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.

Hepatitis B virus (HBV) is one of the public-health issues worldwide. Approximately two billion people are infected with HBV, and about 350 million people are chronic carriers globally. About 3% of the world population is infected with hepatitis C virus (HCV). Oncology patients receiving packed red blood cell suspensions and other blood products usually are in the high-risk group for infections due to these viruses. The aim of the study was to detect the seroprevalence of hepatitis B and hepatitis C among chemotherapy patients at the Oncology Department of the Tepecik Education and Research Hospital. HBsAg, anti-HBs, anti-HBcIgM, anti-HBc total and anti-HCV assays were studied by enzyme immunoassay method (Diasorin, Italy) in serum samples of patients (n=448) referred to the Department of Oncology of the Tepecik Education and Research Hospital during 1 June 2006–1 January 2007. Of the 448 patients, 19 (4.2%) were HBsAg-positive, and three (0.7%) had anti-HCV positivity. In this study, the seroprevalence of HBV was similar to previous data in Turkey. This could be due to widespread vaccination programmes. The seroprevalence of low anti-HCV may be because of controlled blood transfusion. Oncology patients should be monitored for their protective antibody levels against HBV, and they must be included in the vaccination programme. Their anti-HCV status should also be checked as well. DOI: http://dx.doi.org/10.3329/jhpn.v29i6.9903 JHPN 2011; 29(6): 652-655

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.

Background: Klebsiella pneumoniae is an important nosocomial pathogen that can lead to high morbidity and mortality. ESBL and carbapenamase producing strains may cause epidemic situations. The aim of our study was to investigate the molecular epidemiology and clonal relationship between carbapenem resistant K. pneumoniae strains isolated from our hospital during a three month period. Methods: Fourteen carbapenem resistant K. pneumoniae strains isolated during April 1st-June 30th 2013 were included. The identification and the antibiotic susceptibility of the strains were studied by Vitek 2 Compact (Biomerieux, France) system. The carbapenemase production of the isolates were investigated by Modified Hodge assay. The bla(OXA) of the strains was investigated by in house PCR. The clonal relationship between the isolates were studied by pulsed-field gel electrophoresis (PFGE) and automatized repetitive extragenic palindromic PCR (Rep-PCR, DiversiLab sistemi, Biomerieux, France) methods. Results: All the K. pneumoniae isolates were carbapenem resistant; they were all susceptible to gentamycin and colistin. All of them had bla(OXA-48). The genotyping analysis revealed that eight isolates were in the same cluster both by Rep-PCR (similarity border >= 95%) and PFGE (Tennover criteriae) analysis. The other isolates did not belong to any other clusters. The strains that are in the same cluster are isolated from the Anesthesiology Intensive Care Unit during a three month period. The cluster ration by both methods was 57%. Conclusions: All K. pneumoniae strains possessed bla(OXA-48). The clonal spreading was particularly detected in Anesthesiology Intensive Care Unit. Molecular epidemiological monitorization of nosocomial pathogens may prevent the spread of these multidrug resistant pathogens. (C) 2018 The Authors. Published by Elsevier Limited on behalf of King Saud Bin Abdulaziz University for Health Sciences.

Objective: S maltophilia is an opportunistic pathogen found predominantly in the enviroment and hospital setting. Invasive procedures and treatment methods, instruments used for diagnosis and treatment and irrational antibotic use play major role in spread of this pathogen.

Introduction: Mucormycosis is an acute onset, invasive, fungal infection, characterized by organ involvement, and caused by Mucor, Rhizopus, or Absidia. Our aim was to present a case of mucormycotic infection and emphasize its importance in a diabetic immunosuppressed patient with acute myeloid leukemia (AML). Case presentation: A 68-year-old hypertensive and diabetic male patient with a diagnosis of AML developed respiratory failure and exhibited diffuse bilateral consolidation in high-resolution computed tomography (HRCT). The treatment plan involved chemotherapy with cytarabine (200 mg/m2/day for 7 days) and daunorubicin (60 mg/m2/day for 3 days) starting on 20 July 2022. Posaconazole prophylactic treatment was initiated on 23 July 2022, to prevent fungal infections. Five days later there was a black necrotic appearance on the left wing of the nose. The patient underwent excision of the left wing of the nose. Mucor was detected in the excision tissue both histopathologically and in culture. A culture under lactophenol cotton blue (LFCB) staining displaying hyphal structures of Mucor was obtained. The patient died of progressive pneumonia and sepsis. Conclusions: Mucormycosis is an infection with high mortality, and should be considered in the early stages of diagnosis when dealing with immunosuppression patients.