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 human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and carcinogenesis. Studies suggest that alterations in this microbiota contribute to the development and progression of genitourinary cancers, emphasizing the concept of oncobiome, which refers to microbial genetic contributions to cancer. Similarly, gut microbiota can influence hormone levels and systemic inflammation, impacting cancers such as cervical and prostate cancer. Advanced studies indicate that microbial communities in genitourinary cancers have distinct profiles that may serve as diagnostic biomarkers or therapeutic targets. Dysbiosis of the urinary microbiota correlates with bladder and kidney cancer. Additionally, gut microbiota influence the effectiveness of cancer treatments. However, further research is necessary to clarify causality, the role of microbial metabolites, and hormonal regulation. The aim of this review is to understand that these dynamics present opportunities for innovative cancer diagnostics and therapies, highlighting the need for integration of microbiology, oncology, and genomics to explore the role of microbiota in genitourinary cancers. For this, a comprehensive search of relevant databases was conducted, applying specific inclusion and exclusion criteria to identify studies examining the association between microbiota and urogenital cancers. Research into the mechanisms by which microbiota influence urogenital cancers may pave the way for new diagnostic and therapeutic approaches, ultimately improving patient outcomes.

Introduction: Helicobacter pylori is a Gram-negative, microaerophilic bacterium that colonizes human gastric mucosa. Gastric ulcer, duodenal ulcer, chronic atrophic gastritis, mucosa-associated lymphoid tissue lymphoma, and stomach adenocarcinoma are associated with H. pylori as the etiological agent. Cytotoxin-associated gene A (cagA), which is one of the most important virulence factors of H. pylori, encodes a 120–145 kDa protein. The prevalence of cagA genes shows differences in H. pylori infections based on geographical area, and cagA-positive H. pylori strains play an important role in pathogenesis of gastric carcinoma. Methodology: The aim of this study was to detect the prevalence of cagA and vacA genes in H. pylori isolates in adult patient groups in the southeastern region of Turkey. The presence of H. pylori was investigated in gastric biopsy specimens using the culture method, and polymerase chain reaction (PCR) analysis was performed to detect the presence of the cagA and vacA s1 genes. Results: H. pylori was detected in 65% (84/129) of patients who had gastrointestinal complaints. The number of vacA s1 and cagA genes of isolates were 44 (74.5%) and 31 (52.5%), respectively. Conclusions: H. pylori infection in southeastern region of Turkey with are comparable to those in developed countries. Patients with cagA- and vacA-positive H. pylori have a higher risk of severe inflammation and atrophy and should therefore be monitored for the development of gastric cancer.

Geotrichum is a species of fungi that can be found in every environment in nature, in soil, in water and in air. As it can be found in plants and in cereals and milk products, it has also been shown to be found in normal human flora (mucus and faeces). Geotrichum candidum, mostly saprophytic, can cause clinical picture called Geotrichosis. Neoplasms, leukosis, HIV infection, diabetes mellitus, and kidney transplantation are generally the underlying diseases in such cases. In a case in which we detected G.candidum reproduction in urinary tract infection, we aimed to present the case with its clinic findings and to review the literature.

In this study, it was aimed to retrospectively evaluate the anti-Toxoplasma IgG, IgM and avidity index results of patients who were requested for Toxoplasma serology in our hospital between 01.01.2017 and 31.12.2021. Anti-Toxoplasma antibodies are studied with Abbott Architect İ2000 SR device that using the chemiluminescent microparticle immunoassay method (CMIA), according to the company's recommendations. The age, gender, nationality, sending clinic/polyclinic, and pregnancy status information of patients were scanned from the hospital system. In the five-year period between 2017 and 2021, 29.58% of anti-Toxoplasma IgG tests requested from 12694 patients and 0.94% of anti-Toxoplasma IgM tests sent from 12546 patients were found positive. It is striking that the number of test requests is higher in women. IgG positivity is highest in women in the age group of 30-39 (9.97%), and in men in the age group of 60-69 (6.97%). IgM positivity is higher in both women and men in the 20-29 age group (0.48% and 0.38%, respectively). Anti-Toxoplasma IgG was positive in 27.78% and IgM in 0.64% of the pregnant women. IgG positivity in Turkish and Syrian pregnant women were determined as 25.88%; 47.10% and IgM positivity as 0.49% and 1.83%, respectively, and the difference was statistically significant (p<0.001). Our anti-Toxoplasma antibody positivity was found to be compatible with studies conducted in different centers in our country. The fact that IgM positivity in women is high in the 20-29 age group, which is the childbearing age, emphasizes the importance of screening before and during pregnancy. Consistent with other studies in the literature, the rate of seropositivity in Syrian pregnant women was found to be higher than Turkish. This is important in terms of showing the effect of socio-cultural behaviors on prevalence.

<%=header_description %> <%=header_description %> Kateter ile İlişkili Hastane Enfeksiyonlarından İzole Edilen Metisiline Dirençli Stafilokoklarda Biyofilm ile İlişkili Antibiyotik Duyarlılığının Araştırılması Investigation of Biofilm-Associated Antibiotic Susceptibilities of Methicillin-Resistant Staphylococci Isolated from Catheter-Related Nosocomial Infections