Integrating Genomics and Metabolomics to Identify Lactic Acid Bacteria With Broad-Spectrum Antimicrobial Activity and Validation in a Bread System.

Abstract

Foodborne diseases and microbial spoilage remain major threats to food safety and shelf life. This study systematically evaluated Lactiplantibacillus plantarum C-35 for antimicrobial activity, mechanisms, genomic safety, metabolite profile, and application in bread. Among 27 lactic acid bacterial strains, L. plantarum C-35 showed strong broad-spectrum inhibition against Escherichia coli, Staphylococcus aureus, Aspergillus niger, and Penicillium solitum, significantly outperforming L. plantarum ATCC 8014 (p < 0.05). Neutralization reduced residual activity to approximately 35%-55%, whereas protease-treated cell-free supernatant generally retained more than 60% activity, indicating that organic acids were the major antimicrobial contributors and proteinaceous substances played a secondary role. Scanning electron microscopy (SEM) revealed cell shrinkage, membrane disruption, spore collapse, and surface deformation in treated microorganisms. Whole-genome sequencing identified a 2.95 Mb genome with 2803 protein-coding genes and four predicted secondary metabolite biosynthetic gene clusters, whereas no antibiotic resistance or virulence-associated genes meeting the screening criteria were detected. LC-MS metabolomics identified 14 antimicrobial-associated compounds and 416 significantly differential metabolites between L. plantarum C-35 and L. plantarum ATCC 8014, further supporting its enhanced bioactivity. Luteolin, mangiferin, indole-3-lactic acid, glutaric acid, and naringenin were enriched in L. plantarum C-35 and may contribute synergistically to its antimicrobial effects. In bread, visible mold appeared on Days 6, 8, and 10 in the control, L. plantarum ATCC 8014, and L. plantarum C-35 groups, respectively, demonstrating its practical preservation potential. Together, these findings indicate that the strain-specific genomic and metabolomic features of L. plantarum C-35 are associated with its strong antimicrobial performance and support its potential application as a clean-label biopreservative in bread systems.