Microbiology Research

Background: Infections caused by Staphylococcus aureus are a health problem worsened by antibiotic resistance. New drugs, including those inhibiting virulence and resistance mechanisms, are needed. This study aimed to evaluate the anti-growth, anti-virulence, and anti-biofilm activities of Trametes villosa. (2) Methods: Fractions were obtained from the basidiomata of T. villosa. Anti-growth, anti-hemolysis, and anti-biofilm activities were tested against S. aureus strains using resazurin microtiter, blood cell lysis, and crystal violet assays, respectively. Cytotoxicity was evaluated in Vero and HaCaT cells using sulforhodamine B. The active fractions were subjected to GC-MS analysis and molecular docking with S. aureus quorum-sensing receptors. Results: The n-hexane and ethyl acetate (EtOAc) fractions exhibited anti-growth activity against all strains (MIC: 31.2–2000 µg/mL). These fractions also displayed anti-hemolysis (IC₅₀ = 33.8 ± 1.1–53.8 ± 5.1 µg/mL) and anti-biofilm formation activity (IC₅₀ = 106.6 ± 4.8–383.4 ± 31.4 µg/mL), while exhibiting low cytotoxicity in Vero and HaCat. GC-MS analysis revealed that both active fractions mainly contained alkanes, aldehydes, and fatty acids. Molecular docking revealed that isovanillic acid, identified in the EtOAc fraction, exhibited optimal interactions with S. aureus quorum-sensing receptors AgrA and SarA. (4) Conclusions: Our research highlights the potential of T. villosa as a source of bioactive compounds effective against S. aureus.

Carbapenem-resistant Enterobacterales (CREs) pose a critical threat to global public health, largely driven by the enzymatic activity of Klebsiella pneumoniae carbapenemase-2 (KPC-2), a class A serine β-lactamase that hydrolyzes most β-lactam antibiotics. While β-lactamase inhibitors like avibactam offer temporary relief, emerging KPC variants demand novel, sustainable inhibitory scaffolds. This study aimed to identify and characterize potential natural inhibitors of KPC-2 from Pongamia pinnata, leveraging a comprehensive in silico workflow. A curated library of 86 phytochemicals was docked against the active site of KPC-2 (PDB ID: 3DW0). The top-performing ligands were subjected to ADMET profiling (pkCSM), and 100 ns molecular dynamics simulations (GROMACS) to evaluate structural stability and interaction persistence, using avibactam as control. Ponganone V exhibited the most favorable binding energy (−9.0 kcal/mol), engaging Ser70 via a hydrogen bond and forming π–π interactions with Trp105. Glabrachromene II demonstrated a broader interaction network but reduced long-term stability. ADMET analysis confirmed high intestinal absorption, non-mutagenicity, and absence of hERG inhibition for both ligands. Molecular dynamics simulations revealed that Ponganone V maintained compact structure and stable hydrogen bonding throughout the 100 ns trajectory, closely mirroring the behavior of avibactam, whereas Glabrachromene II displayed increased fluctuation and loss of compactness beyond 80 ns. Principal Component Analysis (PCA) further supported these findings, with Ponganone V showing restricted conformational motion and a single deep free energy basin, while avibactam and Glabrachromene II exhibited broader conformational sampling and multiple energy minima. The integrated computational findings highlight Ponganone V as a potent and pharmacologically viable natural KPC-2 inhibitor, with strong binding affinity, sustained structural stability, and minimal toxicity. This study underscores the untapped potential of Pongamia pinnata phytochemicals as future anti-resistance therapeutics and provides a rational basis for their experimental validation.

Gut microbiota dysbiosis is increasingly being recognized as a major contributor to host metabolic imbalance, immune dysfunction, and neurophysiological disorders. Probiotics are known to modulate intestinal metabolism and exert systemic effects through the gut–brain axis. Herein, we evaluated the safety and probiotic potential of Pediococcus acidilactici SWP-CGPA01 (SWP-CGPA01) under antibiotic-induced microbiota dysbiosis. Genomic and phenotypic analyses verified its safety profile, supporting its suitability for use in food and nutritional applications. In a mouse model of antibiotic-induced dysbiosis, SWP-CGPA01 supplementation alleviated diarrhea and restored hippocampal brain-derived neurotrophic factor expression. These findings demonstrate that SWP-CGPA01 is a safe and functionally active probiotic with the potential to maintain gastrointestinal and neurotrophic homeostasis under gut microbiota dysbiosis.