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

Abstract

The molecular mechanisms underlying fish tolerance to soybean meal (SBM) remain unclear. Identifying these mechanisms would be beneficial, as this trait favors growth. Two fish replicates from 19 experimental families were fed fishmeal-(100FM) or SBM-based diets supplemented with saponin (50SBM + 2SPN) from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (HG-50SBM + 2SPN, 170 ± 18 mg) or lower (LG-50SBM + 2SPN, 76 ± 10 mg) weight gain on 50SBM + 2SPN for intestinal transcriptomic analysis. A histological evaluation confirmed middle intestinal inflammation in the LG- vs. HG-50SBM + 2SPN group. Enrichment analysis of 665 differentially expressed genes (DEGs) identified pathways associated with immunity and lipid metabolism. Genes linked to intestinal immunity were downregulated in HG fish (mpx, cxcr3.2, cftr, irg1l, itln2, sgk1, nup61l, il22), likely dampening inflammatory responses. Conversely, genes involved in retinol signaling were upregulated (rbp4, stra6, nr2f5), potentially favoring growth by suppressing insulin responses. Genes associated with lipid metabolism were upregulated, including key components of the SREBP (mbtps1, elov5l, elov6l) and cholesterol catabolism (cyp46a1), as well as the downregulation of cyp7a1. These results strongly suggest that transcriptomic changes in lipid metabolism mediate SBM tolerance. Genotypic variations in DEGs may become biomarkers for improving early selection of fish tolerant to SMB or others plant-based diets.

A Multidisciplinary Approach Evaluating Soybean Meal-Induced Enteritis in Rainbow Trout Oncorhynchus mykiss

“…Our search for indicative parameters for SBM-induced enteritis at the molecular level turned out to be more challenging than expected. The histopathological analysis suggested that molecular markers were likely to be encountered in the intestine, as supported by recent studies in various fish species [40,54,55]. However, as these investigations require the killing and dissection of the animals, we first screened for potential markers that could be detected in small blood volumes taken non-lethally from farmed fish [56].…”

Metabolomic and Transcriptomic Profiles after Immune Stimulation in the Zebrafish Testes

“…LPS treatment altered the expression of some genes with known function in the reproduction system such as zp3 [107,108], as well as others in the fish gonads that have not been described previously in fish. Examples include tgfb1a function in testicular immune homeostasis in sheep [109], and cyp46a1 function in intestine after enriched diets [110] and cldn5b involvement in the blood-testis-barrier in mice [111].…”