Lactobacillus plantarum NCU116 is the first sequenced strain derived from traditional Chinese sauerkraut (TCS). Since NCU116 manifested outstanding probiotic effects in vitro and in vivo, it is crucial to comprehend a clear genetic background for NCU116. Functional re-annotation and comparative analysis were performed to excavate the unique and representative genes in NCU116, in order to investigate its metabolic preference and adaptive mechanism. Horizontal gene transfer (HGT) seemed to occur frequently, which endows NCU116 with a strong ability to transport carbohydrates, as a strain-specific fructose/mannose-PTS was identified, and opu and osmC coding genes were retrieved as NCU116-specific. In addition, a strain-specific type I R/M system and several prophage loci were found in NCU116, which could play vital roles in self-defense mechanism. Pathways of bacterial metabolism on plant-related substrates fermentation were then generated by reconstruction of associated pathways. Moreover, a unique potential plantaricin-producing locus with high homology to that of JDM1 was defined in the genome of NCU116, which could be very important for the preservation of fermented-food. Our results would provide critical basis for the application of NCU116 in food and pharmaceuticals industries.