Dietary Soybean and Kappaphycus sp. Differentially Modulate Gut Microbiota Diversity and Predicted Functional Profile in Nile Tilapia (Oreochromis niloticus).

Diet composition shapes gut microbiota, influencing nutrient utilization, health, and growth. The shift toward sustainable ingredients such as soybean meal (SB) and seaweed (SW) requires an understanding of their effects on the gut microbiota. This study investigated how SB and SW diets modulate gut microbiota and predicted functional profile in Nile tilapia. Fish were assigned to four dietary treatments for 62 days: fishmeal (FM), SB, SW, and a natural meal (NM, non-formulated diet). Gut microbiota were characterized using 16S rRNA gene sequencing, and functional potential was inferred using PICRUSt2. Diet significantly influenced microbial beta diversity (PERMANOVA, R2 = 0.60, F = 4.05, p = 0.001). Alpha diversity was highest in the SW and lowest in the NM, with a significant difference detected only between these groups. Fusobacteriota and Pseudomonadota predominated across treatments, while Cetobacterium was consistently identified as a core genus. SB and SW diets were associated with distinct taxonomic and predicted functional profiles. SB diet showed higher representation of pathways related to nucleotide turnover, central carbon metabolism, and stress response, and was associated with growth performance. SW showed higher predicted abundances of amino acid biosynthesis and carbohydrate metabolism pathways, and achieved the highest protein digestibility. In contrast, NM showed lower predicted functional potential and lower growth indices. Overall, SB and SW were associated with changes in microbial composition and predicted metabolic functions while maintaining relatively stable core microbiota. These findings support the relevance of gut microbiota as a biological indicator when evaluating sustainable feed ingredients for Nile tilapia aquaculture.