Environmental biofilms reshape gut microecology and host metabolism in Strongylocentrotus intermedius under industrial recirculating versus coastal cage aquaculture: A multi-omics study
Strongylocentrotus intermedius (S. intermedius) is a commercially important aquaculture species in northern China. Currently, suspended cage culture in open coastal waters and land-based culture in industrial recirculating aquaculture systems (IRAS) are practiced in parallel. However, the latter is often associated with reduced growth performance and elevated health risks, while the underlying microecological mechanisms remain insufficiently resolved. Given that substrate-associated biofilms may function both as reservoirs of environmental microorganisms and as carriers of quorum-sensing signals and metabolic products, this study was designed within an integrated framework linking environmental biofilms, gut microbiota, and host function. Comparative analyses were conducted on water, biofilm, and gut samples collected from both coastal and industrialized aquaculture systems. A multi-omics strategy was employed, combining 16S rRNA amplicon sequencing, metagenomics, untargeted metabolomics, quantitative analysis of acyl-homoserine lactone (AHL) signaling molecules, and assays of digestive enzyme activities, to elucidate the coupling between environmental microbiota and host gut functionality under different culture modes.