ArticleScientific reports2021
Benchmarking DNA isolation kits used in analyses of the urinary microbiome.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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Who cites it
28 citing papers in PubMed, 41 citations in OpenAlex.
- Impact of sample processing method and volume on 16 S rRNA profiling of the urobiome.BMC microbiology · 2026Article
- 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 impact of DNA extraction methods on species quantification and apparent community composition of in vitro oral biofilms.FEMS microbiology letters · 2026Article
- Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems.Frontiers in microbiology · 2026Review
- Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.International journal of molecular sciences · 2025Article
- Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.Microbiome · 2025Article
- The Prostate Microbiome Is Associated With Prostate Size and PSA Level, Independent of Age, in BPH Patients.The Prostate · 2025Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Textile dye removal using diatomite nanocomposites: a metagenomic study in photosynthetic microalgae-assisted microbial fuel cells.RSC advances · 2025Article
- De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.Microbiome · 2025Article
- Optimizing a modified cetyltrimethylammonium bromide protocol for fungal DNA extraction: Insights from multilocus gene amplification.Open life sciences · 2025Article
- Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.Frontiers in microbiomes · 2025Article
- State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.Frontiers in reproductive health · 2025Review
- Exploring urinary microbiome: insights into neurogenic bladder and improving management of urinary tract infections.Frontiers in cellular and infection microbiology · 2025Review
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- 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
- Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies.Applied microbiology and biotechnology · 2024Article
- Current Trends and Challenges of Microbiome Research in Bladder Cancer.Current oncology reports · 2024Review
- Synthesis of current pediatric urinary microbiome research.Frontiers in pediatrics · 2024Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.