ReviewEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2019
Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory.
Review in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers, 1 of them a synthesis that pooled it.
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.
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Who cites it
152 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease.Molecular psychiatry · 2023Pooled it
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- The diagnostic potential of combined quantitative polymerase chain reaction and next-generation sequencing using the same primers for periprosthetic joint infection.Microbiology spectrum · 2026Article
- An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.Advances in therapy · 2026Review
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.Microbiology spectrum · 2026Article
- Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship.EBioMedicine · 2026Article
- Application of targeted next-generation sequencing in the etiological diagnosis of peritoneal dialysis-associated peritonitis: a single-center prospective cohort study.International urology and nephrology · 2026Article
- Point of care antimicrobial susceptibility testing.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Review
- Medical software for precision diagnostics of infection with immunoprofiling and artificial intelligence.Journal of translational medicine · 2026Review
- Review
- Detection of Pathogens by a Novel User-Developed Broad-Range BR 16S PCR rRNA Polymerase Chain Reaction/Gene Sequencing Assay: Multiyear Experience in a Large Canadian Healthcare Zone.Microorganisms · 2026Article
- Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods and a Vagina-Specific 16S rRNA Gene Database.Microorganisms · 2026Article
- Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.Journal of oral microbiology · 2026Article
- Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.Molecular biomedicine · 2025Review
- A Review on the Role of Oral Bacteria in Stroke.International journal of molecular sciences · 2025Review
- Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.Molecular & cellular proteomics : MCP · 2025Review
- Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.Environmental microbiology reports · 2025Article
- Hospital Wastewater Surveillance and Antimicrobial Resistance: A Narrative Review.Microorganisms · 2025Review
- Metagenomics and its impact on environmental and therapeutic microbiology.Archives of microbiology · 2025Review
- Next-generation sequencing of the tonsillar microbiome in severe acute tonsillitis: comparison with healthy controls and culture-based findings.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
92 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
Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of ('difficult-to-culture') microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform ('MYcrobiota') is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.
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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.