Integrated meta-omics uncovering the mechanisms of Lactobacillus salivarius to improve Oreochromis niloticus intestine health

Oreochromis niloticus represents a critically important species in the aquaculture industry due to its economic significance. Probiotics used as feed additives are known to enhance the growth performance and health of tilapia. However, the underlying mechanisms by which these benefits are conferred remain poorly understood. Here, we demonstrate that Lactobacillus salivarius exhibits significant growth performance-enhancing effects when used as a feed additive. Utilizing multi-omics approaches, our results revealed that L. salivarius significantly modulates the composition and abundance of the intestinal microbiota. Bile acids, choline, and tryptophan were identified as pivotal factors in the microbial-mediated modulation of systemic metabolism. Additionally, we have delineated a single-cell atlas of the tilapia intestine for the first time, discovering that L. salivarius_01 increases the populations of intestinal epithelial cells, immune cells, and epithelial stem cells. A broad spectrum of developmentally relevant genes and pathways were found to be activated. This study significantly advances the application of probiotics in promoting sustainable aquaculture practices. Overall design: Single-cell transcriptomics of tilapia gut tissues were determined for probiotic-treated and untreated groups, respectively.