Response patterns and community assembly processes of gut microbiota in grass carp subjected to various protein sources and their implications for growth and metabolism.

Feed nutrients are crucial in shaping the gut microbial community, especially for complex interactions. While much research focused on the impacts of dietary protein levels, exploration of protein sources remains insufficient. Accordingly, this study specifically investigated the effects of four protein sources [Clostridium autoethanolicum protein (CAP), cottonseed protein concentrate (CPC), Chlorella vulgaris meal (CVP), and Tenebrio molitor meal (TM)] replacing dietary soybean meal on microbial co-occurrence networks and key metabolic taxa. A 56-day feeding trial involved 1500 grass carp (20.00 g) fed five experimental diets, each incorporating one of the experimental protein sources. Results revealed that CPC and CVP diets improved the weight gain and specific growth rate, with the CPC group demonstrating the highest biomass gain and the CVP group exhibiting the best feed conversion ratio. Findings further indicated that SM-free diets enhanced intestinal immunity and barrier function while negatively impacting microbial diversity. Additional profiling revealed that each treatment exhibited distinct abundance profiles and unique species, with Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla and key genera such as Bacteroides, Erysipelatoclostridium, and Cetobacterium. Stochastic mechanisms drove the community assembly process, and prolonged SM-free diets led to simplified networks with increased generalists and specialists. Functional gene analysis highlighted roles in amino acid, carbohydrate, and lipid metabolism, underscoring the impact of protein sources on aquatic microbial communities and host-microbiome interactions. Overall, the study suggests the potential suitability of several protein sources as soybean meal substitutes, emphasizing the importance of further investigation into optimal inclusion levels for diverse proteins.