A multi-omics characterization of the gut microbiota of weaned piglets in response to Lactobacillus plantarum supplementation

Weaning is a critical developmental stage in piglets and is frequently associated with intestinal dysfunction, diarrhea, and growth retardation due to abrupt dietary and environmental changes. Probiotics have been explored as antibiotic alternatives to alleviate postweaning stress, and Lactobacillus plantarum has shown potential for modulating the gut microbiota and improving intestinal health. However, most previous studies have relied on single-omics approaches, limiting mechanistic understanding of host–microbiome interactions. This study employed an integrated multi-omics approach combining ileal transcriptomics, fecal microbiomics, and metabolomics to investigate the effects of dietary L. plantarum supplementation in weaned piglets. Six piglets were assigned to either a control or L. plantarum-supplemented group for two weeks. RNA sequencing, 16S rRNA gene sequencing, and gas chromatography mass spectrometry based metabolomics were conducted, followed by integrative analysis using MIMOSA2 and MetaboAnalyst. Transcriptomic analysis identified 1,229 differentially expressed genes enriched in immune-related pathways, including NF-κB and IgA signaling, as well as epithelial barrier regulation. Microbiome profiling revealed increased microbial diversity, enrichment of Lactobacillus, and reduced abundance of Shigella. Functional prediction suggested enhanced innate immune responsiveness. Integrated metabolome–transcriptome analysis highlighted lipid and amino acid metabolic pathways linking microbial metabolites with host gene expression. Overall, L. plantarum supplementation induced coordinated host–microbiome adaptations associated with reduced oxidative stress, improved intestinal barrier stability, and enhanced immune resilience. These findings provide mechanistic evidence supporting L. plantarum as a promising nutritional strategy to mitigate postweaning stress and improve piglet intestinal health.