Whole Genome Sequencing and Extracellular Metabolite Profiling of Lactiplantibacillus plantarum FRT4: Insights into Probiotic Functionality

Lactiplantibacillus plantarum is a widely studied probiotic species with significant strain-specific functional diversity, yet the molecular mechanisms underlying these variations remain largely unexplored. In this study, whole genome sequencing (WGS) and untargeted metabolomics were employed to comprehensively characterize the genetic architecture and extracellular metabolic profile of Lp. plantarum FRT4 (CGMCC 17955), a probiotic strain previously studied for its metabolic effects in animal models. WGS revealed a circular chromosome and five plasmids, encoding 3301 protein-coding genes enriched in amino acid biosynthesis, carbohydrate metabolism, and environmental response pathways. Carbohydrate-active enzymes (CAZy) annotation revealed 135 carbohydrate-active enzyme genes, dominated by glycoside hydrolases and glycosyl transferases. Untargeted metabolomic analysis comparing the fermentation supernatant of FRT4 with non-inoculated MRS medium revealed significant alterations in metabolite composition, including elevated levels of acetylcholine, nicotinamide adenine dinucleotide (NAD), and trans-3-coumarate, and reduced levels of uridine, inosine, and fructose-1-phosphate, indicating active modulation of neurotransmission, redox balance, and purine metabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment showed significant regulation of pathways related to amino acid metabolism, carbon metabolism, and cofactor biosynthesis. These findings highlight the metabolic versatility and functional potential of FRT4, offering mechanistic insights into its probiotic effects and providing a basis for its potential application in fermentation-based formulations.