Integrated genomic and functional analysis elucidates the probiotic properties and host responses of Enterococcus...

The global aquaculture industry is severely impacted by infectious diseases and excessive antibiotic use, necessitating the development of sustainable probiotic alternatives. Enterococcus faecium has demonstrated efficacy as an emerging feed additive in fish aquaculture, yet its application in Pacific white shrimp (Litopenaeus vannamei), the dominant farmed crustacean species worldwide, remains insufficiently characterized due to a lack of integrated studies combining genomic analysis with functional validation in aquaculture practice. To bridge this gap, we evaluated E. faecium LYB as a novel probiotic for L. vannamei through integrated genomics and functional assays. Genomic analysis revealed stress tolerance, adhesion, and immunomodulation traits linked to improved shrimp performance. Bioinformatic screening detected no high-risk virulence genes (IS16, hylEfm, esp). Phenotypic validation remains necessary to assess biosafety risks for aquaculture use. Functional validation demonstrated that dietary supplementation with E. faecium LYB at 1.0 × 10¹¹ CFU/kg optimally enhanced shrimp growth performance, upregulated Imd/Toll and mTOR signaling effectors, and increased survival against Vibrio parahaemolyticus challenge. This study provides the first comprehensive genome-supported and dose-optimized evidence for E. faecium's probiotic efficacy in L. vannamei, resolving prior knowledge gaps by simultaneously characterizing host response and bacterial functional traits. This work advances the rational development of Enterococcus-based probiotics for crustacean aquaculture, offering a sustainable strategy to enhance global food security while reducing antibiotic dependence in aquaculture systems.