Abstract Feeding strategies critically influence intestinal homeostasis in farmed fish, however, their underlying regulatory mechanisms remain poorly understood. Nibea coibor , a fish species with local characteristics in Zhanjiang (Guangdong Province, China), was chosen as the experimental model for studying feeding strategies. This study employed integrated multi-omics analyses to systematically dissect the multidimensional regulatory networks of four different feeding strategies on intestinal morphology, transcriptome, and microbiota in Nibea coibor . Feeding strategies reshaped gut microbiota composition and significantly altered gene expression. Compared with daytime feeding (DF), continuous fasting (CF) induced villus atrophy and goblet cell loss, disrupted microbial homeostasis ( Vibrio , Actinomyces , Photobacterium , and Akkermansia upregulation), and triggered transcriptional reprogramming ( pfkfb4 , pla2g12b , rptor , and pecam1 downregulation; col1a upregulation). In contrast, intermittent fasting (IF, two-day fasting/one-day feeding) achieved optimal intestinal health with the highest goblet cell density, villus height, and microbial diversity, suggesting microbiota-mediated gut plasticity and adaptation. Nighttime feeding (NF) elicited minor downregulation of energy metabolism genes without causing significant morphological or microbial alterations, indicating limited short-term circadian effects. Finally, the PLS-PM model delineated the cascade regulatory relationships linking gut microbiota, transcriptome, and intestinal morphology. These findings highlight intermittent fasting as a promising strategy to sustain intestinal homeostasis through microbiota-host synergy, while underscoring the risks of prolonged fasting-induced metabolic and barrier dysfunction. This work provides valuable insights for refining feeding protocols in marine fish aquaculture, especially N. coibor .
Qu et al. (Mon,) studied this question.