WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

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Subject: search.filters.subject.Antimicrobial Activity

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  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Pangenome Analysis and Genome-Guided Probiotic Evaluation of Cyclic Dipeptides Producing Levilactobacillus Brevis DY55bre Strain From a Lactic Acid Fermented Shalgam to Assess Its Metabolic, Probiotic Potentials, and Cytotoxic Effects on Colorectal Cancer Cells
    (Springer, 2025-10-01) Yetiman, Ahmet E.; Horzum, Mehmet; Kanbur, Ertan; Cadir, Mehmet; Bahar, Dilek; Gurbuz, Serife; Akbulut, Mikail
    This study investigates the genetic, metabolic, and probiotic characteristics of Levilactobacillus brevis DY55bre, a strain isolated from the traditional Turkish fermented beverage, shalgam. Whole-genome sequencing revealed a circular genome of 2.485 Mb with a GC content of 45.72%, predicted 2791 genes, and multiple CRISPR-Cas systems. Pangenome analysis demonstrated an open structure, with 18.9% core genes and 103 strain-specific genes, highlighting its genetic diversity. The DY55bre exhibits heterofermentative carbohydrate metabolism due to the presence of the araBAD operon and the lack of 1-phosphofructokinase (pfK) and fructose-1,6-bisphosphate aldolase enzymes. Probiotic evaluation revealed firm survival under simulated gastrointestinal conditions, including resistance to acidic pH (as low as 3.0) and bile salts (up to 1%), along with significant adhesion to intestinal epithelial cell lines (HT29;59.3%, Caco-2;87%, and DLD-1;60.8%). The strain exhibited high auto-aggregation (84.55%) and cell surface hydrophobicity (56.69%), essential for gut colonization. Safety assessments confirmed its non-hemolytic nature and absence of horizontally acquired antibiotic resistance genes. Notably, GC-MS analysis identified bioactive cyclic dipeptides, Cyclo(D-Phe-L-Pro) and Cyclo(L-Leu-L-Pro), which demonstrated cytotoxic effects against colorectal cancer cell lines, with IC50 values of 7.71 mg/mL for HT29 and 3.19 mg/mL for DLD-1. The cell-free supernatant exhibited antimicrobial activity against pathogens, likely due to the synergistic effects of cyclic dipeptides, organic acids, and other metabolites. Antioxidant assays revealed significant ABTS+ (76.63%) and DPPH (34.25%) radical scavenging activities, while cholesterol assimilation tests showed a 27.29% reduction. These findings position the DY55bre as a promising candidate for functional foods, nutraceuticals, and therapeutic applications, warranting further in vivo validation.
  • Article
    Citation - WoS: 22
    Citation - Scopus: 28
    Prediction of Linear Cationic Antimicrobial Peptides Active Against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models
    (MDPI, 2022-04-03) Soylemez, Ummu Gulsum; Yousef, Malik; Kesmen, Zulal; Buyukkiraz, Mine Erdem; Bakir-Gungor, Burcu
    Antimicrobial peptides (AMPs) are considered as promising alternatives to conventional antibiotics in order to overcome the growing problems of antibiotic resistance. Computational prediction approaches receive an increasing interest to identify and design the best candidate AMPs prior to the in vitro tests. In this study, we focused on the linear cationic peptides with non-hemolytic activity, which are downloaded from the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). Referring to the MIC (Minimum inhibition concentration) values, we have assigned a positive label to a peptide if it shows antimicrobial activity; otherwise, the peptide is labeled as negative. Here, we focused on the peptides showing antimicrobial activity against Gram-negative and against Gram-positive bacteria separately, and we created two datasets accordingly. Ten different physico-chemical properties of the peptides are calculated and used as features in our study. Following data exploration and data preprocessing steps, a variety of classification algorithms are used with 100-fold Monte Carlo Cross-Validation to build models and to predict the antimicrobial activity of the peptides. Among the generated models, Random Forest has resulted in the best performance metrics for both Gram-negative dataset (Accuracy: 0.98, Recall: 0.99, Specificity: 0.97, Precision: 0.97, AUC: 0.99, F1: 0.98) and Gram-positive dataset (Accuracy: 0.95, Recall: 0.95, Specificity: 0.95, Precision: 0.90, AUC: 0.97, F1: 0.92) after outlier elimination is applied. This prediction approach might be useful to evaluate the antibacterial potential of a candidate peptide sequence before moving to the experimental studies.
  • Article
    Citation - WoS: 15
    Citation - Scopus: 16
    Natural Molecule-Incorporated Magnetic Organic-Inorganic Nanoflower: Investigation of Its Dual Fenton Reaction-Dependent Enzyme-Like Catalytic Activities With Cyclic Use
    (Wiley-VCH Verlag GmbH, 2023-04-03) Dadi, Seyma; Cardoso, Marlon Henrique; Mandal, Amit Kumar; Franco, Octavio Luiz; Ildiz, Nilay; Ocsoy, Ismail
    The functional organic-inorganic hybrid nanoflowers (hNFs) have recently attracted considerable attention due to enhanced catalytic activity and stability. The main purpose of this study is to synthesize new Fenton reagents and investigate their catalytic activity, dye degradation performance and antimicrobial activity. This magnetic gallic acid nanoflowers (FeGANF) were self-assembled via incorporating magnetic nanoparticles (Fe3O4 NPs) into gallic acid (GA) as organic part and copper(II) phosphate (Cu-3(PO4)(2)) as inorganic parts. The FeGANF were characterized by SEM, EDX, FT-IR and XRD. The peroxidase-like activity and dye degradation performance of FeGANF and GANF based on Fenton reaction in the presence of H2O2 was studied toward guaiacol as substrate, using methylene blue (MB) and congo red (CR) as a cationic and anionic dyes, respectively. FeGANF shows much high catalytic activity and decoloration efficiency (97 % for MB and 99 % for CR) because of dual active center in Fenton reaction on the surface of FeGANF. FeGANF exhibited more antimicrobial activity against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, and Candida albicans ATCC 10231 than that of the GA and GANF. The results of these studies suggest that magnetic hNFs has proved to be promising Fenton reagents for biological and environmental applications including treatment of wastewater.