Dietary inclusion of plant ingredients induces epigenetic changes in the intestine of zebrafish.

Epigenetic modifications, such as DNA methylation, can be regulated by nutrition and dietary factors. There has been a large increase in the use of sustainable plant-based protein sources in fish feed due to limitations of fishmeal resources that are needed to sustain a rapidly growing aquaculture industry. With this huge transition from marine ingredients to plant-based diets, fish are abruptly introduced to changes in dietary composition and exposed to a variety of phytochemicals, some of which reported to cause epigenetic changes in mammals. However, the effect of plant ingredients on the epigenome of fish is barely understood. In the present study, the nutriepigenomic effects of the addition of pea, soy and wheat gluten protein concentrates to aquafeeds was investigated using zebrafish as a model. A genome-wide analysis of DNA methylation patterns was performed by reduced representation bisulfite sequencing to examine global epigenetic alterations in the mid intestine after a 42-day feeding trial. We found that inclusion of 30% of wheat gluten, pea and soy protein concentrate in the diet induced epigenetic changes in the mid intestine of zebrafish. A large number of genes and intergenic regions were differentially methylated with plant-based diet. The genes concerned related to immunity, NF-κB system, ubiquitin-proteasome pathway, MAPK pathway and the antioxidant defense system. Epigenetic regulation of biological processes including neurogenesis, cell adhesion, response to stress and immunity were also observed. Ultimately, the observed epigenetic changes may enable zebrafish to rapidly regulate inflammation and maintain intestinal homeostasis when fed plant protein-based diets.