HOLOFISH

For sustainability of aquaculture, carnivorous fish such as rainbow trout have to change their “menu” from fish-based diet to diet free of fish resources. Feed producers have commonly replaced fish ingredients (oil and proteins) by plant ingredients. However, there is still a major problem of growth performance of fish fed with a full plant-based diet due to a decrease in feed intake and feed efficiency. In addition, in many fish species fed with fishmeal and fish oil, dietary digestible carbohydrate (CHO) supply can improve protein utilization for growth (protein sparing effect) and decrease nitrogen waste. In this context, the HOLOFISH project aims to study the partial replacement of plant proteins by digestible dietary carbohydrates (ie starch easy to produce) in rainbow trout fed with full plant-based diet with different CHO/protein ratios from the first feeding stage to the juvenile stage (6 months). We will focus our study for the first time on the whole gut ecosystem: the gut microbiome and gut metabolic response using a multi-omics strategy using 2 complementary approaches. The first one is an in vivo approach to test the beneficial effects of including digestible carbohydrates in an all-plant based diet on the fish growth performance. We will characterize the key role of the gut microbiome to understand the metabolic utilization of dietary carbohydrates through multi-omics studies (metagenomics, metatranscriptomics, metabolomics). The host response will be studied using plasma metabolomics, metatranscriptomics, epigenetics and structure of intestinal epithelium. The second approach is an in vitro approach by using rainbow trout intestinal epithelial intestinal cells of rainbow trout to identify molecular mechanisms that explain the cross-talk between the microbiome and the host intestine. We will test the bacterial metabolites identified in the first approach directly on the change in metabolic gene expression, enzyme activities and epigenetics changes.