Proteomic mechanisms underlying soybean meal‐induced enteritis resistance in selected rainbow trout
Bibliographic record
Abstract
Abstract Soybean meal‐induced enteritis (SBMIE) remains a major barrier to reducing fishmeal use in salmonid aquaculture. This study evaluated physiological and molecular responses associated with SBMIE resistance in rainbow trout ( Oncorhynchus mykiss ) by comparing a commercial strain (Com) and a selectively bred strain (Sel) with over two decades of selection for plant‐based diet tolerance. Both strains were fed either a traditional fishmeal‐based (FM) or high‐soybean meal plant‐based (PM) diet for 7 months. Growth performance was monitored monthly, and intestinal histology and proteomics were assessed at early (2‐month) and late (7‐month) timepoints. The Sel strain consistently outperformed the Com strain in final weight, weight gain and feed conversion ratio ( p < 0.05), with no differences in feed intake or mortality ( p > 0.05). Average weight gain was greatest in the Sel strain across diets (497.3 g on PM; 610.2 g on FM), while Com trout gained less, particularly when fed the PM diet (387.9 g on PM; 482.6 g on FM). Significant strain by diet interactions in distal intestinal histology ( p < 0.05) indicated that only the Com strain developed SBMIE on the PM diet, characterized by shortened, widened villi, mucosal fold clubbing, and inflammatory infiltration. Ordinal histopathology scoring confirmed interactions for goblet cells, submucosa, lamina propria, and inflammatory cell counts ( p < 0.05), confirming the SBMIE susceptibility in the Com strain. Label‐free proteomics identified only 18 significantly altered proteins (FDR ≤0.05, |log 2 FC| ≥1), exclusively in plasma, despite pronounced intestinal pathology in Com PM. Key plasma DEPs included upregulation of the inflammasome sensor Nlrp1 in Com PM relative to Com FM, providing molecular evidence for systemic inflammation linked to SBMIE. Exploratory gene set enrichment analysis revealed distinct functional profiles, notably heightened stress, DNA damage, and innate immune signaling (e.g., TLR pathways) in Com PM intestine, while inflammatory signatures were absent in Sel PM. These findings highlight coordinated histological and molecular adaptations underpinning SBMIE resistance in the Sel strain, demonstrate the utility of plasma proteomics for detecting systemic biomarkers like Nlrp1, and emphasizes the combined roles of diet and genetics in improving feed flexibility and sustainability in aquaculture.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".