Background: Methicillin resistance is a serious health concern since it has spread among Staphylococcus aureus and coagulase-negative Staphylococci (CoNS) that are frequent community and nosocomial pathogens worldwide. Methicillin-resistant strains are often resistant to other classes of antibiotics, making their treatment difficult. Nigella sativa oil is known to be active against Gram-positive cocci, yet its in vitro cytotoxicity is rarely investigated, is a proper and powerful candidate for treatment of methicillin-resistant isolates. Objectives: The aim of this study is to evaluate the in vitro antibacterial activity and cytotoxicity effect of N. sativa oil. Materials and Methods: The minimal inhibitory concentrations (MICs) of N. sativa oil were determined by broth microdilution method against four different American Type Culture Collection strains, 45 clinical isolates of methicillin-resistant S. aureus (MRSA), and 77 methicillin-resistant CoNS (MRCoNS). The effects of different dilutions (0.25 μg/mL, 0.5 μg/mL, and 1 μg/mL) of N. sativa oil on the proliferation of gingival fibroblasts were evaluated. Results: The MIC values of N. sativa oil against clinical isolates of Staphylococci were between <0.25 μg/mL and 1.0 μg/mL. Compared to the control group, there was no cytotoxic effect on the proliferation of the gingival fibroblasts. Conclusion: In the present study, the oil of N. sativa was very active against MRSA and MRCoNS and had no in vitro cytotoxicity at relevant concentrations. These findings emphasize that there is a requirement for further clinical trials on N. sativa oil for "safe" medical management of infections caused by methicillin-resistant Staphylococci. Abbreviation used: ATCC: American Type Culture Collection; CLSI: Clinical and Laboratory Standards Institute; CoNS: Coagulase-negative Staphylococci; DMEM: Dulbecco's modified Eagle's medium; DMSO: Dimethyl sulfoxide; FBS: Fetal bovine serum; HGF: Human gingival fi broblast; MIC: Minimal inhibitory concentration; MRCoNS: Methicillin-resistant CoNS;MRSA: Methicillin-resistant S. aureus

The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.

The aim of this study was to evaluate the antibacterial effect of conventional glass ionomer cement with the addition of antibacterial constituents in its liquid preparation. Two groups of glass ionomers prepared with propolis and chlorhexidine and a third group without any additive used as control were sterilized by low-temperature hydrogen peroxide plasma sterilizer at the sterilization unit. Seven to eight disk-shaped restorative materials of each group were placed on the Mueller Hinton Agar with sheep blood 5% v/v, on which Streptococcus mutans inoculated. The plates were incubated at 37°C in 5% CO₂ for 24 to 48 hours. After 24-hour and 48-hour-incubation, inhibition zone diameters of each restorative materials were measured. No distinct inhibition zone was reported; only a slight zone (6 mm) around the contact surfaces of each material was observed after the 24-hour and 48-hour incubations. No significant difference was observed in the inhibition zone diameters between the two test groups and control. Within the limitations of this study, results revealed that there was no antibacterial difference among glass ionomers prepared with propolis and chlorhexidine.

Objective: The influence of intrauterine and perinatal infections on fetal and neonatal mortality rates and childhood morbidity is substantial. Toxoplasmosis gondii, cytomegalovirus (CMV), and rubella are widely recognized as the major causative agents of in utero infection. The surveillance of preventable and treatable diseases within populations at risk are crucial for public health. The objective of this study is to investigate the seropositivity rates and avidity incidences of T. gondii, CMV, and rubella in pregnant women during the first trimester. Methods: The electrochemiluminescence immunoassay method (Elecsys, Roche, Germany) was employed for the detection of the anti-Toxo IgM, anti-Toxo IgG, anti-CMV IgM, anti-CMV IgG, anti-rubella IgM, and anti-rubella IgG during the time period of January 1, 2021, to June 15, 2023. The anti-Toxo IgG, anti-CMV, and anti-rubella IgG avidity tests were performed with the enzyme-linked fluorescent assay method (VIDAS, bioMérieux, France). Results: The T. gondii IgM incidance was 2.1%; and the T. gondii IgG seroprevalance was 22%. For T. gondii, low avidity was observed in 13.6% (n = 31) of cases, while high avidity index was detected in 75.8% (n = 172) of cases. The anti-CMV IgM incidance was 1.6%; while IgG seroprevalance was 96.9%. The IgG avidity with a high index for CMV was determined as 99.4%. The anti-rubella IgM incidance was 0.8%; while the IgG seroprevalance was found to be 98.7%. The IgG avidity with a high index for Rubella was 99.1%. Conclusion: Seroprevalance of T.gondii, CMV, and rubella may vary according to geographical and socioeconomic conditions. Treatment for T. gondii diagnosed during pregnancy, preventive behavioral measures for CMV and vaccination against rubella prior to pregnancy may help reduce congenital infections. The prioritization of T. gondii, CMV, and rubella screening in high-risk populations, including women of reproductive age and pregnant women, is crucial for public health.

Objective: To assess secondary bacterial pneumonia agents and antibiotic resistance rates in patients with COVID-19 pneumonia and to compare findings with the pre-pandemic period. Materials and Methods: Bacteria grown in endotracheal aspirate fluid and bronchoalveolar fluid samples of patients diagnosed with COVID-19 between January 2020 and December 2020, and antibiotic resistance rates were retrospectively compared with samples of the year before the pandemic. Isolates were identified at the species level with an automated system (VITEK 2, bioMérieux, France), and antimicrobial susceptibility was determined according to EUCAST criteria. Results: A total of 900 culture results were examined in 2019. Acinetobacter baumannii was detected in 36%, Klebsiella pneumoniae in 23%, Pseudomonas aeruginosa in 14%, and Staphylococcus aureus in 8%. In 2020, 660 culture results were examined, and the same bacteria were detected in 43%, 23%, 16%, and 5%, respectively. K. pneumoniae's resistance to third-generation cephalosporins, and A. baumannii's resistance to gentamycin and tobramycin, were found to have increased significantly during the pandemic period. Conclusions: The growth of multidrug-resistant Gram-negative bacteria was frequently detected in respiratory secretions obtained during the COVID-19 pandemic. Regional bacterial agents and antibiotic resistance profiles should be clarified, and empirical therapy should be selected accordingly in COVID-19.