Abstract
To investigate the mechanisms by which bacterial-algal consortia (Chlorella and Effective Microorganisms) enhance the growth performance and muscle quality of Crucian carp (Carassius auratus) in an ecological aquaculture model, this study conducted a 90-day pond experiment comparing a traditional aquaculture group (TA) with a bacterial-algal ecological aquaculture group (EA). Compared with the TA group, the EA group showed significantly improved growth performance, increased polyunsaturated fatty acids (including linoleic acid, arachidonic acid, and DHA), and enriched volatile flavor compounds (alcohols and esters imparting fruity and floral aromas). Mechanistically, the EA group exhibited enhanced intestinal morphology (elevated villus height and microvillus length) and digestive enzyme activities (amylase and lipase). 16S rRNA sequencing and untargeted metabolomics revealed a remodeling of gut microbiota with enrichment of beneficial genera (Romboutsia and Cetobacterium), alongside upregulated lipid metabolism pathways (linoleic acid metabolism and PPAR signaling) and amino acid metabolism. Spearman correlation analysis confirmed strong positive links between these beneficial bacteria and key flavor-related metabolites. Collectively, these findings demonstrate that the bacterial-algal consortium does not merely serve as a nutritional supplement but rather optimizes intestinal structure, enhances digestive function, remodels gut microbial composition, and suggests a potential role of hosting metabolic networks, primarily through the gut–metabolism axis. This study provides a theoretical foundation for developing green and healthy aquaculture technologies for Crucian carp.