Integrated transcriptomic and metabolomic analysis of the antibacterial mechanism of Rhizoma Coptidis extract against Staphylococcus epidermidis ATCC 35984

Abstract Background Biofilm formation is a key virulence factor in Staphylococcus epidermidis . Rhizoma Coptidis , the medicinal root of Coptis chinensis , has been traditionally used in Chinese medicine for its broad-spectrum antimicrobial properties. Results This study investigated the antibacterial and anti-biofilm effects of Rhizoma Coptidis extract against S. epidermidis ATCC 35984. UPLC-MS/MS analysis revealed the chemical composition of the extract. The extract significantly reduced ATPase and succinate dehydrogenase activities, decreased membrane potential, and disrupted cell wall and membrane integrity. These effects led to increased extracellular alkaline phosphatase activity and leakage of proteins and nucleic acids. Anti-biofilm activity was further confirmed using scanning electron microscopy and confocal laser scanning microscopy. Transcriptomic and metabolomic analyses identified significant changes in 366 genes and 286 metabolites after treatment. Integrated omics analysis suggested that the extract impaired cell membrane and wall integrity, disrupted amino acid and nucleic acid metabolism, inhibited the TCA cycle, reduced nitrate reductase activity, suppressed efflux systems, and hindered biofilm formation. Conclusions The study provides new insights into the antibacterial and anti-biofilm mechanisms of Rhizoma Coptidis extract against S. epidermidis , highlighting its potential as a therapeutic agent for combating biofilm-associated infections.