Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis

Abstract

Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

Intestinal Transcriptome Analysis Reveals Enrichment of Genes Associated with Immune and Lipid Mechanisms, Favoring Soybean Meal Tolerance in High-Growth Zebrafish (Danio Rerio)

“…In HG-50SBM + 2SPN fish, cyp27a1.2 , cyp27a1.4 , and cyp7a1 were downregulated, while cyp46a1.1 was upregulated, suggesting a metabolic redirection towards 24(S)-hydroxycholesterol, leading to suppression of Th17 differentiation. These results are consistent with those reported by Abernathy et al [ 81 ], where liver tissues from rainbow trout tolerant to a plant diet were subjected to functional analysis. These authors documented upregulated cytochrome P450A1 and T cell signaling, which suppressed interleukin-17 receptor E-like (IL17REL) expression.…”

“…Thus, upregulation of il-17 is directly related to intestinal inflammation found in fish that cannot tolerate plant-based diets. These authors suggest that tolerant fish display different autoimmune or other detoxification responses to utilize plant proteins, avoiding the onset of enteritis [ 81 ].…”

Investigating Both Mucosal Immunity and Microbiota in Response to Gut Enteritis in Yellowtail Kingfish

“…Fermentation of soybean meal prior to feeding has also been tested in turbot with encouraging results, suppressing the intestinal inflammation and enhancing the intestinal integrity [ 45 ]. Furthermore, efforts in selecting resistant fish with increased tolerance to plant diets have been made in some species such as rainbow trout ( Oncorhynchus mykiss ) [ 46 ]. In yellowtail kingfish, efforts in finding alternatives to soybean meal showed that poultry byproduct, faba bean and lupin kernel meals represent good protein sources compared to corn gluten and blood meals [ 47 ].…”

Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

“…Effects of plant-based diets have been largely studied, but only few transcriptomic studies have analysed the effect of fish genetic background. Overall, these studies indicated only a limited number of genes to be differentially expressed according to the genotype in RBT [ 20 , 21 ], in salmon [ 11 ] or in sea bass [ 14 ]. In the present experiment, we found a high number of genes differentially expressed between genotypes, with a cut-off p-value corrected for multiple testing, controlling thus the number of false positives.…”

“…A study on European sea bass revealed differences between two families characterized by their different abilities to use a plant-based diet [ 14 ]. And only two studies focused on RBT, and analysed two families with different ability to grow with a diet devoid of fishmeal [ 20 , 21 ].…”