Integrated Transcriptomic and Metabolomic Analysis Reveals the Antibacterial Mechanisms of the Novel Peptide FxCy2 Against Helicobacter pylori

Antibiotic resistance and gut microbiota dysbiosis have become major challenges to Helicobacter pylori eradication therapy. This growing threat has prompted an urgent search for alternative antimicrobial strategies. Among them, antimicrobial peptides (AMPs) represent a promising class of bioactive molecules with multifaceted mechanisms that minimize the side effects of antibiotics. In the previous study, we obtained a novel AMP, FxCy2, from the fermentation product of Lactobacillus paracasei, which exhibited strong inhibitory activity against Helicobacter pylori. This study further investigates the underlying anti-Helicobacter pylori mechanisms by combining transcriptomics and metabolomics. FxCy2 treatment disrupted membrane integrity, increased permeability, and induced leakage of intracellular nucleic acids, proteins, and Mg2+, indicating severe membrane damage. Additionally, multi-omics analyses revealed that FxCy2 primarily disrupted key biological processes, including oxidative phosphorylation, amino acid metabolism, and nucleotide biosynthesis. These disturbances impaired energy metabolism and disrupted membrane formation. Furthermore, FxCy2 suppressed virulence by targeting secretion and adhesion systems, and molecular docking suggested stable hydrogen-bond interactions with the virulence-associated proteins CagA and UreB, potentially disrupting their functions. Overall, these findings provide novel insights into the anti-Helicobacter pylori mechanisms of FxCy2 and support its potential as a sustainable, non-antibiotic therapeutic strategy for Helicobacter pylori-associated infections.