ArticlePLoS pathogens2014
Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.
Article in PLoS pathogens, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
What it found
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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.
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
97 citing papers in PubMed, 193 citations in OpenAlex.
- Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.Current opinion in infectious diseases · 2026Review
- Metagenomic sequencing in encephalitis diagnostics: Challenges and opportunities in clinical settings.PloS one · 2026Article
- Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.Microbiology spectrum · 2025Article
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Development and application of a whole transcriptome sequencing assay for the detection of gene fusions in clinical cancer specimens.BMC cancer · 2025Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Why is next-generation sequencing essential in modern virology?The Journal of general virology · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Anthocyanins from pomegranate peel (Heliyon · 2024Article
- Clinical applications of metagenomics next-generation sequencing in infectious diseases.Journal of Zhejiang University. Science. B · 2024Review
- Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.BMC medical genomics · 2024Article
- sRNAflow: A Tool for the Analysis of Small RNA-Seq Data.Non-coding RNA · 2024Article
- Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization.Access microbiology · 2024Article
- Decoding the Link between Periodontitis and Neuroinflammation: The Journey of Bacterial Extracellular Vesicles.Current genomics · 2023Article
- Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.International journal of chronic obstructive pulmonary disease · 2023Article
- De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.Nature communications · 2022Article
- Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases.The clinical respiratory journal · 2022Review
- The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families.Scientific reports · 2022Article
- Metagenomics-enabled microbial surveillance.Nature microbiology · 2022Review
- Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics.Scientific reports · 2022Article
37 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
9 authors at 4 institutions in 1 country.
Funding
Abstract
The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.
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.