Enteromyxum leei-associated emaciation in olive flounder is linked to intestinal microbiome dysbiosis and predicted functional shifts

Emaciation disease associated with the intestinal myxozoan Enteromyxum leei is a major constraint in olive flounder aquaculture, yet its microbiome component remains poorly understood. Here, we combined E. leei -specific PCR, relative condition factor (rCF), and full-length 16S rRNA gene sequencing of the posterior intestine to compare naturally infected and uninfected fish. Infected fish showed markedly reduced rCF, confirming severe emaciation. Alpha-diversity indices did not differ significantly between groups, although richness-related indices tended to be lower in infected fish. Bray–Curtis beta-diversity analysis indicated an infection-associated shift in community composition, whereas weighted UniFrac showed no significant group effect. Taxonomic profiling revealed higher relative representation of Proteobacteria/Vibrionaceae lineages in infected fish and reduced Spirochaetota and several commensal Firmicutes lineages. Differential abundance analyses (ANCOM-BC, DESeq2 and LEfSe) consistently identified amplicon sequence variants (ASVs) assigned to Photobacterium damselae , Vibrio harveyi , Vibrio alginolyticus , Haemophilus parainfluenzae, and other opportunistic lineages as infection-associated taxa, whereas controls were enriched in lactic acid- and short-chain fatty acid-associated genera such as Lactococcus , Weissella and Bifidobacterium . BLASTn showed high 16S sequence similarity for most major infection-associated ASVs, but species-level assignments were treated as putative because closely related marine Gammaproteobacteria may not be fully resolved by 16S rRNA sequences alone. PICRUSt2 analysis predicted differences in functional potentials related to central metabolism, motility, membrane transport, siderophore and lipopolysaccharide biosynthesis, xenobiotic/bile acid metabolism, and glycan-related functions. Overall, these results link E. leei -associated emaciation in olive flounder to infection-associated intestinal microbiome restructuring and predicted functional shifts, and identify candidate microbial indicators for future validation.