Gut microbiota and growth differentiation in koi carp with identification of a growth promoting Exiguobacterium sp. strain WY(Y)3.

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 S rRNA sequencing to characterize the intestinal landscape and to discover a significant taxonomic shift in koi (Cyprinus carpio) 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 Exiguobacterium 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 cm; 20.81 ± 1.33 g) harbored markedly higher proportions of Cyanobacteriota, Actinobacteriota, Chloroflexota, and notably Exiguobacterium sp., alongside enhanced metabolic pathways related to secondary metabolite biosynthesis compared with the SG fish. A piscine-derived strain, Exiguobacterium 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 Exiguobacterium 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 (p < 0.05). Collectively, dietary inclusion of 1 × 106 CFU/g of Exiguobacterium sp. WY(Y)3 effectively promotes growth through microbiota restructuring and metabolic optimization, supporting its potential as a probiotic in aquaculture nutrition.