<p>Discovering specific microbial markers and probiotics related to rapid growth offers a route for developing targeted feed solutions. This study was conducted in two phases: Phase I: Using 16&#xa0;S rRNA sequencing to characterize the intestinal landscape and to discover a significant taxonomic shift in koi (<i>Cyprinus carpio</i>) that grow fast (FG) and grow slow (SG). Phase II: A dietary intervention trial was implemented across four experimental cohorts: a negative control (NC) fed a basal diet and three treatment groups (C1, C2, and C3) supplemented with <i>Exiguobacterium</i> sp. strain WY(Y)3 at escalating concentrations of 1 × 10⁶, 1 × 10⁷, and 1 × 10⁸ CFU/g, respectively. The FG fish (11.44 ± 0.61&#xa0;cm; 20.81 ± 1.33&#xa0;g) harbored markedly higher proportions of Cyanobacteriota, Actinobacteriota, Chloroflexota, and notably <i>Exiguobacterium</i> sp., alongside enhanced metabolic pathways related to secondary metabolite biosynthesis compared with the SG fish. A piscine-derived strain, <i>Exiguobacterium</i> sp. WY(Y)3, isolated from the FG, significantly improved growth performance when supplemented in feed, with the 1 × 10⁶ CFU/g producing the best overall outcomes (WGR = 186.26 ± 1.07 and FCR = 1.437 ± 0.08), including higher gut microbial diversity and stability. Integrated microbiome and metabolomic analyses revealed that supplementation with <i>Exiguobacterium</i> enhances growth performance by reshaping gut microbial composition and regulating host energy metabolism. This includes the downregulation of fatty acid β-oxidation and pyruvate metabolism pathways, alongside the upregulation of bile acid synthesis and vitamin-associated pathways (<i>p</i> &lt; 0.05). Collectively, dietary inclusion of 1 × 10⁶ CFU/g of <i>Exiguobacterium</i> sp. WY(Y)3 effectively promotes growth through microbiota restructuring and metabolic optimization, supporting its potential as a probiotic in aquaculture nutrition.</p> Graphical Abstract <p></p>