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.

Objectives: We aimed to investigate retrospectively the association between the development of surgical wound infection after orthopedic surgery, and neutrophil/lymphocyte ratio (NLR) and platelet/lymphocyte ratio (PLR) obtained from complete blood count results. Methods: A total of 120 patients who underwent orthopedic surgery between 2018 and 2020 were evaluated retrospectively in our study. Wound culture results, complete blood counts, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) values, orthopedic surgery, and wound types were obtained from the laboratory data administration system. The data were statistically analyzed using SPSS 22.0 software. Results: A total of 70 patients who experienced surgical wound infection (66% males and 34% females) and 50 patients without wound infection (64% males and 36% females) were included in this study. The mean age was 46.8 ± 11.4 years for the patients with infection after surgery and 50.1 ± 11.7 years for the patients without infection. Preoperative CRP, NLR, and PLR, and post-operative white blood cell (WBC), neutrophils, ESR, CRP, NLR, and PLR values were significantly higher, and lymphocyte concentrations were significantly lower in the group with infection, in comparison with those without infection. In the postoperative period, CRP and ESR were high in patients with and without infection, while NLR was increased in only those with infection. A medium-level correlation was found between NLR and PLR, and CRP and ESR. Sensitivity was 66%, and specificity was 68% with a cut-off of >3.5 for NLR, while sensitivity was 42% and specificity was 71% with a cut-off of >135 for PLR. Conclusions: We believe that the estimation of NLR and PLR values before the intervention in patients undergoing orthopedic surgery may be advantageous for identifying infection.

Tuberculosis (TB) continues to pose a significant public health problem worldwide. For mycobacteriology laboratories, it is important to be able to diagnose active cases and to make a differential diagnosis of non-tuberculous mycobacteria (NTM). In this study, it was aimed to retrospectively evaluate the epidemiological status of the Mycobacterium [Mycobacterium tuberculosis complex (MTC) and NTM] obtained from the clinical specimens of patients with TB suspicion, and the resistance rates of MTC isolates against anti-TB drugs. Various clinical samples of TB suspected patients sent to the Balıkesir Atatürk City Hospital Mycobacteriology Laboratory between 2011 and 2019, were included in the study. Microscopy, culture procedures, and the first-line anti-TB drug susceptibility tests were performed according to the instructions. Identification of NTM at the species level could be made during four years including 2012, 2013, 2016, and 2017. In our study, acid fast bacillus (AFB) positivity rate was 4% (1.867/47.235); the culture positivity rate for MTC was 5.1% (1.576/31.017) and 1.1% (333/31.017) for NTM. AFB positivity was detected in 837 (53.1%) of the clinical specimens isolated from MTC. In the presence of AFB positivity, it was determined that bacterial growth was significantly higher in both liquid culture systems (LCS) and Lowenstein-Jensen (LJ) media. The isolation rate of MTC isolates from LCS was determined as 95.3% (1.503/1.576) and the isolation rate from LJ was 67.4% (1.063/1.576). The bacterial growth rate was found to be significantly higher in LCS. The average bacterial growth time (ABGT) of AFB negative samples were 21.79 ± 9.96 days; 13.74 ± 8.13 days for AFB positive samples, and ABGT was significantly shorter in the case of AFB positivity. As the severity of AFB positivity increased, ABGT wasshortened which was statistically significant. While 783 (78%) of the isolates were found to be sensitive to all the tested drugs, 221 (22%) were found to be resistant to at least one drug. Eleven of them (1%) were identified as multidrug resistant-TB (MDR-TB) isolates. In our study, 16 different species were identified among 112 typed NTM isolates. Mycobacterium gordonae (25.0%), Mycobacterium avium complex (17.0%) (Mycobacterium intracellulare-11.6%, Mycobacterium avium-5.4%) and Mycobacterium abscessus (13.3%) were the most frequently isolated NTM species. As a result, nine-year results of the mycobacteriology laboratory in our region were analyzed and the MTC and NTM epidemiological data were determined for the first time.

