Optimizing Feeding Strategies in Marinecultured Nibea Coibor: Gut Digestion-Barrier Trade-Offs Revealed by Transcriptome-Microbiota Integration

Abstract

Feeding strategies critically influence intestinal homeostasis in farmed fish, however, their underlying regulatory mechanisms remain poorly understood. This study employed integrated multi-omics analyses to systematically dissect the multidimensional regulatory networks of four feeding strategies on intestinal morphology, host transcriptome, and microbiota in Nibea coibor, including daytime feeding (DF), intermittent fasting (IF, 2 day fasting/1 day feeding), continuous fasting (CF), and nighttime feeding (NF). Our results demonstrated that feeding regimens significantly reshaped lipid metabolism-related genes (pla2g12b, pecam1b, itgal, col1a) and gut microbial communities (Akkermansia, Photobacterium, Vibrio, Ruminococcaceae.sp). The CF group exhibited a 'metabolic-barrier trade-off' phenotype: col1a (a collagen-coding gene) was markedly upregulated, driving extracellular matrix fibrosis that suppressed goblet cell differentiation. Concurrently, pla2g12b (a phospholipase) downregulation exacerbated lipid metabolic dysfunction. Concurrently, continuous fasting-triggered dysbiosis featured Akkermansia-mediated mucin degradation and pathogenic Vibrio proliferation, alongside depletion of butyrogenic Ruminococcaceae, collectively eroding mucosal integrity. In contrast, IF achieved optimal intestinal health, showing the highest goblet cell density, villus height, and microbial diversity, suggesting microbiota-mediated mucosal resilience. NF mildly downregulated energy metabolism pathways but showed no significant omics-level shifts, indicating limited short-term circadian entrainment. These findings highlight IF as a sustainable strategy to enhance gut homeostasis via microbial stewardship, while prolonged fasting risks irreversible metabolic-barrier collapse. This study provides actionable guidelines for optimizing feeding protocols in N. coibor aquaculture.

Keywords: Nibea coibor, feeding strategies, col1a, Akkermansia, ECM-receptor interaction