Rice-fish co-culture improves carp (Cyprinus carpio) quality by modulating the gut microbiota and metabolites

Rice-fish co-culture systems, as compared to fish monoculture, offer a sustainable agriculture model that balances productivity with environmental conservation. While the important role of gut microbiome in fish growth and health is increasingly recognized, the impact of different farming practices on fish quality and their gut microbiome remains insufficiently understood. To address this gap, we conducted a comprehensive survey of 292 carps (Cyprinus carpio) raised in four rice-fish co-culture systems (RF) across China, comparing them with site-matched pond systems (PF). Through a combination of amplicon sequencing, metabolomic analysis, and bioinformatics, we investigated changes in carp quality, as well as alterations in gut microbiota and metabolites, and explored the potential links between them. Our results reveal that RF system significantly improve carp quality and alter gut metabolite profiles. Further analysis of gut microbial subgroup showed that RF co-culture induced homogenization in the community structure of rare microbial taxa. Ecological network analysis indicated that RF enhances the complexity and stability of microbial networks, particularly among rare taxa, which play a previously underestimated role in gut ecosystems. Community assembly analysis suggested that deterministic processes more strongly shape the microbial communities in carps from RF system, promoting habitat-dependent selection. By developing a bi-network model to explore host-microbe interactions, we identified key microbial taxa, such as Cetobacterium, that are closely associated with beneficial traits in carp quality. Overall, this study highlights the potential of Rice-fish co-culture to foster beneficial host-microbe interactions, providing a microbial ecological perspective on understanding aquaculture safety and sustainability.