Stenotrophomonas maltophilia is an opportunistic pathogen that can cause infections especially in hospital settings and in immunocompromised individuals. Due to its resistance to many broad-spectrum antibiotics, treatment options that can be used in clinical practice are limited. This study aims to evaluate the susceptibility profiles of S. maltophilia isolates to antimicrobial agents commonly used in treatment and to investigate the presence of different classes of integrons and sul genes responsible for resistance. The study included 100 S. maltophilia isolates from various clinical samples sent to Balıkesir University Health Practice and Research Hospital Medical Microbiology Laboratory between 2017 and 2023. The BD Phoenix™ M50 Automated System was used for bacterial identification and antibiotic sensitivity testing. The susceptibility of isolates to trimethoprim-sulfamethoxazole was also studied by disk diffusion method. All isolates were investigated for sul1, sul2 genes and integron-associated integrase genes by polymerase chain reaction. The susceptibility rates of isolates to trimethoprim-sulfamethoxazole, levofloxacin and ceftazidime were determined as 96%, 66% and 38%, respectively. Polymerase chain reaction results showed, intI1 and sul1 genes were found to be positive together in two isolates resistant to trimethoprim-sulfamethoxazole, while sul1 and sul2 genes were found in two separate isolates sensitive to trimethoprim-sulfamethoxazole. The intI2 gene was not detected in any isolate. This study addresses the clinically important problems of S. maltophilia infections, which are increasingly difficult to treat due to intrinsic and acquired resistance mechanisms. By providing valuable information on antimicrobial susceptibility and resistance profiles of S. maltophilia isolates, it contributes to national data and guides efforts to control resistance and promote rational antibiotic use.

Aim: Infections of sterile body fluids (SBFs) require rapid and accurate diagnosis and treatment, since their morbidities and mortalities are high. To achieve this goal, definite epidemiologic data is absolutely required, since empiric and preemptive treatments are mainly based on this. The aim of this study was to evaluate infectious agents isolated from SBFs, susceptibility results and molecular analysis (PCR) data, retrospectively. Material and Method: Clinical samples of SBFs (Cerebrospinal, pleural, peritoneal, pericardial and synovial fluids) obtained from January 2017 to December 2020 in Atatürk City Hospital (tertiary center) were included. Identification of bacterial and fungal agents and antibiotic susceptibility were done by conventional and automated system (BD Phoenix™, Becton Dickinson Co., Sparks, MD, USA). Löwenstein-Jensen media and BACTEC Mycobacteria Growth Indicator Tube 960 (Becton Dickinson Co., Sparks, MD, USA) were used for mycobacterial analysis. Bosphore Viral Meningitis Panel Multiplex PCR Kit (Anatolia Geneworks, İstanbul, Turkey) were applied to detect HSV-1, HSV-2, VZV, Enterovirus and/or Parechovirus. Results: A total of 221 (9.74%) organisms were detected among 2269 samples. Particularly common gram negative bacterial agents covered the top of the list (Escherichia coli, Pseudomonas spp., Klebsiella spp. and Acinetobacter baumannii-Acinetobacter calcoaceticus complex). Staphylococcus aureus was the most frequent gram positive strain, followed by enteroccocci. Most of the A. baumannii isolates were multidrug resistant, Pseudomonas spp. showed over than 20% resistance rate to ceftazidime, cefepime and piperacillin-tazobactam. All enterococci were vancomycin-susceptible, one S. aureus strain was methicillin-resistant. All Mycobacterium tuberculosis complex isolates were found to be susceptible to first-line anti-tuberculosis drugs. Conclusions: Continuous laboratory surveillance even in local phase is important to guide clinicians. Even though our data did not show significant changes, improvements on laboratory capabilities and clinical awareness must be done. Isolation rates might be underestimated due to requirement of improvements in our laboratory, especially about sampling, anaerobe transportation and usage of blood culture vials.