# Evaluating the Impact of Two Different Diets on the Protein Profile of the Brain, Liver, and Intestine of the Barramundi

## TL;DR

This study shows how different diets affect protein levels in the brain, liver, and intestine of barramundi, revealing changes in iron metabolism and digestion.

## Contribution

The study uses proteomics to demonstrate diet-induced molecular changes in aquaculture species across multiple organs.

## Key findings

- Diet B increased iron concentrations in brain, liver, and intestine as measured by ICP-MS.
- Dietary differences caused significant changes in protein abundance, with up to 16.59% in the intestine.
- Ferroptosis pathways and digestive proteases were upregulated in diet B-fed fish.

## Abstract

Background: Commercial feed formulations are increasingly being evaluated for their nutritional impacts on aquaculture species, yet the molecular consequences of commonly used commercial diets remain underexplored. Methods: This study investigated the effects of two commercial diets, diet A (higher land animal protein) and diet B (higher fish meal content), on the protein profile in the brain, liver, and intestine of barramundi (Lates calcarifer). A 12-week feeding trial was conducted with controlled water quality, and proteomic profiling was performed using data-independent acquisition. Results: Differential analysis revealed consistent changes between diets across all tissues, with a higher percentage of differentially abundant proteins observed in between-diet comparisons (12.99% in brain, 12.73% in liver, and 16.59% in intestine) than within-diet controls (<8%), confirming a measurable dietary effect size. In total, 3901 proteins in the brain, 3660 in the liver, and 5025 in the intestine were quantified. Functional enrichment highlighted upregulation of ferroptosis pathways, downregulation of apelin signaling in the brain, and increased digestive proteases in the liver. ICP-MS confirmed elevated iron concentrations in the brain, liver, and intestine of fish fed on diet B. Conclusions: These findings demonstrate that molecular pathways linked to iron metabolism, digestion, and growth regulation are very sensitive to dietary composition, highlighting how proteomics can help identify subtle impacts of compositional differences in aquaculture feeding. Although physiological parameters did not differ significantly, the proteomic alterations observed across tissues likely indicate organ-specific metabolic adaptations to the differing nutrient availability between diets.