Community Structure and Functional Prediction of Gut Microbiota in Mandarin Fish (Siniperca Chuatsi) Under Different Culture and Feeding Conditions

This study investigated the effects of culture systems and feed types on the gut microbiota of mandarin fish (Siniperca chuatsi), using three production culture modes: pond–live bait (CE), pond–artificial feed (CS), and RAS–artificial feed (GS). Under identical pond culture conditions, CS fish fed compound feed had higher relative abundances of carbohydrate-metabolizing Bacteroidota and Firmicutes than CE. The CS group showed higher α-diversity, but β-diversity analysis indicated no significant community difference (p = 0.36), demonstrating that feed replacement only induced mild microbial shifts. LEfSe analysis uncovered 17 differential taxa: homeostasis-related genera enriched in CS, while the lipid-adapted Macellibacteroides prevailed in CE. Under identical artificial feed conditions, switching culture mode from pond (CS) to industrial RAS (GS) drastically reduced gut microbial diversity and simplified community structure. GS exhibited a sharp rise in Fusobacteriota, with Cetobacterium (64.94%) becoming the single dominant genus. α-diversity was lower in GS than CS, and β-diversity confirmed highly distinct community profiles between the two groups (p = 0.004). LEfSe detected 43 differential taxa with diverse metabolic genera abundant in CS. No PICRUSt2-inferred KEGG pathways remained significant after FDR correction in the above two comparison groups, so these functional trends are only for reference.