IntroductionThe intensive farming of crucian carp (Carassius auratus) often compromises fish health and increases disease susceptibility, driving interest in probiotic interventions as sustainable alternatives to antibiotics. However, the in vivo efficacy and mechanistic basis of Weissella cibaria strains in freshwater fish remain poorly understood.MethodsA bacteriocin-producing strain, Weissella cibaria XN-2a, was isolated from fish viscera and supplemented in the diet of crucian carp at an initial viable dose of 2.74 × 1010 CFU/g feed (freshly prepared and replaced every 3 days) for 30 days, followed by a challenge with Aeromonas hydrophila. Growth performance, immune parameters, intestinal histology, and gut metagenomic profiles were compared between the probiotic-fed group (XS) and the control group (XD).ResultsProbiotic supplementation significantly improved weight gain (28.17% vs. 13.98%), feed conversion ratio (1.88 ± 0.32 vs. 2.58 ± 0.27, p < 0.05), and post-challenge survival (50% vs. 0%) (p < 0.001). The XS group exhibited enhanced intestinal morphology (higher mucosal fold height and FH/IFD ratio, lower inter-fold distance), elevated IgM and SOD activities, and reduced post-challenge IL-6 and MDA levels. Metagenomic analysis revealed that the probiotic reshaped the gut microbiota from a pathogen-associated virulence profile (LPS, flagella, enterobactin) toward a commensal profile enriched in T6SS/T2SS and alternative siderophores, without increasing the overall antibiotic resistance burden. The butanoate metabolism pathway showed differences consistent with increased butyrate synthesis potential, with enrichment of butyrate-synthetic enzymes (e.g., enoyl-CoA hydratase, acetolactate decarboxylase) in XS and butyrate-diverting enzymes in XD. CAZy profiling further showed enrichment of antibacterial (GH25/GH73) and antioxidant (AA4) gene families in XS, with Weissella as a major contributor.DiscussionThese findings suggest that dietary Weissella cibaria XN-2a enhances growth performance, intestinal health, and disease resistance in crucian carp, potentially through a dual mechanism involving bacteriocin-mediated microbiota modulation and enhanced butyrate synthesis potential. Further investigations, including direct metabolite quantification, are warranted to validate these mechanistic inferences.