Feeding substrate shapes biofloc and intestinal microbiota dynamics in indoor culture of common carp ( Cyprinus carpio )

This study evaluated the effects of wheat (WH) and wheat–sugar (WHSU) biofloc substrate systems on growth performance, intestinal microbiota, and biofloc-associated bacterial communities of common carp (Cyprinus carpio) over a 104–day rearing period. Final body weight, daily weight gain, and feed conversion ratio were not significant between WH and WHSU groups (p > 0.05). There was no significant effect of treatments on the condition factor of fish (p > 0.05). High-throughput 16S rRNA gene sequencing for biofloc and fish digesta generated high-quality datasets (Q30 > 94%), with no sequencing bias among treatments. Significantly higher richness and evenness were observed in biofloc (BF) communities compared with posterior intestine (PI) samples (p < 0.05). Beta diversity (UniFrac, Bray–Curtis, Jaccard) consistently demonstrated strong habitat-driven segregation between PI and BF microbiota. At the phylum level, both BF and PI communities were dominated by Fusobacteriota, Pseudomonadota, and Bacteroidota. At the family level, Fusobacteriaceae were prevalent in both habitats, and Cetobacterium was the dominant genus in BF and PI samples. LEfSe analysis identified distinct diet-associated biomarkers: WHSU biofloc was enriched in Gammaproteobacteria and carbohydrate-degrading taxa, whereas WH biofloc favoured Verrucomicrobiota and Bdellovibrionota. In the intestine, both WH and WHSU treatments altered community structure relative to the control, with enrichment of Actinomycota and Rhodobacterales lineages. Overall, WH biofloc system substantially restructured microbial communities, highlighting habitat-specific ecological dynamics and functional redundancy within aquaculture BF systems.