Meta-analysis of gut microbiome in largemouth bass (Micropterus salmoides) under different aquaculture systems

The teleost gastrointestinal tract hosts metabolically active microbial assemblages that play critical roles in nutrient use, immune regulation, physiology, behavior, growth, reproduction, and health status. However, the extent to which aquaculture production systems restructure these communities remains poorly defined. In this study, metagenomic sequencing was applied to characterize gut microbiota in largemouth bass ( Micropterus salmoides ) reared under four representative farming conditions: industrial aquaculture (IA), captive pond-based farming (CA), ordinary pond aquaculture with healthy fish (PH), and ordinary pond aquaculture with diseased fish (PD). Results revealed that the four groups exhibited pronounced differences in microbial diversity, taxonomic composition, functional capacity, carbohydrate-active enzyme profiles, and antibiotic resistance genes (ARGs). Notably, bacterial taxa accounted for more than 95% of the gut microbial communities across all groups. IA fish showed greater microbial richness and diversity than CA and PH fish, consistent with a more complex and potentially more stable intestinal ecosystem under industrialized rearing conditions. Taxonomic profiling at both the phylum and genus levels identified production system-specific microbial signatures. In particular, opportunistic pathogens, including Aeromonas veronii and Aeromonas hydrophila , were disproportionately enriched in CA fish, suggesting a microbiota profile associated with increased disease vulnerability. Functional prediction analysis further indicated distinct metabolic states among groups, with purine and fatty acid metabolism enriched in PD fish, potentially reflecting disease-associated disruption of host-microbiota interactions. Carbohydrate-active enzyme analysis revealed substantial variation in microbial carbohydrate-processing potential, whereas ARG profiling indicated that farming conditions were linked to distinct gut resistome patterns. Collectively, these findings identify aquaculture regimes as a key ecological driver of intestinal microbiome structure in largemouth bass and provide a mechanistic basis for optimizing microbiome-informed health management in aquaculture systems.