ArticlePloS one2014
Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
188 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of the factors influencing microbial colonization of the preterm infant gut.Gut microbesPooled it
- Usability of rectal swabs for microbiome sampling in a cohort study of hematological and oncological patients.PloS one · 2019Trial
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- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Microbial and immune determinants of disease severity and death in pediatric pneumonia.medRxiv : the preprint server for health sciences · 2026Article
- Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.Current opinion in ophthalmology · 2026Review
- Amphibians After Disease-Induced Declines: Genetic Insights Into Population Recoveries.Molecular ecology · 2026Article
- Maternal factors associate with microbiota-derived extracellular vesicle profiles in pregnancy: a clinical cohort study.BMC medicine · 2026Article
- Integration of human microbiota (SIHUMIx) and zebrafish models reveals microbiome-mediated host responses to azoxystrobin.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.BMC bioinformatics · 2026Article
- Investigating the lasting effects of SARS-CoV-2 infection and the lung microbiome: no persistent microbial alterations in recovered COVID-19 patients with persistent radiological or respiratory abnormalities.Access microbiology · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Do Shifts in Honeybee Crop Microbiota Enable Ethanol Accumulation? A Comparative Analysis of Caged and Foraging Bees.Microbial ecology · 2025Article
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- Identifying the location-dependent adipose tissue bacterial DNA signatures in obese patients that predict body weight loss.Gut microbes · 2025Article
- Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.Microbiology spectrum · 2025Article
- Is Osteoarthritis a State of Joint Dysbiosis?Antibiotics (Basel, Switzerland) · 2025Review
- CleanSeqU algorithm for decontamination of catheterized urine 16S rRNA sequencing data.Scientific reports · 2025Article
128 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 "1000 Genomes Project" sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.
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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.