Integrated bioassays and metabolomics identify Cleome noeana as a promising antibacterial candidate

Antimicrobial resistance has intensified the search for novel antibacterial agents from underexplored desert flora. This study compared three arid-region Cleome species to identify the most active candidate against Escherichia coli, Salmonella enterica, and Staphylococcus aureus, and to relate its antibacterial performance to metabolite composition and compatibility with bacteriophage treatment. An in vitro workflow combined crude-extract antibacterial screening, agar diffusion assays, time-kill kinetics, and untargeted GC-MS metabolomics coupled with multivariate analysis. Among the tested species, Cleome noeana exhibited the broadest and strongest antibacterial activity, with minimum inhibitory concentrations of 6.25-25 mg/mL and MBC/MIC ratios ≤ 4. Inhibition zone diameters were inversely correlated with MIC values. Time-kill assays demonstrated that C. noeana extracts reduced viable bacterial counts more rapidly than bacteriophages or antibiotics alone, while extract-phage combinations achieved >99% inhibition within 4 h, indicating phage compatibility with accelerated killing rather than true synergism. Untargeted metabolomic profiling tentatively associated antibacterial activity with phenolic acids, terpenoids, and long-chain fatty acids, including caffeic acid, α-terpineol, and myristic acid. Overall, Cleome noeana emerges as a promising antibacterial species from desert ecosystems and a plant extract compatible with bacteriophage-based approaches, supporting further targeted isolation and in vivo evaluation of its bioactive constituents.