ArticlePloS one2019
Optimizing bacterial DNA extraction in urine.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- Age-related changes in the gut microbiota of a long-lived seabird suggest divergence from mammalian models.Royal Society open science · 2026Article
- Impact of sample processing method and volume on 16 S rRNA profiling of the urobiome.BMC microbiology · 2026Article
- Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay.Microbiology spectrum · 2026Article
- Multiplexed Isothermal Amplification Assay for the Detection ofACS omega · 2026Article
- A rapid ionic liquid-based DNA extraction method for molecular diagnostics of urinary tract infections.Microbiology spectrum · 2026Article
- Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.Investigative and clinical urology · 2025Article
- A MALDI-TOF nucleic acid mass spectrometry assay for rapid detection of fiveFrontiers in cellular and infection microbiology · 2025Article
- Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain.Viruses · 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
- Microbial DNA extraction method for avian feces and preen oil from diverse species.Ecology and evolution · 2024Article
- Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices.Annals of clinical microbiology and antimicrobials · 2024Article
- Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia.Scientific reports · 2023Article
- Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics.Clinical biochemistry · 2023Review
- Article
- Time and temperature stability ofFrontiers in veterinary science · 2023Article
- Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota.International journal of molecular sciences · 2022Article
- Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing.mSystems · 2021Article
- Urethral Microbiota in Men: Association of Haemophilus influenzae and Mycoplasma penetrans With Nongonococcal Urethritis.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Benchmarking DNA isolation kits used in analyses of the urinary microbiome.Scientific reports · 2021Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Urine is an acceptable, non-invasive sample for investigating the human urogenital microbiota and for the diagnosis of sexually transmitted infections. However, low quantities of bacterial DNA and PCR inhibitors in urine may prevent efficient PCR amplification for molecular detection of bacteria. Furthermore, cold temperatures used to preserve DNA and bacteria in urine can promote precipitation of crystals that interfere with DNA extraction. Saline, Dulbecco's Phosphate Buffered Saline, or Tris-EDTA buffer were added to urine from adult men to determine if crystal precipitation could be reversed without heating samples beyond ambient temperature. Total bacterial DNA concentrations and PCR inhibition were measured using quantitative PCR assays to compare DNA yields with and without buffer addition. Dissolution of crystals with Tris-EDTA prior to urine centrifugation was most effective in increasing bacterial DNA recovery and reducing PCR inhibition. DNA recovery using Tris-EDTA was further tested by spiking urine with DNA from bacterial isolates and median concentrations of Lactobacillus jensenii and Escherichia coli 16S rRNA gene copies were found to be higher in urine processed with Tris-EDTA. Maximizing bacterial DNA yield from urine may facilitate more accurate assessment of bacterial populations and increase detection of specific bacteria in the genital tract.
Indexed as
Identifiers
What OpenQuestion holds
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.