Dataset supporting the study: "Genomic and Functional Characterization of Novel Probiotic Strains from Traditional Fermented Dairy Products in Alleviating DSS-Induced Colitis"

In this study,three previously uncharacterized strains—Lacticaseibacillus rhamnosus L.r1, Lacticaseibacillus rhamnosus L.r2, and Lactiplantibacillus plantarum subsp. plantarum L.p—were isolated and identified. Their probiotic features were assessed through acid and bile salt tolerance tests, survival in simulated gastrointestinal fluids, cell surface hydrophobicity, and auto-aggregation capacity. Additionally, cell-free supernatants from these isolates exhibited broad-spectrum antimicrobial activity against several pathogenic bacteria. Whole-genome sequencing and comparative genomic analysis revealed the presence of an LPH homologue gene implicated in anti-inflammatory processes, along with gene clusters encoding secondary metabolites such as RiPP-like and terpene-precursor compounds. In a DSS-induced murine colitis model, administration of L.r1, L.r2, or L.p significantly ameliorated colon damage, up-regulated the expression of ZO-1, Occludin, and IL-10, and down-regulated IL-6. Fecal microbiome sequencing and functional prediction indicated that intervention with these strains restored gut microbiota balance, promoted the enrichment of beneficial genera including Akkermansia, Pediococcus, and Bacteroides, and suppressed microbial pathways related to antibiotic resistance and carbohydrate transport.