ArticleInternational journal of molecular sciences2022
Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 12 citations in OpenAlex.
- A rapid ionic liquid-based DNA extraction method for molecular diagnostics of urinary tract infections.Microbiology spectrum · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- The stone-degrading metabolic potential of the urinary microbiome: Sexual dimorphism and dysbiosis in urolithiasis.AIMS microbiology · 2026Article
- Mechanisms of microbiome-immune interactions in bladder cancer and targeted regulatory strategies.Frontiers in immunology · 2026Review
- State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.Frontiers in reproductive health · 2025Review
- Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Dysbiosis in Human Urinary Microbiota May Differentiate Patients with a Bladder Cancer.International journal of molecular sciences · 2024Article
- Korean urobiome platform (KUROM) study for acute uncomplicated sporadic versus recurrent cystitis in women: Clinical significance.Investigative and clinical urology · 2024Article
- Synthesis of current pediatric urinary microbiome research.Frontiers in pediatrics · 2024Review
- Urinary Microbiome of Reproductive-Age Asymptomatic European Women.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in molecular biology have been successfully applied to the exploration of microbiota from various fluids. However, the urinary microbiota remains poorly explored, as its analysis requires specific technical considerations. Indeed, urine is a low microbial biomass environment, in which the representativity of each bacterium must be respected to obtain accurate data. Thus, sensitive extraction methods must be used to obtain good quality DNA while preserving the proportions between species. To address this, we compared the efficiency of five extraction methods on artificial urine samples spiked with low amounts of four bacteria species. The quality of the DNA obtained was further evaluated by different molecular biology approaches, including quantitative PCR and amplicon-based next-generation sequencing (NGS). Although two extraction methods allowed DNA of sufficient quality for NGS analysis to be obtained, one kit extracted a larger amount of DNA, which is more suitable for the detection of low-abundant bacteria. Results from the subsequent assessment of this kit on 29 human clinical samples correlated well with results obtained using conventional bacterial urine culture. We hope that our work will make investigators aware of the importance of challenging and adapting their practice in terms of the molecular biology approaches used for the exploration of microbiota.
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