Comprehensive analysis of microbiome and transcriptome revealed the mechanisms of <i>Flammulina velutipes</i> stem‐base enhance intestinal health in <i>Gymnocypris eckloni</i>

Although Flammulina velutipes residues are increasingly used in fish feeds, their mode of action in the gut is poorly defined. Here, we show that feeding Gymnocypris eckloni diets supplemented with F. velutipes stem-base (FVS) or its polysaccharides (FVP) selectively enhance foregut morphology-increasing both villus height and muscle layer thickness-without affecting mid- or hindgut regions. Transcriptome profiling revealed that 1831 differentially expressed genes (DEGs) were generated by FVS diet in the foregut mainly enriched in the signalling pathways related to DNA replication, fat digestion and absorption and HIF-1 signalling pathway. In addition, the differential genes between the FVP group and the control group were enriched in cell adhesion molecules, MAPK signalling pathway and cytokine-cytokine receptor interaction. Consistent with this, KEGG enrichment highlighted HIF-1α and MAPK as key pathways activated by FVS and FVP, respectively. Importantly, FVP also shifted the gut microbiota composition, boosting Weissella and other putative beneficial bacteria. These findings imply that F. velutipes has the potential to strengthen the intestinal barrier and improve intestinal health, offering valuable insights for the aquaculture of G. eckloni.