Farming Mode Drives Gut Microbiota Structure in Mandarin Fish: Diet Drives Functional Adaptation While Environment Drives Community Simplification

Abstract This study investigated the effects of farming modes (pond vs. industrial recirculating aquaculture system, RAS) and feed types (live bait vs. artificial feed) on the gut microbiota of mandarin fish ( Siniperca chuatsi ). Three experimental groups were set: pond farming with live bait (CE group), pond farming with artificial feed (CS group), and industrial RAS farming with artificial feed (GS group). All the groups were dominated by Fusobacteriota, Bacteroidota, Proteobacteria, and Firmicutes, but their abundances varied markedly. GS formed a simplified community dominated by Cetobacterium (64.94%) genus, unlike the balanced compositions of CE and CS. The CS exhibited the highest species richness (Chao1, ACE) and diversity (Shannon, Simpson), while the GS had the lowest diversity. Beta diversity analysis showed no significant difference between the CE and CS groups (p = 0.36), but a highly significant difference between the GS and CS groups (p = 0.004). LEfSe analysis identified 43 differential taxonomic units (from phylum to genus) between the GS and CS groups, far more than the 22 differential genera between the CE and CS groups. PICRUSt2 functional prediction indicated that artificial feed drove functional adaptation of gut microbiota (e.g., enriched nutrient transport and digestion pathways in the CS group), while the industrial environment induced simplification of microbial functions (e.g., focused genetic information processing pathways in the GS group). Collectively, this study demonstrates that farming environment plays a dominant role in shaping the gut microbiota of mandarin fish, leading to community simplification, while diet mainly regulates microbial functional adaptation.